Starting phenix.real_space_refine on Sat Dec 16 14:03:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/12_2023/6co7_7542_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/12_2023/6co7_7542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/12_2023/6co7_7542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/12_2023/6co7_7542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/12_2023/6co7_7542_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/12_2023/6co7_7542_updated.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.008 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 20 5.49 5 S 188 5.16 5 Na 3 4.78 5 C 23024 2.51 5 N 5648 2.21 5 O 6368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 895": "NH1" <-> "NH2" Residue "A ARG 935": "NH1" <-> "NH2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A ARG 947": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A ARG 1016": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 642": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 820": "NH1" <-> "NH2" Residue "B ARG 895": "NH1" <-> "NH2" Residue "B ARG 935": "NH1" <-> "NH2" Residue "B ARG 941": "NH1" <-> "NH2" Residue "B ARG 947": "NH1" <-> "NH2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B ARG 1016": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B ARG 1132": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ARG 642": "NH1" <-> "NH2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C ARG 820": "NH1" <-> "NH2" Residue "C ARG 895": "NH1" <-> "NH2" Residue "C ARG 935": "NH1" <-> "NH2" Residue "C ARG 941": "NH1" <-> "NH2" Residue "C ARG 947": "NH1" <-> "NH2" Residue "C ARG 960": "NH1" <-> "NH2" Residue "C ARG 1016": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C ARG 1132": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 619": "NH1" <-> "NH2" Residue "D ARG 642": "NH1" <-> "NH2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D ARG 820": "NH1" <-> "NH2" Residue "D ARG 895": "NH1" <-> "NH2" Residue "D ARG 935": "NH1" <-> "NH2" Residue "D ARG 941": "NH1" <-> "NH2" Residue "D ARG 947": "NH1" <-> "NH2" Residue "D ARG 960": "NH1" <-> "NH2" Residue "D ARG 1016": "NH1" <-> "NH2" Residue "D ARG 1091": "NH1" <-> "NH2" Residue "D ARG 1132": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35255 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 366 Unusual residues: {' CA': 1, ' NA': 3, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-2': 8, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 363 Unusual residues: {' CA': 1, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-2': 8, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 363 Unusual residues: {' CA': 1, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-2': 8, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 363 Unusual residues: {' CA': 1, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-2': 8, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Time building chain proxies: 18.57, per 1000 atoms: 0.53 Number of scatterers: 35255 At special positions: 0 Unit cell: (149.35, 149.35, 159.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 188 16.00 P 20 15.00 Na 3 11.00 O 6368 8.00 N 5648 7.00 C 23024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A1017 " " NAG F 1 " - " ASN B1017 " " NAG G 1 " - " ASN C1017 " " NAG H 1 " - " ASN D1017 " Time building additional restraints: 15.72 Conformation dependent library (CDL) restraints added in 6.6 seconds 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 12 sheets defined 57.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.18 Creating SS restraints... Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 153 through 170 removed outlier: 4.082A pdb=" N ILE A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.193A pdb=" N MET A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.944A pdb=" N MET A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'A' and resid 450 through 462 removed outlier: 5.294A pdb=" N ALA A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 485 through 493 Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.708A pdb=" N LEU A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'A' and resid 593 through 601 Processing helix chain 'A' and resid 606 through 626 Processing helix chain 'A' and resid 634 through 658 Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.705A pdb=" N GLN A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 Processing helix chain 'A' and resid 689 through 692 No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 695 through 705 Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.975A pdb=" N TYR A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 749 removed outlier: 3.595A pdb=" N GLU A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 828 through 835 removed outlier: 3.841A pdb=" N PHE A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 860 Processing helix chain 'A' and resid 871 through 873 No H-bonds generated for 'chain 'A' and resid 871 through 873' Processing helix chain 'A' and resid 877 through 898 Processing helix chain 'A' and resid 905 through 912 Processing helix chain 'A' and resid 917 through 937 removed outlier: 4.279A pdb=" N PHE A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE A 937 " --> pdb=" O ILE A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 967 removed outlier: 5.229A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 962 " --> pdb=" O ILE A 958 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 967 " --> pdb=" O GLN A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1007 Proline residue: A 973 - end of helix removed outlier: 3.760A pdb=" N GLN A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A 983 " --> pdb=" O GLN A 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1035 removed outlier: 3.778A pdb=" N VAL A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix removed outlier: 3.565A pdb=" N MET A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR A1035 " --> pdb=" O TYR A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1043 No H-bonds generated for 'chain 'A' and resid 1040 through 1043' Processing helix chain 'A' and resid 1058 through 1074 Proline residue: A1063 - end of helix Processing helix chain 'A' and resid 1077 through 1113 removed outlier: 4.232A pdb=" N GLU A1090 " --> pdb=" O ASN A1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG A1091 " --> pdb=" O TYR A1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A1097 " --> pdb=" O GLN A1093 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A1098 " --> pdb=" O GLU A1094 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR A1105 " --> pdb=" O LYS A1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1135 removed outlier: 3.823A pdb=" N LEU A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A1129 " --> pdb=" O GLY A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1181 Processing helix chain 'A' and resid 1184 through 1209 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 153 through 170 removed outlier: 4.081A pdb=" N ILE B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 4.193A pdb=" N MET B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.944A pdb=" N MET B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 421 through 431 Processing helix chain 'B' and resid 434 through 440 Processing helix chain 'B' and resid 450 through 462 removed outlier: 5.294A pdb=" N ALA B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.709A pdb=" N LEU B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 579 through 589 Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 606 through 626 Processing helix chain 'B' and resid 634 through 658 Processing helix chain 'B' and resid 660 through 668 removed outlier: 3.705A pdb=" N GLN B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 Processing helix chain 'B' and resid 689 through 692 No H-bonds generated for 'chain 'B' and resid 689 through 692' Processing helix chain 'B' and resid 695 through 705 Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.974A pdb=" N TYR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 749 removed outlier: 3.595A pdb=" N GLU B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 Processing helix chain 'B' and resid 828 through 835 removed outlier: 3.841A pdb=" N PHE B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 860 Processing helix chain 'B' and resid 871 through 873 No H-bonds generated for 'chain 'B' and resid 871 through 873' Processing helix chain 'B' and resid 877 through 898 Processing helix chain 'B' and resid 905 through 912 Processing helix chain 'B' and resid 917 through 937 removed outlier: 4.279A pdb=" N PHE B 936 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 967 removed outlier: 5.229A pdb=" N ILE B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER B 961 " --> pdb=" O PHE B 957 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 962 " --> pdb=" O ILE B 958 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 964 " --> pdb=" O ARG B 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 967 " --> pdb=" O GLN B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1007 Proline residue: B 973 - end of helix removed outlier: 3.760A pdb=" N GLN B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN B 983 " --> pdb=" O GLN B 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1035 removed outlier: 3.778A pdb=" N VAL B1027 " --> pdb=" O ILE B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix removed outlier: 3.566A pdb=" N MET B1034 " --> pdb=" O PRO B1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR B1035 " --> pdb=" O TYR B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1043 No H-bonds generated for 'chain 'B' and resid 1040 through 1043' Processing helix chain 'B' and resid 1058 through 1074 Proline residue: B1063 - end of helix Processing helix chain 'B' and resid 1077 through 1113 removed outlier: 4.233A pdb=" N GLU B1090 " --> pdb=" O ASN B1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B1091 " --> pdb=" O TYR B1087 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B1095 " --> pdb=" O ARG B1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B1097 " --> pdb=" O GLN B1093 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS B1098 " --> pdb=" O GLU B1094 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR B1105 " --> pdb=" O LYS B1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B1106 " --> pdb=" O PHE B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1135 removed outlier: 3.823A pdb=" N LEU B1128 " --> pdb=" O LEU B1124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B1129 " --> pdb=" O GLY B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1181 Processing helix chain 'B' and resid 1184 through 1209 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 153 through 170 removed outlier: 4.081A pdb=" N ILE C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 removed outlier: 4.193A pdb=" N MET C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 221 No H-bonds generated for 'chain 'C' and resid 218 through 221' Processing helix chain 'C' and resid 268 through 279 removed outlier: 3.944A pdb=" N MET C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 329 through 338 Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'C' and resid 421 through 431 Processing helix chain 'C' and resid 434 through 440 Processing helix chain 'C' and resid 450 through 462 removed outlier: 5.293A pdb=" N ALA C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 485 through 493 Processing helix chain 'C' and resid 500 through 510 removed outlier: 3.708A pdb=" N LEU C 504 " --> pdb=" O THR C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 542 through 544 No H-bonds generated for 'chain 'C' and resid 542 through 544' Processing helix chain 'C' and resid 579 through 589 Processing helix chain 'C' and resid 593 through 601 Processing helix chain 'C' and resid 606 through 626 Processing helix chain 'C' and resid 634 through 658 Processing helix chain 'C' and resid 660 through 668 removed outlier: 3.705A pdb=" N GLN C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 685 Processing helix chain 'C' and resid 689 through 692 No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 695 through 705 Processing helix chain 'C' and resid 715 through 723 removed outlier: 3.975A pdb=" N TYR C 723 " --> pdb=" O LEU C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 749 removed outlier: 3.595A pdb=" N GLU C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 828 through 835 removed outlier: 3.842A pdb=" N PHE C 833 " --> pdb=" O ARG C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 860 Processing helix chain 'C' and resid 871 through 873 No H-bonds generated for 'chain 'C' and resid 871 through 873' Processing helix chain 'C' and resid 877 through 898 Processing helix chain 'C' and resid 905 through 912 Processing helix chain 'C' and resid 917 through 937 removed outlier: 4.280A pdb=" N PHE C 936 " --> pdb=" O ILE C 932 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE C 937 " --> pdb=" O ILE C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 967 removed outlier: 5.229A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER C 961 " --> pdb=" O PHE C 957 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU C 962 " --> pdb=" O ILE C 958 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C 964 " --> pdb=" O ARG C 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 967 " --> pdb=" O GLN C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1007 Proline residue: C 973 - end of helix removed outlier: 3.759A pdb=" N GLN C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN C 983 " --> pdb=" O GLN C 979 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1035 removed outlier: 3.778A pdb=" N VAL C1027 " --> pdb=" O ILE C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix removed outlier: 3.565A pdb=" N MET C1034 " --> pdb=" O PRO C1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR C1035 " --> pdb=" O TYR C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1043 No H-bonds generated for 'chain 'C' and resid 1040 through 1043' Processing helix chain 'C' and resid 1058 through 1074 Proline residue: C1063 - end of helix Processing helix chain 'C' and resid 1077 through 1113 removed outlier: 4.231A pdb=" N GLU C1090 " --> pdb=" O ASN C1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG C1091 " --> pdb=" O TYR C1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP C1095 " --> pdb=" O ARG C1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP C1097 " --> pdb=" O GLN C1093 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS C1098 " --> pdb=" O GLU C1094 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR C1105 " --> pdb=" O LYS C1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C1106 " --> pdb=" O PHE C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1135 removed outlier: 3.823A pdb=" N LEU C1128 " --> pdb=" O LEU C1124 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C1129 " --> pdb=" O GLY C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1155 through 1181 Processing helix chain 'C' and resid 1184 through 1209 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 153 through 170 removed outlier: 4.082A pdb=" N ILE D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.193A pdb=" N MET D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 221 No H-bonds generated for 'chain 'D' and resid 218 through 221' Processing helix chain 'D' and resid 268 through 279 removed outlier: 3.944A pdb=" N MET D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 315 Processing helix chain 'D' and resid 329 through 338 Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 375 through 385 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 421 through 431 Processing helix chain 'D' and resid 434 through 440 Processing helix chain 'D' and resid 450 through 462 removed outlier: 5.294A pdb=" N ALA D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 479 through 482 No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 500 through 510 removed outlier: 3.708A pdb=" N LEU D 504 " --> pdb=" O THR D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 593 through 601 Processing helix chain 'D' and resid 606 through 626 Processing helix chain 'D' and resid 634 through 658 Processing helix chain 'D' and resid 660 through 668 removed outlier: 3.705A pdb=" N GLN D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 685 Processing helix chain 'D' and resid 689 through 692 No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 695 through 705 Processing helix chain 'D' and resid 715 through 723 removed outlier: 3.974A pdb=" N TYR D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 749 removed outlier: 3.595A pdb=" N GLU D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 819 Processing helix chain 'D' and resid 828 through 835 removed outlier: 3.842A pdb=" N PHE D 833 " --> pdb=" O ARG D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 860 Processing helix chain 'D' and resid 871 through 873 No H-bonds generated for 'chain 'D' and resid 871 through 873' Processing helix chain 'D' and resid 877 through 898 Processing helix chain 'D' and resid 905 through 912 Processing helix chain 'D' and resid 917 through 937 removed outlier: 4.280A pdb=" N PHE D 936 " --> pdb=" O ILE D 932 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE D 937 " --> pdb=" O ILE D 933 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 967 removed outlier: 5.229A pdb=" N ILE D 955 " --> pdb=" O SER D 951 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE D 956 " --> pdb=" O LEU D 952 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER D 961 " --> pdb=" O PHE D 957 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU D 962 " --> pdb=" O ILE D 958 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN D 963 " --> pdb=" O VAL D 959 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE D 964 " --> pdb=" O ARG D 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL D 967 " --> pdb=" O GLN D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 1007 Proline residue: D 973 - end of helix removed outlier: 3.760A pdb=" N GLN D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN D 983 " --> pdb=" O GLN D 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP D 984 " --> pdb=" O LYS D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1035 removed outlier: 3.778A pdb=" N VAL D1027 " --> pdb=" O ILE D1023 " (cutoff:3.500A) Proline residue: D1030 - end of helix removed outlier: 3.566A pdb=" N MET D1034 " --> pdb=" O PRO D1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR D1035 " --> pdb=" O TYR D1031 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1043 No H-bonds generated for 'chain 'D' and resid 1040 through 1043' Processing helix chain 'D' and resid 1058 through 1074 Proline residue: D1063 - end of helix Processing helix chain 'D' and resid 1077 through 1113 removed outlier: 4.232A pdb=" N GLU D1090 " --> pdb=" O ASN D1086 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG D1091 " --> pdb=" O TYR D1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP D1095 " --> pdb=" O ARG D1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP D1097 " --> pdb=" O GLN D1093 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS D1098 " --> pdb=" O GLU D1094 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR D1105 " --> pdb=" O LYS D1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP D1106 " --> pdb=" O PHE D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1135 removed outlier: 3.824A pdb=" N LEU D1128 " --> pdb=" O LEU D1124 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D1129 " --> pdb=" O GLY D1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 1155 through 1181 Processing helix chain 'D' and resid 1184 through 1209 Processing sheet with id= A, first strand: chain 'A' and resid 46 through 48 Processing sheet with id= B, first strand: chain 'A' and resid 97 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 111 through 115 removed outlier: 6.633A pdb=" N PHE A 253 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET A 114 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A 255 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 46 through 48 Processing sheet with id= E, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= F, first strand: chain 'B' and resid 111 through 115 removed outlier: 6.634A pdb=" N PHE B 253 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET B 114 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 255 " --> pdb=" O MET B 114 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 46 through 48 Processing sheet with id= H, first strand: chain 'C' and resid 97 through 99 Processing sheet with id= I, first strand: chain 'C' and resid 111 through 115 removed outlier: 6.633A pdb=" N PHE C 253 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET C 114 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 255 " --> pdb=" O MET C 114 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 46 through 48 Processing sheet with id= K, first strand: chain 'D' and resid 97 through 99 Processing sheet with id= L, first strand: chain 'D' and resid 111 through 115 removed outlier: 6.634A pdb=" N PHE D 253 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET D 114 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU D 255 " --> pdb=" O MET D 114 " (cutoff:3.500A) 1648 hydrogen bonds defined for protein. 4932 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: 12.71 Time building geometry restraints manager: 16.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5620 1.31 - 1.43: 8968 1.43 - 1.56: 20904 1.56 - 1.68: 88 1.68 - 1.81: 344 Bond restraints: 35924 Sorted by residual: bond pdb=" C MET C1007 " pdb=" N PHE C1008 " ideal model delta sigma weight residual 1.330 1.481 -0.151 1.21e-02 6.83e+03 1.56e+02 bond pdb=" C MET A1007 " pdb=" N PHE A1008 " ideal model delta sigma weight residual 1.330 1.481 -0.150 1.21e-02 6.83e+03 1.54e+02 bond pdb=" C MET D1007 " pdb=" N PHE D1008 " ideal model delta sigma weight residual 1.330 1.481 -0.150 1.21e-02 6.83e+03 1.54e+02 bond pdb=" C MET B1007 " pdb=" N PHE B1008 " ideal model delta sigma weight residual 1.330 1.480 -0.150 1.21e-02 6.83e+03 1.53e+02 bond pdb=" C29 POV B3004 " pdb="C210 POV B3004 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 35919 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.05: 976 107.05 - 113.87: 19883 113.87 - 120.68: 15101 120.68 - 127.50: 12024 127.50 - 134.32: 344 Bond angle restraints: 48328 Sorted by residual: angle pdb=" N PRO B 8 " pdb=" CA PRO B 8 " pdb=" CB PRO B 8 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.47e+01 angle pdb=" N PRO C 8 " pdb=" CA PRO C 8 " pdb=" CB PRO C 8 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.47e+01 angle pdb=" N PRO D 8 " pdb=" CA PRO D 8 " pdb=" CB PRO D 8 " ideal model delta sigma weight residual 103.36 110.42 -7.06 8.80e-01 1.29e+00 6.44e+01 angle pdb=" N PRO A 8 " pdb=" CA PRO A 8 " pdb=" CB PRO A 8 " ideal model delta sigma weight residual 103.36 110.42 -7.06 8.80e-01 1.29e+00 6.43e+01 angle pdb=" N PRO D 50 " pdb=" CA PRO D 50 " pdb=" CB PRO D 50 " ideal model delta sigma weight residual 103.25 110.60 -7.35 1.05e+00 9.07e-01 4.90e+01 ... (remaining 48323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 21212 25.39 - 50.79: 696 50.79 - 76.18: 120 76.18 - 101.57: 32 101.57 - 126.96: 12 Dihedral angle restraints: 22072 sinusoidal: 9704 harmonic: 12368 Sorted by residual: dihedral pdb=" CA SER C1010 " pdb=" C SER C1010 " pdb=" N PRO C1011 " pdb=" CA PRO C1011 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER A1010 " pdb=" C SER A1010 " pdb=" N PRO A1011 " pdb=" CA PRO A1011 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER D1010 " pdb=" C SER D1010 " pdb=" N PRO D1011 " pdb=" CA PRO D1011 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 22069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3634 0.058 - 0.115: 1339 0.115 - 0.173: 305 0.173 - 0.231: 88 0.231 - 0.289: 10 Chirality restraints: 5376 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.97e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.94e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.76e+00 ... (remaining 5373 not shown) Planarity restraints: 5996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A3011 " 0.147 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV A3011 " -0.351 2.00e-02 2.50e+03 pdb="C210 POV A3011 " 0.345 2.00e-02 2.50e+03 pdb="C211 POV A3011 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C3011 " -0.146 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV C3011 " 0.351 2.00e-02 2.50e+03 pdb="C210 POV C3011 " -0.345 2.00e-02 2.50e+03 pdb="C211 POV C3011 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B3011 " 0.147 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV B3011 " -0.351 2.00e-02 2.50e+03 pdb="C210 POV B3011 " 0.345 2.00e-02 2.50e+03 pdb="C211 POV B3011 " -0.140 2.00e-02 2.50e+03 ... (remaining 5993 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 76 2.64 - 3.20: 29590 3.20 - 3.77: 51404 3.77 - 4.33: 72316 4.33 - 4.90: 119864 Nonbonded interactions: 273250 Sorted by model distance: nonbonded pdb="NA NA A4001 " pdb="NA NA A4002 " model vdw 2.070 1.900 nonbonded pdb=" O VAL B 859 " pdb=" OG SER C1010 " model vdw 2.384 2.440 nonbonded pdb=" O VAL A 859 " pdb=" OG SER B1010 " model vdw 2.384 2.440 nonbonded pdb=" O VAL C 859 " pdb=" OG SER D1010 " model vdw 2.390 2.440 nonbonded pdb=" OG SER A1010 " pdb=" O VAL D 859 " model vdw 2.393 2.440 ... (remaining 273245 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 6 through 1210 or (resid 3002 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3004 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3006 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3007 or resid 3009)) selection = (chain 'B' and (resid 6 through 1210 or (resid 3001 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3003 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3005 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3006 or (resid 3008 and (name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C310 or name C311 or name C312)))) selection = (chain 'C' and (resid 6 through 1210 or (resid 3001 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3003 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3005 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3006 or (resid 3008 and (name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C310 or name C311 or name C312)))) selection = (chain 'D' and (resid 6 through 1210 or (resid 3012 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3014 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3001 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or (resid 3002 and (name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C310 or name C311 or name C312 or name C313 or name C314 or name C315 or na \ me C316)) or (resid 3004 and (name C31 or name C32 or name C33 or name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C310 or name C311 \ or name C312)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic 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: 3.350 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: 0.030 Extract box with map and model: 14.430 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 91.710 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 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 0.202 35924 Z= 0.686 Angle : 1.390 20.322 48328 Z= 0.794 Chirality : 0.064 0.289 5376 Planarity : 0.012 0.266 5992 Dihedral : 14.009 126.964 14072 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 0.33 % Allowed : 2.44 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.00 (0.11), residues: 4196 helix: -0.51 (0.09), residues: 2544 sheet: -1.65 (0.31), residues: 180 loop : -2.67 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 885 HIS 0.004 0.001 HIS D1126 PHE 0.015 0.002 PHE D1085 TYR 0.012 0.001 TYR B 229 ARG 0.009 0.001 ARG B1059 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 784 time to evaluate : 3.871 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 791 average time/residue: 0.5417 time to fit residues: 661.9881 Evaluate side-chains 448 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 444 time to evaluate : 3.855 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3088 time to fit residues: 7.5866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 332 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 385 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN B 513 GLN C 513 GLN D 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4968 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35924 Z= 0.201 Angle : 0.582 8.511 48328 Z= 0.296 Chirality : 0.041 0.162 5376 Planarity : 0.004 0.050 5992 Dihedral : 12.590 89.332 6072 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 0.92 % Allowed : 7.67 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.52 (0.12), residues: 4196 helix: 0.85 (0.10), residues: 2544 sheet: -1.57 (0.30), residues: 256 loop : -2.36 (0.14), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 705 HIS 0.003 0.001 HIS B 250 PHE 0.013 0.001 PHE D 584 TYR 0.022 0.001 TYR C 312 ARG 0.006 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 483 time to evaluate : 4.075 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 501 average time/residue: 0.5387 time to fit residues: 420.0109 Evaluate side-chains 441 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 424 time to evaluate : 3.874 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3256 time to fit residues: 15.5692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 320 optimal weight: 50.0000 chunk 262 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 385 optimal weight: 0.7980 chunk 416 optimal weight: 7.9990 chunk 343 optimal weight: 4.9990 chunk 382 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 309 optimal weight: 4.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS A1086 ASN B 250 HIS B1086 ASN C 250 HIS C1086 ASN D 250 HIS D1086 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4979 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35924 Z= 0.354 Angle : 0.623 8.395 48328 Z= 0.315 Chirality : 0.045 0.165 5376 Planarity : 0.005 0.050 5992 Dihedral : 11.592 84.712 6072 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 1.58 % Allowed : 8.31 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.35 (0.13), residues: 4196 helix: 0.87 (0.10), residues: 2568 sheet: -1.23 (0.30), residues: 256 loop : -2.14 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 705 HIS 0.005 0.001 HIS C 250 PHE 0.017 0.002 PHE C 584 TYR 0.019 0.002 TYR B 229 ARG 0.007 0.001 ARG C 676 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 421 time to evaluate : 3.863 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 33 residues processed: 468 average time/residue: 0.5463 time to fit residues: 398.7920 Evaluate side-chains 439 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 406 time to evaluate : 3.712 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2929 time to fit residues: 23.2903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 1.9990 chunk 290 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 42 optimal weight: 0.0040 chunk 184 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 387 optimal weight: 0.9980 chunk 409 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 366 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: