Starting phenix.real_space_refine (version: dev) on Fri Feb 24 13:14:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/02_2023/6bwd_7297.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/02_2023/6bwd_7297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/02_2023/6bwd_7297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/02_2023/6bwd_7297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/02_2023/6bwd_7297.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/02_2023/6bwd_7297.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 681": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 681": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 673": "NH1" <-> "NH2" Residue "C ARG 770": "NH1" <-> "NH2" Residue "C ARG 853": "NH1" <-> "NH2" Residue "D ARG 455": "NH1" <-> "NH2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 681": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Residue "D ARG 856": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23187 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5613 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 227} Link IDs: {'CIS': 48, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 887 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 345 Chain: "B" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5618 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 226} Link IDs: {'CIS': 47, 'PTRANS': 27, 'TRANS': 696} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 650 Unresolved non-hydrogen angles: 880 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 5628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5628 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 223} Link IDs: {'CIS': 45, 'PTRANS': 27, 'TRANS': 698} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 640 Unresolved non-hydrogen angles: 867 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 326 Chain: "D" Number of atoms: 5593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5593 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 232} Link IDs: {'CIS': 46, 'PTRANS': 27, 'TRANS': 697} Chain breaks: 15 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 674 Unresolved non-hydrogen angles: 910 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 360 Chain: "A" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 212 Unusual residues: {' MG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 142 Unusual residues: {' MG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 280 Unusual residues: {'Y01': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {' MG': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 13.79, per 1000 atoms: 0.59 Number of scatterers: 23187 At special positions: 0 Unit cell: (136.53, 136.53, 152.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 122 16.00 Mg 5 11.99 O 4082 8.00 N 3822 7.00 C 15156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 904 " distance=2.02 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 904 " distance=2.02 Simple disulfide: pdb=" SG CYS C 711 " - pdb=" SG CYS C 721 " distance=2.02 Simple disulfide: pdb=" SG CYS D 894 " - pdb=" SG CYS D 904 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.58 Conformation dependent library (CDL) restraints added in 3.0 seconds 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 0 sheets defined 71.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 273 through 285 removed outlier: 4.071A pdb=" N UNK A 285 " --> pdb=" O UNK A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.856A pdb=" N GLU A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.761A pdb=" N HIS A 417 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 418 " --> pdb=" O HIS A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 418' Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.555A pdb=" N LYS A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.971A pdb=" N ILE A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 597 through 604 removed outlier: 3.540A pdb=" N SER A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.581A pdb=" N LEU A 612 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 613 " --> pdb=" O LEU A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 609 through 613' Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.891A pdb=" N ILE A 623 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 689 through 714 removed outlier: 4.133A pdb=" N LEU A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 removed outlier: 4.265A pdb=" N VAL A 727 " --> pdb=" O GLN A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 758 removed outlier: 3.788A pdb=" N TRP A 757 " --> pdb=" O LYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER A 765 " --> pdb=" O TYR A 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 777 " --> pdb=" O PHE A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 removed outlier: 3.903A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 819 removed outlier: 3.830A pdb=" N ARG A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 814 " --> pdb=" O TRP A 810 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 815 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 832 removed outlier: 4.087A pdb=" N TYR A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 861 removed outlier: 3.550A pdb=" N PHE A 839 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 841 " --> pdb=" O ASN A 837 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 844 " --> pdb=" O TYR A 840 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 849 " --> pdb=" O MET A 845 " (cutoff:3.500A) Proline residue: A 855 - end of helix removed outlier: 4.002A pdb=" N ILE A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 880 removed outlier: 4.587A pdb=" N HIS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Proline residue: A 878 - end of helix Processing helix chain 'A' and resid 910 through 922 removed outlier: 3.506A pdb=" N ALA A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 920 " --> pdb=" O ALA A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE A 944 " --> pdb=" O GLN A 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 970 through 974 Processing helix chain 'A' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1031 through 1068 removed outlier: 3.665A pdb=" N ILE A1035 " --> pdb=" O SER A1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 273 through 285 removed outlier: 4.072A pdb=" N UNK B 285 " --> pdb=" O UNK B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.857A pdb=" N GLU B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.760A pdb=" N HIS B 417 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 418 " --> pdb=" O HIS B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 418' Processing helix chain 'B' and resid 435 through 442 removed outlier: 3.555A pdb=" N LYS B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 470 removed outlier: 3.970A pdb=" N ILE B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU B 491 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN B 538 " --> pdb=" O GLN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'B' and resid 574 through 587 Processing helix chain 'B' and resid 597 through 604 removed outlier: 3.770A pdb=" N SER B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 613 removed outlier: 4.257A pdb=" N MET B 611 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 612 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 613 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.890A pdb=" N ILE B 623 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 687 Processing helix chain 'B' and resid 689 through 714 removed outlier: 4.133A pdb=" N LEU B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 714 " --> pdb=" O PHE B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 743 removed outlier: 4.266A pdb=" N VAL B 727 " --> pdb=" O GLN B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 758 removed outlier: 3.788A pdb=" N TRP B 757 " --> pdb=" O LYS B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER B 765 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 777 " --> pdb=" O PHE B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.902A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 819 removed outlier: 3.831A pdb=" N ARG B 813 " --> pdb=" O PHE B 809 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 814 " --> pdb=" O TRP B 810 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 815 " --> pdb=" O TYR B 811 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 816 " --> pdb=" O VAL B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 832 removed outlier: 4.086A pdb=" N TYR B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 861 removed outlier: 3.549A pdb=" N PHE B 839 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE B 841 " --> pdb=" O ASN B 837 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B 844 " --> pdb=" O TYR B 840 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 849 " --> pdb=" O MET B 845 " (cutoff:3.500A) Proline residue: B 855 - end of helix removed outlier: 4.004A pdb=" N ILE B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 880 removed outlier: 4.587A pdb=" N HIS B 877 " --> pdb=" O ASP B 873 " (cutoff:3.500A) Proline residue: B 878 - end of helix Processing helix chain 'B' and resid 910 through 922 removed outlier: 3.507A pdb=" N ALA B 916 " --> pdb=" O PRO B 912 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 920 " --> pdb=" O ALA B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE B 944 " --> pdb=" O GLN B 940 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 947 " --> pdb=" O ALA B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 970 through 974 Processing helix chain 'B' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1026 No H-bonds generated for 'chain 'B' and resid 1024 through 1026' Processing helix chain 'B' and resid 1031 through 1068 removed outlier: 3.666A pdb=" N ILE B1035 " --> pdb=" O SER B1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 54 through 64 Processing helix chain 'C' and resid 91 through 103 removed outlier: 4.071A pdb=" N UNK C 103 " --> pdb=" O UNK C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.857A pdb=" N GLU C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU C 131 " --> pdb=" O PRO C 127 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.761A pdb=" N HIS C 234 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 235 " --> pdb=" O HIS C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.556A pdb=" N LYS C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 287 removed outlier: 3.971A pdb=" N ILE C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 302 through 320 removed outlier: 4.284A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.809A pdb=" N GLN C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.809A pdb=" N SER C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 430 removed outlier: 4.914A pdb=" N MET C 428 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 429 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU C 430 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 440 removed outlier: 3.891A pdb=" N ILE C 440 " --> pdb=" O MET C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 506 through 531 removed outlier: 4.132A pdb=" N LEU C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 4.266A pdb=" N VAL C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.789A pdb=" N TRP C 574 " --> pdb=" O LYS C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 596 removed outlier: 3.873A pdb=" N SER C 582 " --> pdb=" O TYR C 578 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 593 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 3.903A pdb=" N ILE C 619 " --> pdb=" O ALA C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.831A pdb=" N ARG C 630 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU C 631 " --> pdb=" O TRP C 627 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 632 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 633 " --> pdb=" O VAL C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 removed outlier: 4.086A pdb=" N TYR C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY C 649 " --> pdb=" O VAL C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 678 removed outlier: 3.550A pdb=" N PHE C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 661 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 666 " --> pdb=" O MET C 662 " (cutoff:3.500A) Proline residue: C 672 - end of helix removed outlier: 4.003A pdb=" N ILE C 676 " --> pdb=" O PRO C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 697 removed outlier: 4.586A pdb=" N HIS C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Proline residue: C 695 - end of helix Processing helix chain 'C' and resid 727 through 739 removed outlier: 3.506A pdb=" N ALA C 733 " --> pdb=" O PRO C 729 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 755 through 770 removed outlier: 4.240A pdb=" N ILE C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 764 " --> pdb=" O ALA C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 775 Processing helix chain 'C' and resid 787 through 791 Processing helix chain 'C' and resid 818 through 840 removed outlier: 3.893A pdb=" N GLU C 834 " --> pdb=" O GLU C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 843 No H-bonds generated for 'chain 'C' and resid 841 through 843' Processing helix chain 'C' and resid 848 through 885 removed outlier: 3.666A pdb=" N ILE C 852 " --> pdb=" O SER C 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 16 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 236 through 246 Processing helix chain 'D' and resid 273 through 285 removed outlier: 4.071A pdb=" N UNK D 285 " --> pdb=" O UNK D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.856A pdb=" N GLU D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.562A pdb=" N MET D 358 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 removed outlier: 3.761A pdb=" N HIS D 417 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 418 " --> pdb=" O HIS D 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 414 through 418' Processing helix chain 'D' and resid 435 through 442 removed outlier: 3.556A pdb=" N LYS D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.971A pdb=" N ILE D 465 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU D 491 " --> pdb=" O MET D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN D 538 " --> pdb=" O GLN D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 545 Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'D' and resid 574 through 587 Processing helix chain 'D' and resid 597 through 604 removed outlier: 3.802A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 613 removed outlier: 4.256A pdb=" N MET D 611 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 612 " --> pdb=" O ILE D 609 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU D 613 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 3.891A pdb=" N ILE D 623 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 687 Processing helix chain 'D' and resid 689 through 714 removed outlier: 4.132A pdb=" N LEU D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 714 " --> pdb=" O PHE D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 743 removed outlier: 4.266A pdb=" N VAL D 727 " --> pdb=" O GLN D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 758 removed outlier: 3.789A pdb=" N TRP D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER D 765 " --> pdb=" O TYR D 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 773 " --> pdb=" O ALA D 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 805 removed outlier: 3.902A pdb=" N ILE D 802 " --> pdb=" O ALA D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 819 removed outlier: 3.829A pdb=" N ARG D 813 " --> pdb=" O PHE D 809 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 814 " --> pdb=" O TRP D 810 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 815 " --> pdb=" O TYR D 811 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 816 " --> pdb=" O VAL D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 832 removed outlier: 4.086A pdb=" N TYR D 827 " --> pdb=" O GLN D 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY D 832 " --> pdb=" O VAL D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 861 removed outlier: 3.550A pdb=" N PHE D 839 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D 841 " --> pdb=" O ASN D 837 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE D 844 " --> pdb=" O TYR D 840 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 849 " --> pdb=" O MET D 845 " (cutoff:3.500A) Proline residue: D 855 - end of helix removed outlier: 4.003A pdb=" N ILE D 859 " --> pdb=" O PRO D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 880 removed outlier: 4.586A pdb=" N HIS D 877 " --> pdb=" O ASP D 873 " (cutoff:3.500A) Proline residue: D 878 - end of helix Processing helix chain 'D' and resid 910 through 922 removed outlier: 3.506A pdb=" N ALA D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE D 920 " --> pdb=" O ALA D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE D 944 " --> pdb=" O GLN D 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE D 947 " --> pdb=" O ALA D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 953 through 958 Processing helix chain 'D' and resid 970 through 974 Processing helix chain 'D' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU D1017 " --> pdb=" O GLU D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1026 No H-bonds generated for 'chain 'D' and resid 1024 through 1026' Processing helix chain 'D' and resid 1031 through 1068 removed outlier: 3.665A pdb=" N ILE D1035 " --> pdb=" O SER D1031 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 10.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3939 1.32 - 1.44: 6177 1.44 - 1.57: 13281 1.57 - 1.69: 36 1.69 - 1.81: 212 Bond restraints: 23645 Sorted by residual: bond pdb=" CAV Y01 C1303 " pdb=" CAZ Y01 C1303 " ideal model delta sigma weight residual 1.507 1.362 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" CAV Y01 C1306 " pdb=" CAZ Y01 C1306 " ideal model delta sigma weight residual 1.507 1.378 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" CAZ Y01 B1204 " pdb=" CBH Y01 B1204 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAZ Y01 A1203 " pdb=" CBH Y01 A1203 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAV Y01 D1203 " pdb=" CAZ Y01 D1203 " ideal model delta sigma weight residual 1.507 1.390 0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 23640 not shown) Histogram of bond angle deviations from ideal: 93.74 - 103.15: 265 103.15 - 112.56: 12260 112.56 - 121.97: 15124 121.97 - 131.38: 4421 131.38 - 140.79: 159 Bond angle restraints: 32229 Sorted by residual: angle pdb=" C ILE C 167 " pdb=" N GLY C 168 " pdb=" CA GLY C 168 " ideal model delta sigma weight residual 121.41 140.79 -19.38 1.96e+00 2.60e-01 9.78e+01 angle pdb=" C TRP A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta sigma weight residual 122.82 134.84 -12.02 1.42e+00 4.96e-01 7.16e+01 angle pdb=" C TRP B 480 " pdb=" N GLN B 481 " pdb=" CA GLN B 481 " ideal model delta sigma weight residual 122.82 134.83 -12.01 1.42e+00 4.96e-01 7.15e+01 angle pdb=" C TRP C 297 " pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta sigma weight residual 122.82 134.83 -12.01 1.42e+00 4.96e-01 7.15e+01 angle pdb=" C TRP D 480 " pdb=" N GLN D 481 " pdb=" CA GLN D 481 " ideal model delta sigma weight residual 122.82 134.82 -12.00 1.42e+00 4.96e-01 7.14e+01 ... (remaining 32224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 13309 26.92 - 53.84: 407 53.84 - 80.76: 26 80.76 - 107.68: 15 107.68 - 134.60: 6 Dihedral angle restraints: 13763 sinusoidal: 4651 harmonic: 9112 Sorted by residual: dihedral pdb=" CA TRP A 480 " pdb=" C TRP A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta harmonic sigma weight residual 180.00 45.40 134.60 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" CA TRP D 480 " pdb=" C TRP D 480 " pdb=" N GLN D 481 " pdb=" CA GLN D 481 " ideal model delta harmonic sigma weight residual 180.00 45.45 134.55 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA TRP C 297 " pdb=" C TRP C 297 " pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta harmonic sigma weight residual 180.00 45.47 134.53 0 5.00e+00 4.00e-02 7.24e+02 ... (remaining 13760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3292 0.106 - 0.212: 334 0.212 - 0.318: 81 0.318 - 0.425: 43 0.425 - 0.531: 25 Chirality restraints: 3775 Sorted by residual: chirality pdb=" CBF Y01 A1206 " pdb=" CAS Y01 A1206 " pdb=" CBD Y01 A1206 " pdb=" CBH Y01 A1206 " both_signs ideal model delta sigma weight residual False -2.45 -2.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CBG Y01 C1303 " pdb=" CAQ Y01 C1303 " pdb=" CBD Y01 C1303 " pdb=" CBI Y01 C1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CBG Y01 B1205 " pdb=" CAQ Y01 B1205 " pdb=" CBD Y01 B1205 " pdb=" CBI Y01 B1205 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 3772 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 167 " -0.033 2.00e-02 2.50e+03 6.63e-02 4.39e+01 pdb=" C ILE C 167 " 0.115 2.00e-02 2.50e+03 pdb=" O ILE C 167 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY C 168 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 605 " 0.092 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO D 606 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO D 606 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 606 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 353 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C VAL A 353 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL A 353 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE A 354 " 0.023 2.00e-02 2.50e+03 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 1 1.98 - 2.71: 1268 2.71 - 3.44: 32255 3.44 - 4.17: 51645 4.17 - 4.90: 88268 Nonbonded interactions: 173437 Sorted by model distance: nonbonded pdb="MG MG D1201 " pdb=" O HOH D1307 " model vdw 1.254 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH B1301 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH A1304 " model vdw 2.047 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH C1404 " model vdw 2.073 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH D1303 " model vdw 2.079 2.170 ... (remaining 173432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 346 or (resid 347 through 348 and (name N or nam \ e CA or name C or name O or name CB )) or resid 349 through 351 or (resid 352 an \ d (name N or name CA or name C or name O or name CB )) or resid 353 through 362 \ or (resid 363 through 365 and (name N or name CA or name C or name O or name CB \ )) or resid 366 through 432 or (resid 433 through 434 and (name N or name CA or \ name C or name O or name CB )) or resid 435 through 443 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 455 through 484 or (resi \ d 485 and (name N or name CA or name C or name O or name CB )) or resid 486 thro \ ugh 514 or (resid 515 through 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 538 or (resid 539 through 540 and (name N or nam \ e CA or name C or name O or name CB )) or resid 541 through 550 or (resid 551 an \ d (name N or name CA or name C or name O or name CB )) or resid 552 through 1068 \ or resid 1203)) selection = (chain 'B' and (resid 1 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 346 or (resid 347 through 348 an \ d (name N or name CA or name C or name O or name CB )) or resid 349 through 353 \ or (resid 354 through 355 and (name N or name CA or name C or name O or name CB \ )) or resid 356 through 362 or (resid 363 through 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 439 or (resid 440 and (name \ N or name CA or name C or name O or name CB )) or resid 441 through 443 or (resi \ d 454 and (name N or name CA or name C or name O or name CB )) or resid 455 thro \ ugh 484 or (resid 485 and (name N or name CA or name C or name O or name CB )) o \ r resid 486 through 514 or (resid 515 through 516 and (name N or name CA or name \ C or name O or name CB )) or resid 517 through 522 or (resid 523 and (name N or \ name CA or name C or name O or name CB )) or resid 524 through 538 or (resid 53 \ 9 through 540 and (name N or name CA or name C or name O or name CB )) or resid \ 541 through 1068 or resid 1203)) selection = (chain 'C' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 163 or (resid 164 through 165 an \ d (name N or name CA or name C or name O or name CB )) or resid 166 through 170 \ or (resid 171 through 172 and (name N or name CA or name C or name O or name CB \ )) or resid 173 through 179 or (resid 180 through 182 and (name N or name CA or \ name C or name O or name CB )) or resid 183 through 232 or (resid 233 through 23 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 235 through \ 249 or (resid 250 through 251 and (name N or name CA or name C or name O or name \ CB )) or resid 252 through 256 or (resid 257 and (name N or name CA or name C o \ r name O or name CB )) or resid 258 through 300 or (resid 301 through 302 and (n \ ame N or name CA or name C or name O or name CB )) or resid 303 through 331 or ( \ resid 332 through 333 and (name N or name CA or name C or name O or name CB )) o \ r resid 334 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 355 or (resid 356 through 357 and (name N or \ name CA or name C or name O or name CB )) or resid 358 through 885 or resid 130 \ 3)) selection = (chain 'D' and (resid 1 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 353 or (resid 354 through 355 an \ d (name N or name CA or name C or name O or name CB )) or resid 356 through 433 \ or (resid 434 and (name N or name CA or name C or name O or name CB )) or resid \ 435 through 439 or (resid 440 and (name N or name CA or name C or name O or name \ CB )) or resid 441 through 443 or (resid 454 and (name N or name CA or name C o \ r name O or name CB )) or resid 455 through 550 or (resid 551 and (name N or nam \ e CA or name C or name O or name CB )) or resid 552 through 605 or (resid 606 an \ d (name N or name CA or name C or name O or name CB )) or resid 607 through 1068 \ or resid 1203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 5 5.21 5 S 122 5.16 5 C 15156 2.51 5 N 3822 2.21 5 O 4082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.790 Check model and map are aligned: 0.390 Process input model: 59.700 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.230 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.145 23645 Z= 0.718 Angle : 1.653 19.383 32229 Z= 0.858 Chirality : 0.092 0.531 3775 Planarity : 0.009 0.135 3968 Dihedral : 13.726 134.605 7791 Min Nonbonded Distance : 1.254 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.33 % Twisted Proline : 3.70 % Twisted General : 3.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.69 (0.12), residues: 2528 helix: -3.51 (0.09), residues: 1578 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 950 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 628 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 637 average time/residue: 0.3462 time to fit residues: 340.5170 Evaluate side-chains 419 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 417 time to evaluate : 2.477 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2210 time to fit residues: 4.1525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 146 optimal weight: 0.0970 chunk 179 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 578 GLN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1048 GLN B 395 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B 553 ASN B 578 GLN B 590 ASN B 806 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 395 GLN C 540 GLN ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 GLN D 395 GLN D 522 ASN D 538 GLN D 553 ASN D 578 GLN D 590 ASN D 763 ASN ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 HIS D1005 GLN D1014 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 23645 Z= 0.303 Angle : 1.113 18.236 32229 Z= 0.496 Chirality : 0.049 0.259 3775 Planarity : 0.005 0.085 3968 Dihedral : 10.694 111.061 3506 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.18 % Favored : 89.91 % Rotamer Outliers : 4.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.51 % Twisted Proline : 2.78 % Twisted General : 0.90 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.15), residues: 2528 helix: -2.00 (0.11), residues: 1681 sheet: None (None), residues: 0 loop : -3.95 (0.19), residues: 847 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 489 time to evaluate : 2.530 Fit side-chains outliers start: 90 outliers final: 44 residues processed: 541 average time/residue: 0.3235 time to fit residues: 278.7621 Evaluate side-chains 445 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 401 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2112 time to fit residues: 20.3015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 302 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN A 763 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 538 GLN B 896 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 GLN ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1014 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 23645 Z= 0.234 Angle : 1.052 18.732 32229 Z= 0.460 Chirality : 0.047 0.227 3775 Planarity : 0.005 0.071 3968 Dihedral : 9.927 107.016 3506 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.73 % Favored : 89.40 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.51 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.16), residues: 2528 helix: -1.26 (0.12), residues: 1671 sheet: None (None), residues: 0 loop : -3.92 (0.19), residues: 857 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 444 time to evaluate : 2.807 Fit side-chains outliers start: 61 outliers final: 22 residues processed: 481 average time/residue: 0.3217 time to fit residues: 248.9258 Evaluate side-chains 412 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 390 time to evaluate : 2.307 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2574 time to fit residues: 13.2386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.9990 chunk 210 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 297 optimal weight: 0.5980 chunk 146 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 ASN A 806 ASN A 837 ASN C 355 GLN C 580 ASN C 753 ASN C 831 GLN D 395 GLN D 473 GLN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 HIS ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 23645 Z= 0.239 Angle : 1.035 18.214 32229 Z= 0.450 Chirality : 0.046 0.227 3775 Planarity : 0.004 0.060 3968 Dihedral : 9.575 109.210 3506 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.93 % Favored : 89.36 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.51 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.16), residues: 2528 helix: -0.85 (0.13), residues: 1661 sheet: None (None), residues: 0 loop : -3.82 (0.19), residues: 867 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 425 time to evaluate : 2.717 Fit side-chains outliers start: 80 outliers final: 49 residues processed: 473 average time/residue: 0.3342 time to fit residues: 250.3191 Evaluate side-chains 428 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 379 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2221 time to fit residues: 23.5960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 221 optimal weight: 0.1980 chunk 122 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 ASN A 806 ASN A 837 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 ASN B1048 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN C 355 GLN C 580 ASN C 831 GLN ** C 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS D 538 GLN ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 ASN D1014 GLN D1057 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 23645 Z= 0.241 Angle : 1.036 18.248 32229 Z= 0.449 Chirality : 0.046 0.254 3775 Planarity : 0.004 0.048 3968 Dihedral : 9.374 108.490 3506 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.93 % Favored : 89.20 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.51 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.17), residues: 2528 helix: -0.58 (0.13), residues: 1659 sheet: None (None), residues: 0 loop : -3.83 (0.18), residues: 869 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 429 time to evaluate : 2.620 Fit side-chains outliers start: 56 outliers final: 33 residues processed: 461 average time/residue: 0.3344 time to fit residues: 246.3396 Evaluate side-chains 411 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 378 time to evaluate : 2.903 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2454 time to fit residues: 18.3149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.5980 chunk 268 optimal weight: 0.0870 chunk 58 optimal weight: 0.0670 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 ASN A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 193 ASN C 212 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 GLN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 23645 Z= 0.196 Angle : 1.016 18.101 32229 Z= 0.436 Chirality : 0.045 0.214 3775 Planarity : 0.004 0.051 3968 Dihedral : 9.067 107.855 3506 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.38 % Favored : 89.83 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.17), residues: 2528 helix: -0.30 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -3.72 (0.18), residues: 890 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 424 time to evaluate : 2.530 Fit side-chains outliers start: 40 outliers final: 31 residues processed: 442 average time/residue: 0.3335 time to fit residues: 236.0190 Evaluate side-chains 418 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 387 time to evaluate : 2.653 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2754 time to fit residues: 18.9761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3193 > 50: distance: 89 - 94: 31.310 distance: 94 - 95: 40.522 distance: 95 - 96: 44.465 distance: 95 - 98: 28.014 distance: 96 - 97: 18.854 distance: 96 - 106: 38.999 distance: 98 - 99: 24.380 distance: 99 - 100: 43.529 distance: 99 - 101: 13.740 distance: 100 - 102: 26.179 distance: 101 - 103: 18.606 distance: 102 - 104: 17.179 distance: 103 - 104: 18.289 distance: 106 - 107: 38.114 distance: 107 - 108: 46.567 distance: 107 - 110: 18.730 distance: 108 - 109: 55.934 distance: 108 - 120: 23.090 distance: 110 - 111: 33.419 distance: 111 - 112: 13.862 distance: 111 - 113: 9.222 distance: 112 - 114: 17.700 distance: 113 - 115: 23.081 distance: 113 - 116: 32.336 distance: 114 - 115: 25.851 distance: 115 - 117: 27.870 distance: 116 - 118: 14.198 distance: 117 - 119: 16.043 distance: 118 - 119: 8.204 distance: 120 - 121: 21.851 distance: 121 - 122: 25.575 distance: 121 - 124: 22.139 distance: 122 - 123: 35.016 distance: 122 - 128: 16.720 distance: 124 - 125: 46.413 distance: 125 - 126: 27.773 distance: 126 - 127: 17.166 distance: 128 - 129: 50.262 distance: 129 - 130: 7.277 distance: 129 - 132: 44.011 distance: 130 - 131: 23.659 distance: 130 - 136: 5.909 distance: 132 - 133: 21.543 distance: 132 - 134: 48.413 distance: 133 - 135: 21.787 distance: 136 - 137: 10.464 distance: 137 - 138: 24.301 distance: 137 - 140: 43.992 distance: 138 - 139: 41.312 distance: 138 - 147: 28.946 distance: 140 - 141: 36.813 distance: 141 - 142: 33.643 distance: 141 - 143: 13.891 distance: 142 - 144: 46.531 distance: 143 - 145: 34.526 distance: 144 - 146: 33.914 distance: 145 - 146: 16.420 distance: 147 - 148: 39.234 distance: 148 - 149: 41.443 distance: 149 - 150: 21.680 distance: 149 - 151: 36.173 distance: 151 - 152: 37.851 distance: 152 - 153: 38.607 distance: 152 - 155: 40.907 distance: 153 - 154: 42.784 distance: 153 - 160: 28.977 distance: 155 - 156: 31.217 distance: 156 - 157: 31.208 distance: 157 - 158: 37.446 distance: 160 - 161: 41.441 distance: 161 - 162: 25.349 distance: 161 - 164: 8.648 distance: 162 - 163: 23.943 distance: 162 - 167: 45.880 distance: 164 - 165: 6.871 distance: 164 - 166: 24.441 distance: 167 - 168: 35.000 distance: 168 - 169: 39.376 distance: 168 - 171: 9.543 distance: 169 - 170: 37.809 distance: 171 - 172: 11.518 distance: 172 - 173: 14.014 distance: 172 - 174: 30.076 distance: 173 - 175: 17.474 distance: 174 - 176: 20.475 distance: 175 - 177: 13.594 distance: 176 - 177: 19.561 distance: 177 - 178: 47.888 distance: 179 - 180: 7.103 distance: 180 - 181: 57.195 distance: 180 - 183: 39.512 distance: 181 - 182: 37.811 distance: 181 - 184: 31.819