reading topology file parameters/top_all22_prot.inp >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<< >>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< Created by CHARMM version 22 1 aliasing residue HIS to HSD reading topology file parameters/top_all22_prot.inp building segment SEG0 reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 reading residues from pdb file myfile_frag1.pdb extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<< >>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< Created by CHARMM version 22 1 no residue 1 past SER:684 of segment SEG1 aliasing residue HIS to HSD Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom CD1 in residue ILE:657 of segment SEG1 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG1 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEbuilding segment SEG0 reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 reading residues from pdb file myfile_frag1.pdb extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 G2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb extracted 105 residues from pdb file generating structure at end of segment reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom CD1 in residue ILE:569 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG3 no atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG3 no atom CD1 in residue ILE:588 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG3 no atom CD1 in residue ILE:590 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG3 no atom CD1 in residue ILE:596 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:no atom CD1 in residue ILE:657 of segment SEG1 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG1 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfil596 of segment SEG3 no atom CD1 in residue ILE:607 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG3 no atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG3 e_frag3.pdb extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no atom CD1 in residue ILE:631 of segment SEG3 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom CD1 in residue ILE:569 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG3 no atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG3 no atom CD1 in residue ILE:588 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG3 no atom CD1 in residue ILE:590 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG3 no atom CD1 in residue ILE:596 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG3 no atom CD1 in residue ILE:607 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG3 no atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG3 no atom CD1 in residue ILE:631 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 reading topology file parameters/top_all22_prot.inp >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<< >>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< Created by CHARMM version 22 1 reading topology file parameters/top_all22_prot.inp >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<< >>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< Created by CHARMM version 22 1 aliasing residue HIS to HSD building segment SEG0 reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 aliasing residue HIS to HSD building segment SEG0 reading residues from pdb file myfile_frag0.pdb reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 no atom O in residue GLY:723 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 reading residues from pdb file myfile_frag1.pdb no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 extracted 31 residues from pdb file no residue 1 past ARG:549 of segment SEG4 no atom O in residue GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 reading residues from pdb file myfile_frag1.pdb no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 extracted 31 residues from pdb file no atom CD1 in residue ILE:657 of segment SEG1 generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG1 no atom O in residue SER:684 of segment SEG1 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom CD1 in residue ILE:657 of segment SEG1 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue SER:684 of segment SEG1 no atom O in residue PRO:635 of segment SEG2 no atom CD1 in residue ILE:140 of segment SEG4 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag2.pdb Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG4 no atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb no atom CD1 in residue ILE:188 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG4 no atom CD1 in residue ILE:198 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG4 extracted 105 residues from pdb file generating structure at end of segment no atom CD1 in residue ILE:231 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG4 no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom CD1 in residue ILE:237 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG4 no atom CD1 in residue ILE:140 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG4 no atom CD1 in residue ILE:256 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG4 no atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG4 extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no atom CD1 in residue ILE:188 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG4 no atom CD1 in residue ILE:296 of segment SEG4 no residue 1 past GLU:664 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG4 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 no atom CD1 in residue ILE:198 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG4 no atom CD1 in residue ILE:303 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:314 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG4 no atom CD1 in residue ILE:315 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG4 no atom CD1 in residue ILE:327 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG4 no atom CD1 in residue ILE:231 of segment SEG4 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG4 no atom CD1 in residue ILE:237 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG4 no atom CD1 in residue ILE:569 of segment SEG3 no residue 1 past GLU:664 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 no atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG3 no atom CD1 in residue ILE:256 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG4 no atom CD1 in residue ILE:357 of segment SEG4 no atom CD1 in residue ILE:588 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG3 no atom CD1 in residue ILE:590 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG3 no atom CD1 in residue ILE:596 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG3 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom CD1 in residue ILE:607 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG3 no atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG3 no atom CD1 in residue ILE:569 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG3 no atom CD1 in residue ILE:296 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG4 no atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:631 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG3 no atom CD1 in residue ILE:588 of segment SEG3 no atom CD1 in residue ILE:314 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG4 no atom CD1 in residue ILE:590 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG3 no atom CD1 in residue ILE:315 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG4 no atom CD1 in residue ILE:596 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG3 no atom CD1 in residue ILE:414 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:327 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG4 no atom CD1 in residue ILE:423 of segment SEG4 no atom CD1 in residue ILE:607 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG3 no atom O in residue GLU:664 of segment SEG3 no atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb no atom CD1 in residue ILE:444 of segment SEG4 no atom CD1 in residue ILE:631 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG4 no atom CD1 in residue ILE:357 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG4 no atom CD1 in residue ILE:460 of segment SEG4 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG4 no atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb no atom CD1 in residue ILE:414 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:423 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG4 no atom CD1 in residue ILE:507 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG4 no atom CD1 in residue ILE:514 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG4 no atom CD1 in residue ILE:444 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG4 no atom CD1 in residue ILE:533 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG4 no atom CD1 in residue ILE:460 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG4 no atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 building segment SEG5 reading residues from pdb file myfile_frag5.pdb no atom CD1 in residue ILE:507 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG4 no atom CD1 in residue ILE:514 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG4 extracted 57 residues from pdb file generating structure at end of segment no residue 1 before VAL:628 of segment SEG5 Warning: add improper failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-N-CA-C failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-CA-N-HN failed in residue VAL:628 no atom CD1 in residue ILE:533 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 building segment SEG5 reading residues from pdb file myfile_frag5.pdb no residue 1 past SER:684 of segment SEG5 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag5.pdb for segment SEG5 extracted 57 residues from pdb file generating structure at end of segment no residue 1 before VAL:628 of segment SEG5 Warning: add improper failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-N-CA-C failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-CA-N-HN failed in residue VAL:628 no atom CD1 in residue ILE:653 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:653 of segment SEG5 no atom CD1 in residue ILE:657 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG5 no residue 1 past SER:684 of segment SEG5 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-N failed in residue SER:684 no atom O in residue SER:684 of segment SEG5 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG5 building segment SEG6 reading residues from pdb file myfile_frag6.pdb reading coordinates from pdb file myfile_frag5.pdb for segment SEG5 no atom CD1 in residue ILE:653 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:653 of segment SEG5 no atom CD1 in residue ILE:657 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG5 extracted 416 residues from pdb file generating structure at end of segment no atom O in residue SER:684 of segment SEG5 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG5 building segment SEG6 reading residues from pdb file myfile_frag6.pdb extracted 416 residues from pdb file generating structure at end of segment extracted 106 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 no residue 1 before PHE:560 of segment SEG6 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 extracted 106 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG6 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past ASP:665 of segment SEG6 Warning: add bond C(0) N(1) failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add improper failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation CA-C-N-CA failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-O failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-N failed in residue ASP:665 reading coordinates from pdb file myfile_frag6.pdb for segment SEG6 no atom CD1 in residue ILE:569 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:579 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG6 no residue 1 past ASP:665 of segment SEG6 Warning: add bond C(0) N(1) failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add improper failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation CA-C-N-CA failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-O failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-N failed in residue ASP:665 no atom CD1 in residue ILE:588 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG6 no atom CD1 in residue ILE:590 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG6 no atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG6 no atom CD1 in residue ILE:607 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG6 no atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG6 reading coordinates from pdb file myfile_frag6.pdb for segment SEG6 no atom CD1 in residue ILE:631 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG6 no atom CD1 in residue ILE:569 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:579 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG6 no atom CD1 in residue ILE:588 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG6 no atom CD1 in residue ILE:590 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG6 no atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG6 no atom O in residue ASP:665 of segment SEG6 Warning: failed to set coordinate for atom O in residue ASP:665 of segment SEG6 building segment SEG7 reading residues from pdb file myfile_frag7.pdb no atom CD1 in residue ILE:607 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG6 no atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG6 no atom CD1 in residue ILE:631 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG6 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 no atom O in residue ASP:665 of segment SEG6 Warning: failed to set coordinate for atom O in residue ASP:665 of segment SEG6 building segment SEG7 reading residues from pdb file myfile_frag7.pdb reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom CD1 in residue ILE:140 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG4 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG4 no atom CD1 in residue ILE:140 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG4 no atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG4 no atom CD1 in residue ILE:188 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG4 no atom CD1 in residue ILE:198 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG4 no atom CD1 in residue ILE:188 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG4 no atom CD1 in residue ILE:198 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG4 no atom CD1 in residue ILE:231 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG4 no atom CD1 in residue ILE:237 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG4 no atom CD1 in residue ILE:256 of segment SEG4 no atom CD1 in residue ILE:231 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG4 no atom CD1 in residue ILE:237 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG4 extracted 416 residues from pdb file generating structure at end of segment no atom CD1 in residue ILE:256 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG4 no atom CD1 in residue ILE:296 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG4 extracted 416 residues from pdb file generating structure at end of segment no atom CD1 in residue ILE:303 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:314 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG4 no atom CD1 in residue ILE:315 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG4 no residue 1 before VAL:137 of segment SEG7 Warning: add improper failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-N-CA-C failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-CA-N-HN failed in residue VAL:137 no atom CD1 in residue ILE:296 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG4 no atom CD1 in residue ILE:327 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG4 no atom CD1 in residue ILE:303 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:314 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG4 no atom CD1 in residue ILE:315 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG4 no residue 1 before VAL:137 of segment SEG7 Warning: add improper failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-N-CA-C failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-CA-N-HN failed in residue VAL:137 no atom CD1 in residue ILE:327 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG4 no atom CD1 in residue ILE:357 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG4 no atom CD1 in residue ILE:357 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG4 no atom CD1 in residue ILE:414 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:423 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG4 no atom CD1 in residue ILE:444 of segment SEG4 no atom CD1 in residue ILE:414 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:423 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG4 no atom CD1 in residue ILE:460 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG4 no atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG4 no atom CD1 in residue ILE:444 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG4 no atom CD1 in residue ILE:460 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG4 no atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG4 no atom CD1 in residue ILE:507 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG4 no atom CD1 in residue ILE:514 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG4 no atom CD1 in residue ILE:533 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG4 no atom CD1 in residue ILE:507 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG4 no atom CD1 in residue ILE:514 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 building segment SEG5 reading residues from pdb file myfile_frag5.pdb no atom CD1 in residue ILE:533 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 building segment SEG5 reading residues from pdb file myfile_frag5.pdb extracted 57 residues from pdb file generating structure at end of segment no residue 1 before VAL:628 of segment SEG5 Warning: add improper failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-N-CA-C failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-CA-N-HN failed in residue VAL:628 no residue 1 past SER:552 of segment SEG7 Warning: add bond C(0) N(1) failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add improper failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation CA-C-N-CA failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-O failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-N failed in residue SER:552 extracted 57 residues from pdb file generating structure at end of segment no residue 1 before VAL:628 of segment SEG5 Warning: add improper failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-N-CA-C failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-CA-N-HN failed in residue VAL:628 no residue 1 past SER:684 of segment SEG5 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-N failed in residue SER:684 no residue 1 past SER:552 of segment SEG7 Warning: add bond C(0) N(1) failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add improper failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation CA-C-N-CA failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-O failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-N failed in residue SER:552 reading coordinates from pdb file myfile_frag5.pdb for segment SEG5 no residue 1 past SER:684 of segment SEG5 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-N failed in residue SER:684 no atom CD1 in residue ILE:653 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:653 of segment SEG5 reading coordinates from pdb file myfile_frag5.pdb for segment SEG5 no atom CD1 in residue ILE:657 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG5 no atom CD1 in residue ILE:653 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:653 of segment SEG5 no atom O in residue SER:684 of segment SEG5 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG5 building segment SEG6 reading residues from pdb file myfile_frag6.pdb no atom CD1 in residue ILE:657 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG5 no atom O in residue SER:684 of segment SEG5 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG5 building segment SEG6 reading residues from pdb file myfile_frag6.pdb reading coordinates from pdb file myfile_frag7.pdb for segment SEG7 extracted 106 residues from pdb file no atom CD1 in residue ILE:140 of segment SEG7 generating structure at end of segment Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7 no residue 1 before PHE:560 of segment SEG6 no atom CD1 in residue ILE:153 of segment SEG7 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-CA-N-HN failed in residue PHE:560 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG7 extracted 106 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG6 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no atom CD1 in residue ILE:188 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG7 reading coordinates from pdb file myfile_frag7.pdb for segment SEG7 no atom CD1 in residue ILE:140 of segment SEG7 no atom CD1 in residue ILE:198 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG7 no atom CD1 in residue ILE:153 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG7 no residue 1 past ASP:665 of segment SEG6 Warning: add bond C(0) N(1) failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add improper failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation CA-C-N-CA failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-O failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-N failed in residue ASP:665 no atom CD1 in residue ILE:231 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG7 no atom CD1 in residue ILE:237 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG7 no atom CD1 in residue ILE:188 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG7 no atom CD1 in residue ILE:198 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG7 no atom CD1 in residue ILE:256 of segment SEG7 reading coordinates from pdb file myfile_frag6.pdb for segment SEG6 no residue 1 past ASP:665 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG7 Warning: add bond C(0) N(1) failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add improper failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation CA-C-N-CA failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-O failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-N failed in residue ASP:665 no atom CD1 in residue ILE:569 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:579 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG6 no atom CD1 in residue ILE:231 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG7 no atom CD1 in residue ILE:588 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG6 no atom CD1 in residue ILE:590 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG6 no atom CD1 in residue ILE:237 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG7 no atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG6 no atom CD1 in residue ILE:296 of segment SEG7 reading coordinates from pdb file myfile_frag6.pdb for segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:607 of segment SEG6 no atom CD1 in residue ILE:303 of segment SEG7 no atom CD1 in residue ILE:256 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG7 no atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:579 of segment SEG6 no atom CD1 in residue ILE:314 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG7 no atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG7 no atom CD1 in residue ILE:631 of segment SEG6 no atom CD1 in residue ILE:588 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG6 no atom CD1 in residue ILE:590 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG6 no atom CD1 in residue ILE:327 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG7 no atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG6 no atom CD1 in residue ILE:296 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:607 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG6 no atom CD1 in residue ILE:610 of segment SEG6 no atom CD1 in residue ILE:303 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG7 no atom O in residue ASP:665 of segment SEG6 Warning: failed to set coordinate for atom O in residue ASP:665 of segment SEG6 building segment SEG7 reading residues from pdb file myfile_frag7.pdb no atom CD1 in residue ILE:314 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG7 no atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG7 no atom CD1 in residue ILE:357 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG7 no atom CD1 in residue ILE:631 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG6 no atom CD1 in residue ILE:327 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG7 no atom O in residue ASP:665 of segment SEG6 Warning: failed to set coordinate for atom O in residue ASP:665 of segment SEG6 building segment SEG7 reading residues from pdb file myfile_frag7.pdb no atom CD1 in residue ILE:357 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG7 no atom CD1 in residue ILE:414 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG7 no atom CD1 in residue ILE:423 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG7 no atom CD1 in residue ILE:444 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG7 no atom CD1 in residue ILE:414 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG7 no atom CD1 in residue ILE:423 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG7 no atom CD1 in residue ILE:460 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG7 no atom CD1 in residue ILE:465 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG7 no atom CD1 in residue ILE:444 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG7 no atom CD1 in residue ILE:460 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG7 no atom CD1 in residue ILE:465 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG7 no atom CD1 in residue ILE:507 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG7 reading topology file parameters/top_all22_prot.inp reading topology file parameters/top_all22_prot.inp reading topology file parameters/top_all22_prot.inp >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<< >>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< Created by CHARMM version 22 1 reading topology file parameters/top_all22_prot.inp >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<< >>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< Created by CHARMM version 22 1 >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<< >>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< Created by CHARMM version 22 1 aliasing residue HIS to HSD building segment SEG0 no atom CD1 in residue ILE:507 of segment SEG7 >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<< >>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< Created by CHARMM version 22 1 aliasing residue HIS to HSD building segment SEG0 no atom CD1 in residue ILE:514 of segment SEG7 aliasing residue HIS to HSD building segment SEG0 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG7 no atom CD1 in residue ILE:514 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG7 no atom CD1 in residue ILE:533 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG7 no atom O in residue SER:552 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:552 of segment SEG7 guessing coordinates based on topology file Warning: guessing coordinates for 9205 atoms (83 non-hydrogen) Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG7 no atom CD1 in residue ILE:533 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG7 no atom O in residue SER:552 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:552 of segment SEG7 guessing coordinates based on topology file Warning: guessing coordinates for 9205 atoms (83 non-hydrogen) aliasing residue HIS to HSD building segment SEG0 extracted 416 residues from pdb file generating structure at end of segment Warning: poorly guessed coordinates for 40 atoms (16 non-hydrogen) Warning: poorly guessed coordinates for 40 atoms (16 non-hydrogen) extracted 416 residues from pdb file generating structure at end of segment no residue 1 before VAL:137 of segment SEG7 Warning: add improper failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-N-CA-C failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-CA-N-HN failed in residue VAL:137 writing psf file output_psf/1i7x_psfgen_psf.psf writing psf file output_psf/1i7x_psfgen_psf.psf no residue 1 before VAL:137 of segment SEG7 Warning: add improper failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-N-CA-C failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-CA-N-HN failed in residue VAL:137 reading residues from pdb file myfile_frag0.pdb reading residues from pdb file myfile_frag0.pdb reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file generating structure at end of segment extracted 26 residues from pdb file extracted 26 residues from pdb file generating structure at end of segment generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 no residue 1 before GLU:698 of segment SEG0 no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 Warning: add conformation C-CA-N-HN failed in residue GLU:698 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 no residue 1 past SER:552 of segment SEG7 Warning: add bond C(0) N(1) failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add improper failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation CA-C-N-CA failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-O failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-N failed in residue SER:552 total of 18046 atoms total of 18180 bonds total of 32992 angles total of 48050 dihedrals total of 3188 impropers total of 18046 atoms total of 18180 bonds total of 32992 angles total of 48050 dihedrals total of 3188 impropers no residue 1 past SER:552 of segment SEG7 Warning: add bond C(0) N(1) failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add improper failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation CA-C-N-CA failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-O failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-N failed in residue SER:552 reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 building segment SEG1 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 reading residues from pdb file myfile_frag1.pdb reading residues from pdb file myfile_frag1.pdb reading residues from pdb file myfile_frag1.pdb extracted 31 residues from pdb file generating structure at end of segment extracted 31 residues from pdb file extracted 31 residues from pdb file generating structure at end of segment generating structure at end of segment reading coordinates from pdb file myfile_frag7.pdb for segment SEG7 no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 no atom CD1 in residue ILE:140 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7 no atom CD1 in residue ILE:153 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG7 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag7.pdb for segment SEG7 no atom CD1 in residue ILE:140 of segment SEG7 no atom CD1 in residue ILE:188 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG7 no atom CD1 in residue ILE:198 of segment SEG7 no atom CD1 in residue ILE:153 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG7 no atom CD1 in residue ILE:231 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG7 no atom CD1 in residue ILE:188 of segment SEG7 no atom CD1 in residue ILE:237 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG7 no atom CD1 in residue ILE:198 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG7 no atom CD1 in residue ILE:256 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG7 no atom CD1 in residue ILE:231 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG7 no atom CD1 in residue ILE:237 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG7 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom CD1 in residue ILE:657 of segment SEG1 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG1 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom CD1 in residue ILE:657 of segment SEG1 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG1 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom CD1 in residue ILE:657 of segment SEG1 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG1 no atom O in residue SER:684 of segment SEG1 no atom CD1 in residue ILE:296 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 no atom CD1 in residue ILE:256 of segment SEG7 no atom O in residue SER:684 of segment SEG1 no atom O in residue SER:684 of segment SEG1 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:303 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG7 no atom CD1 in residue ILE:314 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG7 no atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG7 no atom CD1 in residue ILE:327 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG7 no atom CD1 in residue ILE:296 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:303 of segment SEG7 no atom CD1 in residue ILE:357 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG7 no atom CD1 in residue ILE:314 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG7 no atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG7 no atom CD1 in residue ILE:327 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG7 no atom CD1 in residue ILE:414 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG7 no atom CD1 in residue ILE:357 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG7 no atom CD1 in residue ILE:423 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG7 no atom CD1 in residue ILE:444 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG7 no atom CD1 in residue ILE:460 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG7 no atom CD1 in residue ILE:465 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG7 no atom CD1 in residue ILE:414 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG7 no atom CD1 in residue ILE:423 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG7 no atom CD1 in residue ILE:444 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG7 no atom CD1 in residue ILE:507 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG7 no atom CD1 in residue ILE:514 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG7 no atom CD1 in residue ILE:460 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG7 no atom CD1 in residue ILE:465 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG7 no atom CD1 in residue ILE:533 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG7 no atom O in residue SER:552 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:552 of segment SEG7 guessing coordinates based on topology file no atom CD1 in residue ILE:507 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG7 no atom CD1 in residue ILE:514 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG7 Warning: guessing coordinates for 9205 atoms (83 non-hydrogen) no atom CD1 in residue ILE:533 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG7 no atom O in residue SER:552 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:552 of segment SEG7 guessing coordinates based on topology file reading residues from pdb file myfile_frag1.pdb building segment SEG2 building segment SEG2 building segment SEG2 Warning: guessing coordinates for 9205 atoms (83 non-hydrogen) extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 Warning: poorly guessed coordinates for 40 atoms (16 non-hydrogen) reading residues from pdb file myfile_frag2.pdb reading residues from pdb file myfile_frag2.pdb reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file extracted 6 residues from pdb file generating structure at end of segment generating structure at end of segment writing psf file output_psf/1i7x_psfgen_psf.psf reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom CD1 in residue ILE:657 of segment SEG1 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG1 extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 no residue 1 before ARG:630 of segment SEG2 no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 Warning: poorly guessed coordinates for 40 atoms (16 non-hydrogen) writing psf file output_psf/1i7x_psfgen_psf.psf total of 18046 atoms total of 18180 bonds total of 32992 angles total of 48050 dihedrals total of 3188 impropers reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 total of 18046 atoms total of 18180 bonds total of 32992 angles total of 48050 dihedrals total of 3188 impropers reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom CD1 in residue ILE:569 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG3 no atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG3 no atom CD1 in residue ILE:588 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG3 no atom CD1 in residue ILE:590 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG3 no atom CD1 in residue ILE:596 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG3 no atom CD1 in residue ILE:607 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG3 no atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG3 no atom CD1 in residue ILE:631 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom CD1 in residue ILE:569 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG3 no atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG3 no atom CD1 in residue ILE:588 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG3 no atom CD1 in residue ILE:590 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG3 no atom CD1 in residue ILE:596 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG3 no atom CD1 in residue ILE:607 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG3 no atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG3 no atom CD1 in residue ILE:631 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom CD1 in residue ILE:569 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG3 no atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG3 no atom CD1 in residue ILE:588 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG3 no atom CD1 in residue ILE:590 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG3 no atom CD1 in residue ILE:596 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG3 no atom CD1 in residue ILE:607 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG3 no atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG3 no atom CD1 in residue ILE:631 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom CD1 in residue ILE:569 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG3 no atom CD1 in residue ILE:579 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG3 no atom CD1 in residue ILE:588 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG3 no atom CD1 in residue ILE:590 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG3 no atom CD1 in residue ILE:596 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG3 no atom CD1 in residue ILE:607 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG3 no atom CD1 in residue ILE:610 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG3 no atom CD1 in residue ILE:631 of segment SEG3 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom CD1 in residue ILE:140 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG4 no atom CD1 in residue ILE:140 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG4 no atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG4 no atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG4 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom CD1 in residue ILE:140 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG4 no atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG4 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 no atom CD1 in residue ILE:188 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG4 no atom CD1 in residue ILE:198 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG4 no atom CD1 in residue ILE:231 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG4 no atom CD1 in residue ILE:237 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG4 no atom CD1 in residue ILE:256 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG4 no atom CD1 in residue ILE:296 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG4 no atom CD1 in residue ILE:303 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:314 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG4 no atom CD1 in residue ILE:315 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG4 no atom CD1 in residue ILE:327 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG4 no atom CD1 in residue ILE:357 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG4 no atom CD1 in residue ILE:188 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG4 no atom CD1 in residue ILE:198 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG4 no atom CD1 in residue ILE:231 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG4 no atom CD1 in residue ILE:237 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG4 no atom CD1 in residue ILE:256 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG4 no atom CD1 in residue ILE:296 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG4 no atom CD1 in residue ILE:303 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:314 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG4 no atom CD1 in residue ILE:315 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG4 no atom CD1 in residue ILE:327 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG4 no atom CD1 in residue ILE:357 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG4 no atom CD1 in residue ILE:188 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG4 no atom CD1 in residue ILE:198 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG4 no atom CD1 in residue ILE:231 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG4 no atom CD1 in residue ILE:237 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG4 no atom CD1 in residue ILE:256 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG4 no atom CD1 in residue ILE:296 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG4 no atom CD1 in residue ILE:303 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:314 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG4 no atom CD1 in residue ILE:315 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG4 no atom CD1 in residue ILE:327 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG4 no atom CD1 in residue ILE:357 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG4 no atom CD1 in residue ILE:414 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:423 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG4 no atom CD1 in residue ILE:444 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG4 no atom CD1 in residue ILE:460 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG4 no atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG4 no atom CD1 in residue ILE:507 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG4 no atom CD1 in residue ILE:514 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG4 no atom CD1 in residue ILE:533 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG4 no atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:414 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:423 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG4 no atom CD1 in residue ILE:444 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG4 no atom CD1 in residue ILE:460 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG4 no atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG4 no atom CD1 in residue ILE:507 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG4 no atom CD1 in residue ILE:514 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG4 no atom CD1 in residue ILE:533 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 building segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:423 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG4 no atom CD1 in residue ILE:444 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG4 no atom CD1 in residue ILE:460 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG4 no atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG4 no atom CD1 in residue ILE:507 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG4 no atom CD1 in residue ILE:514 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG4 no atom CD1 in residue ILE:533 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 building segment SEG5 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom CD1 in residue ILE:140 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG4 no atom CD1 in residue ILE:153 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG4 no atom CD1 in residue ILE:188 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG4 no atom CD1 in residue ILE:198 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG4 no atom CD1 in residue ILE:231 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG4 no atom CD1 in residue ILE:237 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG4 no atom CD1 in residue ILE:256 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG4 no atom CD1 in residue ILE:296 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG4 no atom CD1 in residue ILE:303 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG4 no atom CD1 in residue ILE:314 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG4 no atom CD1 in residue ILE:315 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 building segment SEG5 no atom CD1 in residue ILE:327 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG4 reading residues from pdb file myfile_frag5.pdb reading residues from pdb file myfile_frag5.pdb no atom CD1 in residue ILE:357 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG4 reading residues from pdb file myfile_frag5.pdb extracted 57 residues from pdb file generating structure at end of segment no residue 1 before VAL:628 of segment SEG5 Warning: add improper failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-N-CA-C failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-CA-N-HN failed in residue VAL:628 no atom CD1 in residue ILE:414 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG4 no atom CD1 in residue ILE:423 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG4 no atom CD1 in residue ILE:444 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG4 extracted 57 residues from pdb file generating structure at end of segment no residue 1 before VAL:628 of segment SEG5 Warning: add improper failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-N-CA-C failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-CA-N-HN failed in residue VAL:628 no residue 1 past SER:684 of segment SEG5 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-N failed in residue SER:684 extracted 57 residues from pdb file generating structure at end of segment no residue 1 before VAL:628 of segment SEG5 Warning: add improper failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-N-CA-C failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-CA-N-HN failed in residue VAL:628 no residue 1 past SER:684 of segment SEG5 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-N failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag5.pdb for segment SEG5 no atom CD1 in residue ILE:653 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:653 of segment SEG5 no atom CD1 in residue ILE:657 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG5 reading coordinates from pdb file myfile_frag5.pdb for segment SEG5 no atom CD1 in residue ILE:653 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:653 of segment SEG5 no atom CD1 in residue ILE:657 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG5 no atom CD1 in residue ILE:460 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG4 no atom CD1 in residue ILE:465 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG4 no atom O in residue SER:684 of segment SEG5 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG5 building segment SEG6 no atom O in residue SER:684 of segment SEG5 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG5 no atom CD1 in residue ILE:507 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG4 no atom CD1 in residue ILE:514 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG4 building segment SEG6 reading coordinates from pdb file myfile_frag5.pdb for segment SEG5 no atom CD1 in residue ILE:533 of segment SEG4 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 building segment SEG5 reading residues from pdb file myfile_frag6.pdb reading residues from pdb file myfile_frag6.pdb no atom CD1 in residue ILE:653 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:653 of segment SEG5 no atom CD1 in residue ILE:657 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG5 no atom O in residue SER:684 of segment SEG5 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG5 building segment SEG6 reading residues from pdb file myfile_frag5.pdb extracted 57 residues from pdb file generating structure at end of segment no residue 1 before VAL:628 of segment SEG5 Warning: add improper failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-N-CA-C failed in residue VAL:628 no residue 1 before VAL:628 of segment SEG5 Warning: add conformation C-CA-N-HN failed in residue VAL:628 extracted 106 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG6 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-CA-N-HN failed in residue PHE:560 extracted 106 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG6 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past SER:684 of segment SEG5 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG5 Warning: add conformation N-CA-C-N failed in residue SER:684 reading residues from pdb file myfile_frag6.pdb extracted 106 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG6 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-CA-N-HN failed in residue PHE:560 reading coordinates from pdb file myfile_frag5.pdb for segment SEG5 no atom CD1 in residue ILE:653 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:653 of segment SEG5 no atom CD1 in residue ILE:657 of segment SEG5 Warning: failed to set coordinate for atom CD1 in residue ILE:657 of segment SEG5 no atom O in residue SER:684 of segment SEG5 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG5 building segment SEG6 no residue 1 past ASP:665 of segment SEG6 Warning: add bond C(0) N(1) failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add improper failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation CA-C-N-CA failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-O failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-N failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add bond C(0) N(1) failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add improper failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation CA-C-N-CA failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-O failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-N failed in residue ASP:665 reading residues from pdb file myfile_frag6.pdb no residue 1 past ASP:665 of segment SEG6 Warning: add bond C(0) N(1) failed in residue ASP:665 reading coordinates from pdb file myfile_frag6.pdb for segment SEG6 no residue 1 past ASP:665 of segment SEG6 reading coordinates from pdb file myfile_frag6.pdb for segment SEG6 Warning: add improper failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation CA-C-N-CA failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-O failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-N failed in residue ASP:665 no atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:569 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:579 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG6 no atom CD1 in residue ILE:588 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG6 no atom CD1 in residue ILE:590 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG6 no atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:579 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG6 no atom CD1 in residue ILE:588 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG6 no atom CD1 in residue ILE:590 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG6 no atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG6 no atom CD1 in residue ILE:607 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG6 no atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG6 reading coordinates from pdb file myfile_frag6.pdb for segment SEG6 no atom CD1 in residue ILE:569 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:607 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG6 no atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG6 extracted 106 residues from pdb file generating structure at end of segment no atom CD1 in residue ILE:631 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG6 no atom O in residue ASP:665 of segment SEG6 Warning: failed to set coordinate for atom O in residue ASP:665 of segment SEG6 no atom CD1 in residue ILE:631 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG6 no atom O in residue ASP:665 of segment SEG6 Warning: failed to set coordinate for atom O in residue ASP:665 of segment SEG6 building segment SEG7 no residue 1 before PHE:560 of segment SEG6 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG6 Warning: add conformation C-CA-N-HN failed in residue PHE:560 building segment SEG7 no atom CD1 in residue ILE:579 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG6 no atom CD1 in residue ILE:588 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG6 no atom CD1 in residue ILE:590 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG6 no atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG6 no atom CD1 in residue ILE:607 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG6 no atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG6 no atom CD1 in residue ILE:631 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG6 reading residues from pdb file myfile_frag7.pdb no residue 1 past ASP:665 of segment SEG6 reading residues from pdb file myfile_frag7.pdb Warning: add bond C(0) N(1) failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add improper failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation CA-C-N-CA failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-O failed in residue ASP:665 no residue 1 past ASP:665 of segment SEG6 Warning: add conformation N-CA-C-N failed in residue ASP:665 no atom O in residue ASP:665 of segment SEG6 Warning: failed to set coordinate for atom O in residue ASP:665 of segment SEG6 building segment SEG7 reading coordinates from pdb file myfile_frag6.pdb for segment SEG6 reading residues from pdb file myfile_frag7.pdb no atom CD1 in residue ILE:569 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:569 of segment SEG6 no atom CD1 in residue ILE:579 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:579 of segment SEG6 no atom CD1 in residue ILE:588 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:588 of segment SEG6 no atom CD1 in residue ILE:590 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:590 of segment SEG6 no atom CD1 in residue ILE:596 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:596 of segment SEG6 no atom CD1 in residue ILE:607 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:607 of segment SEG6 no atom CD1 in residue ILE:610 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:610 of segment SEG6 no atom CD1 in residue ILE:631 of segment SEG6 Warning: failed to set coordinate for atom CD1 in residue ILE:631 of segment SEG6 no atom O in residue ASP:665 of segment SEG6 Warning: failed to set coordinate for atom O in residue ASP:665 of segment SEG6 building segment SEG7 reading residues from pdb file myfile_frag7.pdb extracted 416 residues from pdb file generating structure at end of segment extracted 416 residues from pdb file generating structure at end of segment writing pdb file output_psf/1i7x_psfgen_pdb.pdb writing pdb file output_psf/1i7x_psfgen_pdb.pdb extracted 416 residues from pdb file generating structure at end of segment no residue 1 before VAL:137 of segment SEG7 Warning: add improper failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-N-CA-C failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-CA-N-HN failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add improper failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-N-CA-C failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-CA-N-HN failed in residue VAL:137 no residue 1 past SER:552 of segment SEG7 Warning: add bond C(0) N(1) failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add improper failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation CA-C-N-CA failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-O failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-N failed in residue SER:552 no residue 1 before VAL:137 of segment SEG7 Warning: add improper failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-N-CA-C failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-CA-N-HN failed in residue VAL:137 no residue 1 past SER:552 of segment SEG7 Warning: add bond C(0) N(1) failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add improper failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation CA-C-N-CA failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-O failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-N failed in residue SER:552 extracted 416 residues from pdb file generating structure at end of segment no residue 1 before VAL:137 of segment SEG7 Warning: add improper failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-N-CA-C failed in residue VAL:137 no residue 1 before VAL:137 of segment SEG7 Warning: add conformation C-CA-N-HN failed in residue VAL:137 no residue 1 past SER:552 of segment SEG7 Warning: add bond C(0) N(1) failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add improper failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation CA-C-N-CA failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-O failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-N failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add bond C(0) N(1) failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add improper failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation CA-C-N-CA failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-O failed in residue SER:552 no residue 1 past SER:552 of segment SEG7 Warning: add conformation N-CA-C-N failed in residue SER:552 writing pdb file output_psf/1i7x_psfgen_pdb.pdb reading coordinates from pdb file myfile_frag7.pdb for segment SEG7 no atom CD1 in residue ILE:140 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7 no atom CD1 in residue ILE:153 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG7 no atom CD1 in residue ILE:188 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG7 no atom CD1 in residue ILE:198 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG7 no atom CD1 in residue ILE:231 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG7 no atom CD1 in residue ILE:237 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG7 no atom CD1 in residue ILE:256 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG7 reading coordinates from pdb file myfile_frag7.pdb for segment SEG7 no atom CD1 in residue ILE:140 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7 no atom CD1 in residue ILE:153 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG7 no atom CD1 in residue ILE:188 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG7 no atom CD1 in residue ILE:198 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG7 no atom CD1 in residue ILE:231 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG7 no atom CD1 in residue ILE:237 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG7 no atom CD1 in residue ILE:256 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG7 reading coordinates from pdb file myfile_frag7.pdb for segment SEG7 no atom CD1 in residue ILE:140 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7 no atom CD1 in residue ILE:153 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG7 no atom CD1 in residue ILE:188 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG7 no atom CD1 in residue ILE:198 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG7 no atom CD1 in residue ILE:231 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG7 no atom CD1 in residue ILE:237 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG7 no atom CD1 in residue ILE:256 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG7 writing pdb file output_psf/1i7x_psfgen_pdb.pdb reading coordinates from pdb file myfile_frag7.pdb for segment SEG7 no atom CD1 in residue ILE:140 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7 no atom CD1 in residue ILE:153 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:153 of segment SEG7 no atom CD1 in residue ILE:188 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:188 of segment SEG7 no atom CD1 in residue ILE:198 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:198 of segment SEG7 no atom CD1 in residue ILE:231 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:231 of segment SEG7 no atom CD1 in residue ILE:237 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:237 of segment SEG7 no atom CD1 in residue ILE:256 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:256 of segment SEG7 no atom CD1 in residue ILE:296 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:303 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG7 no atom CD1 in residue ILE:314 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG7 no atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG7 no atom CD1 in residue ILE:327 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG7 no atom CD1 in residue ILE:357 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG7 no atom CD1 in residue ILE:414 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG7 no atom CD1 in residue ILE:423 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG7 no atom CD1 in residue ILE:444 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG7 no atom CD1 in residue ILE:460 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG7 no atom CD1 in residue ILE:465 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG7 no atom CD1 in residue ILE:507 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG7 no atom CD1 in residue ILE:514 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG7 no atom CD1 in residue ILE:533 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG7 no atom O in residue SER:552 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:552 of segment SEG7 guessing coordinates based on topology file Warning: guessing coordinates for 9205 atoms (83 non-hydrogen) Warning: poorly guessed coordinates for 40 atoms (16 non-hydrogen) no atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:296 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:303 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG7 no atom CD1 in residue ILE:314 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG7 no atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG7 no atom CD1 in residue ILE:327 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG7 no atom CD1 in residue ILE:357 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG7 no atom CD1 in residue ILE:414 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG7 no atom CD1 in residue ILE:423 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG7 no atom CD1 in residue ILE:444 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG7 no atom CD1 in residue ILE:460 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG7 no atom CD1 in residue ILE:465 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG7 no atom CD1 in residue ILE:507 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG7 no atom CD1 in residue ILE:514 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG7 no atom CD1 in residue ILE:533 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG7 no atom O in residue SER:552 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:552 of segment SEG7 guessing coordinates based on topology file Warning: guessing coordinates for 9205 atoms (83 non-hydrogen) Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:303 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG7 no atom CD1 in residue ILE:314 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG7 no atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG7 no atom CD1 in residue ILE:327 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG7 no atom CD1 in residue ILE:357 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG7 no atom CD1 in residue ILE:414 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG7 no atom CD1 in residue ILE:423 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG7 no atom CD1 in residue ILE:444 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG7 no atom CD1 in residue ILE:460 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG7 no atom CD1 in residue ILE:465 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG7 no atom CD1 in residue ILE:507 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG7 no atom CD1 in residue ILE:514 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG7 no atom CD1 in residue ILE:533 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG7 no atom O in residue SER:552 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:552 of segment SEG7 guessing coordinates based on topology file Warning: guessing coordinates for 9205 atoms (83 non-hydrogen) Warning: failed to set coordinate for atom CD1 in residue ILE:296 of segment SEG7 no atom CD1 in residue ILE:303 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:303 of segment SEG7 no atom CD1 in residue ILE:314 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:314 of segment SEG7 no atom CD1 in residue ILE:315 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:315 of segment SEG7 no atom CD1 in residue ILE:327 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:327 of segment SEG7 no atom CD1 in residue ILE:357 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:357 of segment SEG7 no atom CD1 in residue ILE:414 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:414 of segment SEG7 no atom CD1 in residue ILE:423 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:423 of segment SEG7 no atom CD1 in residue ILE:444 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:444 of segment SEG7 no atom CD1 in residue ILE:460 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:460 of segment SEG7 no atom CD1 in residue ILE:465 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:465 of segment SEG7 no atom CD1 in residue ILE:507 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:507 of segment SEG7 no atom CD1 in residue ILE:514 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:514 of segment SEG7 no atom CD1 in residue ILE:533 of segment SEG7 Warning: failed to set coordinate for atom CD1 in residue ILE:533 of segment SEG7 no atom O in residue SER:552 of segment SEG7 Warning: failed to set coordinate for atom O in residue SER:552 of segment SEG7 guessing coordinates based on topology file Warning: guessing coordinates for 9205 atoms (83 non-hydrogen) Warning: poorly guessed coordinates for 40 atoms (16 non-hydrogen) Warning: poorly guessed coordinates for 40 atoms (16 non-hydrogen) Warning: poorly guessed coordinates for 40 atoms (16 non-hydrogen) writing psf file output_psf/1i7x_psfgen_psf.psf writing psf file output_psf/1i7x_psfgen_psf.psf writing psf file output_psf/1i7x_psfgen_psf.psf total of 18046 atoms total of 18180 bonds total of 32992 angles total of 48050 dihedrals total of 3188 impropers total of 18046 atoms total of 18180 bonds total of 32992 angles total of 48050 dihedrals total of 3188 impropers total of 18046 atoms total of 18180 bonds total of 32992 angles total of 48050 dihedrals total of 3188 impropers writing psf file output_psf/1i7x_psfgen_psf.psf total of 18046 atoms total of 18180 bonds total of 32992 angles total of 48050 dihedrals total of 3188 impropers PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha writing pdb file output_psf/1i7x_psfgen_pdb.pdb writing pdb file output_psf/1i7x_psfgen_pdb.pdb writing pdb file output_psf/1i7x_psfgen_pdb.pdb writing pdb file output_psf/1i7x_psfgen_pdb.pdb PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha