Starting phenix.real_space_refine on Fri Aug 9 09:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/08_2024/5zx5_6975.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/08_2024/5zx5_6975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/08_2024/5zx5_6975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/08_2024/5zx5_6975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/08_2024/5zx5_6975.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/08_2024/5zx5_6975.cif" } resolution = 3.28 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 16752 2.51 5 N 4128 2.21 5 O 4396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "A TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 942": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 1018": "NH1" <-> "NH2" Residue "A ARG 1198": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ARG 750": "NH1" <-> "NH2" Residue "B TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 942": "NH1" <-> "NH2" Residue "B ARG 962": "NH1" <-> "NH2" Residue "B ARG 1018": "NH1" <-> "NH2" Residue "B ARG 1198": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C ARG 639": "NH1" <-> "NH2" Residue "C ARG 699": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C ARG 750": "NH1" <-> "NH2" Residue "C TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 942": "NH1" <-> "NH2" Residue "C ARG 962": "NH1" <-> "NH2" Residue "C ARG 1018": "NH1" <-> "NH2" Residue "C ARG 1198": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 525": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 639": "NH1" <-> "NH2" Residue "D ARG 699": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D ARG 750": "NH1" <-> "NH2" Residue "D TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 942": "NH1" <-> "NH2" Residue "D ARG 962": "NH1" <-> "NH2" Residue "D ARG 1018": "NH1" <-> "NH2" Residue "D ARG 1198": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25440 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6255 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 27, 'TRANS': 786} Chain breaks: 14 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 269 Chain: "B" Number of atoms: 6255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6255 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 27, 'TRANS': 786} Chain breaks: 14 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 269 Chain: "C" Number of atoms: 6255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6255 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 27, 'TRANS': 786} Chain breaks: 14 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 269 Chain: "D" Number of atoms: 6255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6255 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 27, 'TRANS': 786} Chain breaks: 14 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 269 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.23, per 1000 atoms: 0.48 Number of scatterers: 25440 At special positions: 0 Unit cell: (132.84, 132.84, 153.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 164 16.00 O 4396 8.00 N 4128 7.00 C 16752 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 Time building additional restraints: 8.15 Conformation dependent library (CDL) restraints added in 4.1 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 8 sheets defined 67.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 152 through 165 removed outlier: 4.247A pdb=" N LEU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.901A pdb=" N PHE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 366' Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 400 through 403 removed outlier: 4.151A pdb=" N THR A 403 " --> pdb=" O LEU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 403' Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.604A pdb=" N THR A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.897A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.725A pdb=" N LEU A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 488 through 494 Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.580A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.688A pdb=" N ILE A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 4.054A pdb=" N GLN A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 668 removed outlier: 3.509A pdb=" N LEU A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 668 " --> pdb=" O TYR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 680 Processing helix chain 'A' and resid 682 through 701 removed outlier: 3.538A pdb=" N PHE A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 688 " --> pdb=" O ASN A 684 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 691 " --> pdb=" O GLY A 687 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 709 removed outlier: 3.601A pdb=" N LYS A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 removed outlier: 4.043A pdb=" N SER A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 736 through 749 removed outlier: 3.555A pdb=" N SER A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 removed outlier: 4.080A pdb=" N ILE A 762 " --> pdb=" O TRP A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 842 through 850 removed outlier: 3.821A pdb=" N TYR A 846 " --> pdb=" O THR A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 876 removed outlier: 3.556A pdb=" N VAL A 876 " --> pdb=" O PHE A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 906 Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 922 through 944 removed outlier: 3.510A pdb=" N VAL A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 927 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.750A pdb=" N ALA A 960 " --> pdb=" O HIS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 981 removed outlier: 3.867A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 977 " --> pdb=" O TYR A 973 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.542A pdb=" N VAL A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 995 " --> pdb=" O MET A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1023 removed outlier: 3.856A pdb=" N ILE A1006 " --> pdb=" O TYR A1002 " (cutoff:3.500A) Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1030 through 1042 removed outlier: 3.792A pdb=" N LYS A1034 " --> pdb=" O TRP A1030 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS A1039 " --> pdb=" O ASP A1035 " (cutoff:3.500A) Proline residue: A1040 - end of helix Processing helix chain 'A' and resid 1072 through 1087 Processing helix chain 'A' and resid 1087 through 1123 removed outlier: 3.631A pdb=" N ILE A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLN A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A1109 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1121 " --> pdb=" O HIS A1117 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A1122 " --> pdb=" O PHE A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1185 removed outlier: 3.658A pdb=" N LYS A1168 " --> pdb=" O GLU A1164 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A1175 " --> pdb=" O HIS A1171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A1176 " --> pdb=" O ASP A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1192 through 1228 removed outlier: 3.520A pdb=" N GLN A1206 " --> pdb=" O GLU A1202 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A1226 " --> pdb=" O LYS A1222 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1227 " --> pdb=" O ARG A1223 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 152 through 165 removed outlier: 4.247A pdb=" N LEU B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.901A pdb=" N PHE B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 361 through 366' Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 400 through 403 removed outlier: 4.151A pdb=" N THR B 403 " --> pdb=" O LEU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 403' Processing helix chain 'B' and resid 406 through 417 removed outlier: 3.604A pdb=" N THR B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.897A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 451 through 462 removed outlier: 3.725A pdb=" N LEU B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 476 Processing helix chain 'B' and resid 488 through 494 Processing helix chain 'B' and resid 508 through 520 removed outlier: 3.580A pdb=" N VAL B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 537 Processing helix chain 'B' and resid 621 through 632 removed outlier: 3.688A pdb=" N ILE B 627 " --> pdb=" O ASN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 4.054A pdb=" N GLN B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 668 removed outlier: 3.509A pdb=" N LEU B 653 " --> pdb=" O MET B 649 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 682 through 701 removed outlier: 3.538A pdb=" N PHE B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 688 " --> pdb=" O ASN B 684 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 689 " --> pdb=" O ASP B 685 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 691 " --> pdb=" O GLY B 687 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 701 " --> pdb=" O SER B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 removed outlier: 3.601A pdb=" N LYS B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 728 removed outlier: 4.043A pdb=" N SER B 728 " --> pdb=" O LEU B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 736 through 749 removed outlier: 3.555A pdb=" N SER B 744 " --> pdb=" O GLN B 740 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 4.080A pdb=" N ILE B 762 " --> pdb=" O TRP B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 842 through 850 removed outlier: 3.821A pdb=" N TYR B 846 " --> pdb=" O THR B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 876 removed outlier: 3.556A pdb=" N VAL B 876 " --> pdb=" O PHE B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 906 Processing helix chain 'B' and resid 916 through 920 Processing helix chain 'B' and resid 922 through 944 removed outlier: 3.510A pdb=" N VAL B 926 " --> pdb=" O ASP B 922 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 927 " --> pdb=" O TYR B 923 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP B 928 " --> pdb=" O PHE B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 967 removed outlier: 3.750A pdb=" N ALA B 960 " --> pdb=" O HIS B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 981 removed outlier: 3.867A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 977 " --> pdb=" O TYR B 973 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 998 removed outlier: 3.542A pdb=" N VAL B 990 " --> pdb=" O ALA B 986 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS B 995 " --> pdb=" O MET B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1023 removed outlier: 3.856A pdb=" N ILE B1006 " --> pdb=" O TYR B1002 " (cutoff:3.500A) Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1030 through 1042 removed outlier: 3.792A pdb=" N LYS B1034 " --> pdb=" O TRP B1030 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS B1039 " --> pdb=" O ASP B1035 " (cutoff:3.500A) Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1072 through 1087 Processing helix chain 'B' and resid 1087 through 1123 removed outlier: 3.631A pdb=" N ILE B1093 " --> pdb=" O VAL B1089 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B1094 " --> pdb=" O ASN B1090 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU B1101 " --> pdb=" O ASN B1097 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLN B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B1121 " --> pdb=" O HIS B1117 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B1122 " --> pdb=" O PHE B1118 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1185 removed outlier: 3.658A pdb=" N LYS B1168 " --> pdb=" O GLU B1164 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B1175 " --> pdb=" O HIS B1171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B1176 " --> pdb=" O ASP B1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1188 No H-bonds generated for 'chain 'B' and resid 1186 through 1188' Processing helix chain 'B' and resid 1192 through 1228 removed outlier: 3.546A pdb=" N GLN B1206 " --> pdb=" O GLU B1202 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B1209 " --> pdb=" O GLU B1205 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B1226 " --> pdb=" O LYS B1222 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B1227 " --> pdb=" O ARG B1223 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B1228 " --> pdb=" O SER B1224 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 152 through 165 removed outlier: 4.247A pdb=" N LEU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 361 through 366 removed outlier: 3.901A pdb=" N PHE C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 366' Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 400 through 403 removed outlier: 4.151A pdb=" N THR C 403 " --> pdb=" O LEU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 403' Processing helix chain 'C' and resid 406 through 417 removed outlier: 3.604A pdb=" N THR C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 428 removed outlier: 3.897A pdb=" N ALA C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.725A pdb=" N LEU C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 476 Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 508 through 520 removed outlier: 3.580A pdb=" N VAL C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 537 Processing helix chain 'C' and resid 621 through 632 removed outlier: 3.688A pdb=" N ILE C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 4.054A pdb=" N GLN C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 668 removed outlier: 3.509A pdb=" N LEU C 653 " --> pdb=" O MET C 649 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN C 668 " --> pdb=" O TYR C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 680 Processing helix chain 'C' and resid 682 through 701 removed outlier: 3.538A pdb=" N PHE C 686 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 689 " --> pdb=" O ASP C 685 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 691 " --> pdb=" O GLY C 687 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 699 " --> pdb=" O GLU C 695 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 700 " --> pdb=" O GLN C 696 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 701 " --> pdb=" O SER C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 709 removed outlier: 3.601A pdb=" N LYS C 707 " --> pdb=" O THR C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 removed outlier: 4.043A pdb=" N SER C 728 " --> pdb=" O LEU C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 736 through 749 removed outlier: 3.555A pdb=" N SER C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET C 748 " --> pdb=" O SER C 744 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 749 " --> pdb=" O ASP C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 removed outlier: 4.080A pdb=" N ILE C 762 " --> pdb=" O TRP C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 842 through 850 removed outlier: 3.821A pdb=" N TYR C 846 " --> pdb=" O THR C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 876 removed outlier: 3.556A pdb=" N VAL C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 906 Processing helix chain 'C' and resid 916 through 920 Processing helix chain 'C' and resid 922 through 944 removed outlier: 3.510A pdb=" N VAL C 926 " --> pdb=" O ASP C 922 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER C 927 " --> pdb=" O TYR C 923 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP C 928 " --> pdb=" O PHE C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 967 removed outlier: 3.750A pdb=" N ALA C 960 " --> pdb=" O HIS C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 981 removed outlier: 3.867A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 977 " --> pdb=" O TYR C 973 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 998 removed outlier: 3.542A pdb=" N VAL C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY C 994 " --> pdb=" O VAL C 990 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS C 995 " --> pdb=" O MET C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1023 removed outlier: 3.856A pdb=" N ILE C1006 " --> pdb=" O TYR C1002 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1030 through 1042 removed outlier: 3.792A pdb=" N LYS C1034 " --> pdb=" O TRP C1030 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS C1039 " --> pdb=" O ASP C1035 " (cutoff:3.500A) Proline residue: C1040 - end of helix Processing helix chain 'C' and resid 1072 through 1087 Processing helix chain 'C' and resid 1087 through 1123 removed outlier: 3.631A pdb=" N ILE C1093 " --> pdb=" O VAL C1089 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C1094 " --> pdb=" O ASN C1090 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLN C1102 " --> pdb=" O ASN C1098 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C1109 " --> pdb=" O ALA C1105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C1121 " --> pdb=" O HIS C1117 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C1122 " --> pdb=" O PHE C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1185 removed outlier: 3.658A pdb=" N LYS C1168 " --> pdb=" O GLU C1164 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C1175 " --> pdb=" O HIS C1171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C1176 " --> pdb=" O ASP C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1188 No H-bonds generated for 'chain 'C' and resid 1186 through 1188' Processing helix chain 'C' and resid 1192 through 1228 removed outlier: 3.546A pdb=" N GLN C1206 " --> pdb=" O GLU C1202 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C1209 " --> pdb=" O GLU C1205 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C1226 " --> pdb=" O LYS C1222 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER C1227 " --> pdb=" O ARG C1223 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C1228 " --> pdb=" O SER C1224 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 152 through 165 removed outlier: 4.247A pdb=" N LEU D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 272 Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.901A pdb=" N PHE D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 361 through 366' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 400 through 403 removed outlier: 4.151A pdb=" N THR D 403 " --> pdb=" O LEU D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 403' Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.604A pdb=" N THR D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 428 removed outlier: 3.897A pdb=" N ALA D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 449 Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.725A pdb=" N LEU D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 476 Processing helix chain 'D' and resid 488 through 494 Processing helix chain 'D' and resid 508 through 520 removed outlier: 3.580A pdb=" N VAL D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 529 Processing helix chain 'D' and resid 530 through 537 Processing helix chain 'D' and resid 621 through 632 removed outlier: 3.688A pdb=" N ILE D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 4.054A pdb=" N GLN D 643 " --> pdb=" O ARG D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 668 removed outlier: 3.509A pdb=" N LEU D 653 " --> pdb=" O MET D 649 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN D 668 " --> pdb=" O TYR D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 680 Processing helix chain 'D' and resid 682 through 701 removed outlier: 3.538A pdb=" N PHE D 686 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 691 " --> pdb=" O GLY D 687 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN D 700 " --> pdb=" O GLN D 696 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 701 " --> pdb=" O SER D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 711 removed outlier: 3.601A pdb=" N LYS D 707 " --> pdb=" O THR D 703 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 4.043A pdb=" N SER D 728 " --> pdb=" O LEU D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 735 Processing helix chain 'D' and resid 736 through 749 removed outlier: 3.555A pdb=" N SER D 744 " --> pdb=" O GLN D 740 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET D 748 " --> pdb=" O SER D 744 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 749 " --> pdb=" O ASP D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 removed outlier: 4.080A pdb=" N ILE D 762 " --> pdb=" O TRP D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 771 Processing helix chain 'D' and resid 842 through 850 removed outlier: 3.821A pdb=" N TYR D 846 " --> pdb=" O THR D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 876 removed outlier: 3.556A pdb=" N VAL D 876 " --> pdb=" O PHE D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 906 Processing helix chain 'D' and resid 916 through 920 Processing helix chain 'D' and resid 922 through 944 removed outlier: 3.510A pdb=" N VAL D 926 " --> pdb=" O ASP D 922 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER D 927 " --> pdb=" O TYR D 923 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP D 928 " --> pdb=" O PHE D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 967 removed outlier: 3.750A pdb=" N ALA D 960 " --> pdb=" O HIS D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 981 removed outlier: 3.867A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 977 " --> pdb=" O TYR D 973 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 978 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 998 removed outlier: 3.542A pdb=" N VAL D 990 " --> pdb=" O ALA D 986 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY D 994 " --> pdb=" O VAL D 990 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS D 995 " --> pdb=" O MET D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1023 removed outlier: 3.856A pdb=" N ILE D1006 " --> pdb=" O TYR D1002 " (cutoff:3.500A) Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1030 through 1042 removed outlier: 3.792A pdb=" N LYS D1034 " --> pdb=" O TRP D1030 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS D1039 " --> pdb=" O ASP D1035 " (cutoff:3.500A) Proline residue: D1040 - end of helix Processing helix chain 'D' and resid 1072 through 1087 Processing helix chain 'D' and resid 1087 through 1123 removed outlier: 3.631A pdb=" N ILE D1093 " --> pdb=" O VAL D1089 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D1094 " --> pdb=" O ASN D1090 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU D1101 " --> pdb=" O ASN D1097 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLN D1102 " --> pdb=" O ASN D1098 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D1109 " --> pdb=" O ALA D1105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D1121 " --> pdb=" O HIS D1117 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D1122 " --> pdb=" O PHE D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1185 removed outlier: 3.658A pdb=" N LYS D1168 " --> pdb=" O GLU D1164 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D1175 " --> pdb=" O HIS D1171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D1176 " --> pdb=" O ASP D1172 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1188 No H-bonds generated for 'chain 'D' and resid 1186 through 1188' Processing helix chain 'D' and resid 1192 through 1228 removed outlier: 3.546A pdb=" N GLN D1206 " --> pdb=" O GLU D1202 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D1226 " --> pdb=" O LYS D1222 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D1227 " --> pdb=" O ARG D1223 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D1228 " --> pdb=" O SER D1224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 288 removed outlier: 6.214A pdb=" N ALA A 287 " --> pdb=" O LYS A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 287 through 288 removed outlier: 6.214A pdb=" N ALA B 287 " --> pdb=" O LYS B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'C' and resid 287 through 288 removed outlier: 6.214A pdb=" N ALA C 287 " --> pdb=" O LYS C 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'D' and resid 287 through 288 removed outlier: 6.214A pdb=" N ALA D 287 " --> pdb=" O LYS D 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 1266 hydrogen bonds defined for protein. 3774 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: 7.39 Time building geometry restraints manager: 9.05 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: 4835 1.32 - 1.45: 6425 1.45 - 1.57: 14470 1.57 - 1.69: 2 1.69 - 1.82: 284 Bond restraints: 26016 Sorted by residual: bond pdb=" CAI Y01 D1302 " pdb=" CAK Y01 D1302 " ideal model delta sigma weight residual 1.492 1.366 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CAV Y01 A1304 " pdb=" CAZ Y01 A1304 " ideal model delta sigma weight residual 1.507 1.382 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" CAI Y01 A1304 " pdb=" CAK Y01 A1304 " ideal model delta sigma weight residual 1.492 1.368 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAV Y01 C1302 " pdb=" CAZ Y01 C1302 " ideal model delta sigma weight residual 1.507 1.383 0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" CAV Y01 D1302 " pdb=" CAZ Y01 D1302 " ideal model delta sigma weight residual 1.507 1.385 0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 26011 not shown) Histogram of bond angle deviations from ideal: 89.06 - 99.01: 45 99.01 - 108.96: 2960 108.96 - 118.91: 18641 118.91 - 128.86: 13522 128.86 - 138.81: 248 Bond angle restraints: 35416 Sorted by residual: angle pdb=" N LEU A 298 " pdb=" CA LEU A 298 " pdb=" C LEU A 298 " ideal model delta sigma weight residual 111.28 125.33 -14.05 1.09e+00 8.42e-01 1.66e+02 angle pdb=" N GLU B 476 " pdb=" CA GLU B 476 " pdb=" C GLU B 476 " ideal model delta sigma weight residual 110.52 96.24 14.28 1.48e+00 4.57e-01 9.31e+01 angle pdb=" N GLU D 476 " pdb=" CA GLU D 476 " pdb=" C GLU D 476 " ideal model delta sigma weight residual 110.52 96.27 14.25 1.48e+00 4.57e-01 9.27e+01 angle pdb=" N GLU C 476 " pdb=" CA GLU C 476 " pdb=" C GLU C 476 " ideal model delta sigma weight residual 110.52 96.30 14.22 1.48e+00 4.57e-01 9.24e+01 angle pdb=" N GLU A 476 " pdb=" CA GLU A 476 " pdb=" C GLU A 476 " ideal model delta sigma weight residual 110.55 98.84 11.71 1.35e+00 5.49e-01 7.52e+01 ... (remaining 35411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 15359 22.47 - 44.93: 464 44.93 - 67.40: 72 67.40 - 89.86: 5 89.86 - 112.33: 12 Dihedral angle restraints: 15912 sinusoidal: 6344 harmonic: 9568 Sorted by residual: dihedral pdb=" CA ILE C 297 " pdb=" C ILE C 297 " pdb=" N LEU C 298 " pdb=" CA LEU C 298 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE D 297 " pdb=" C ILE D 297 " pdb=" N LEU D 298 " pdb=" CA LEU D 298 " ideal model delta harmonic sigma weight residual 180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE B 297 " pdb=" C ILE B 297 " pdb=" N LEU B 298 " pdb=" CA LEU B 298 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 15909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3845 0.120 - 0.241: 278 0.241 - 0.361: 42 0.361 - 0.482: 14 0.482 - 0.602: 1 Chirality restraints: 4180 Sorted by residual: chirality pdb=" CA LEU A 298 " pdb=" N LEU A 298 " pdb=" C LEU A 298 " pdb=" CB LEU A 298 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" CBH Y01 B1302 " pdb=" CAT Y01 B1302 " pdb=" CAZ Y01 B1302 " pdb=" CBF Y01 B1302 " both_signs ideal model delta sigma weight residual False -2.85 -2.41 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CBH Y01 A1303 " pdb=" CAT Y01 A1303 " pdb=" CAZ Y01 A1303 " pdb=" CBF Y01 A1303 " both_signs ideal model delta sigma weight residual False -2.85 -2.41 -0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 4177 not shown) Planarity restraints: 4312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 858 " -0.031 2.00e-02 2.50e+03 3.05e-02 1.62e+01 pdb=" CG PHE A 858 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 858 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 858 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 858 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 858 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 858 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 858 " -0.031 2.00e-02 2.50e+03 3.05e-02 1.62e+01 pdb=" CG PHE D 858 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE D 858 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE D 858 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 858 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 858 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE D 858 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 858 " 0.031 2.00e-02 2.50e+03 3.05e-02 1.62e+01 pdb=" CG PHE B 858 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 858 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE B 858 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 858 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 858 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE B 858 " -0.005 2.00e-02 2.50e+03 ... (remaining 4309 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7087 2.80 - 3.32: 23325 3.32 - 3.85: 39763 3.85 - 4.37: 49074 4.37 - 4.90: 81733 Nonbonded interactions: 200982 Sorted by model distance: nonbonded pdb=" OG1 THR B 895 " pdb=" O PRO B1130 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR C 895 " pdb=" O PRO C1130 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR D 895 " pdb=" O PRO D1130 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR A 895 " pdb=" O PRO A1130 " model vdw 2.270 3.040 nonbonded pdb=" O GLU D 775 " pdb=" CD1 TYR D 776 " model vdw 2.294 3.340 ... (remaining 200977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 1230 or resid 1301 through 1302)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 6 through 1230 or resid 1301 through 1302)) } 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: 0.870 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 58.400 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.016 0.135 26016 Z= 1.003 Angle : 1.405 14.282 35416 Z= 0.747 Chirality : 0.079 0.602 4180 Planarity : 0.008 0.069 4312 Dihedral : 12.219 112.329 9672 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.02 % Favored : 95.79 % Rotamer: Outliers : 2.12 % Allowed : 3.88 % Favored : 94.00 % 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: -4.97 (0.11), residues: 3136 helix: -3.49 (0.07), residues: 2036 sheet: None (None), residues: 0 loop : -2.49 (0.16), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A 417 HIS 0.019 0.003 HIS C1137 PHE 0.068 0.005 PHE D 858 TYR 0.067 0.004 TYR A 870 ARG 0.019 0.002 ARG D 942 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 681 time to evaluate : 2.752 Fit side-chains REVERT: A 662 MET cc_start: 0.8707 (mtm) cc_final: 0.8288 (mtp) REVERT: A 664 TYR cc_start: 0.8401 (t80) cc_final: 0.8042 (t80) REVERT: A 703 THR cc_start: 0.8979 (p) cc_final: 0.8719 (t) REVERT: A 748 MET cc_start: 0.8413 (mtt) cc_final: 0.8152 (mtm) REVERT: A 984 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7865 (mp10) REVERT: A 1088 MET cc_start: 0.9104 (mmm) cc_final: 0.8791 (mmm) REVERT: A 1089 VAL cc_start: 0.9164 (p) cc_final: 0.8707 (t) REVERT: A 1159 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7763 (tttm) REVERT: A 1168 LYS cc_start: 0.8266 (mttm) cc_final: 0.8062 (mmmt) REVERT: B 662 MET cc_start: 0.8707 (mtm) cc_final: 0.8287 (mtp) REVERT: B 664 TYR cc_start: 0.8404 (t80) cc_final: 0.8039 (t80) REVERT: B 703 THR cc_start: 0.8976 (p) cc_final: 0.8719 (t) REVERT: B 748 MET cc_start: 0.8398 (mtt) cc_final: 0.8140 (mtm) REVERT: B 849 TYR cc_start: 0.8639 (m-10) cc_final: 0.8439 (m-10) REVERT: B 1088 MET cc_start: 0.9108 (mmm) cc_final: 0.8786 (mmm) REVERT: B 1089 VAL cc_start: 0.9170 (p) cc_final: 0.8714 (t) REVERT: B 1168 LYS cc_start: 0.8270 (mttm) cc_final: 0.8062 (mmmt) REVERT: C 662 MET cc_start: 0.8711 (mtm) cc_final: 0.8288 (mtp) REVERT: C 664 TYR cc_start: 0.8390 (t80) cc_final: 0.8041 (t80) REVERT: C 703 THR cc_start: 0.8976 (p) cc_final: 0.8718 (t) REVERT: C 748 MET cc_start: 0.8409 (mtt) cc_final: 0.8152 (mtm) REVERT: C 849 TYR cc_start: 0.8641 (m-10) cc_final: 0.8437 (m-10) REVERT: C 984 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7856 (mp10) REVERT: C 1088 MET cc_start: 0.9102 (mmm) cc_final: 0.8779 (mmm) REVERT: C 1089 VAL cc_start: 0.9175 (p) cc_final: 0.8722 (t) REVERT: C 1168 LYS cc_start: 0.8263 (mttm) cc_final: 0.8058 (mmmt) REVERT: D 662 MET cc_start: 0.8708 (mtm) cc_final: 0.8284 (mtp) REVERT: D 664 TYR cc_start: 0.8395 (t80) cc_final: 0.8040 (t80) REVERT: D 703 THR cc_start: 0.8980 (p) cc_final: 0.8724 (t) REVERT: D 748 MET cc_start: 0.8408 (mtt) cc_final: 0.8153 (mtm) REVERT: D 1088 MET cc_start: 0.9112 (mmm) cc_final: 0.8789 (mmm) REVERT: D 1089 VAL cc_start: 0.9172 (p) cc_final: 0.8712 (t) REVERT: D 1159 LYS cc_start: 0.8305 (mtmm) cc_final: 0.8104 (tttm) REVERT: D 1168 LYS cc_start: 0.8262 (mttm) cc_final: 0.8057 (mmmt) outliers start: 53 outliers final: 22 residues processed: 726 average time/residue: 0.4073 time to fit residues: 447.7275 Evaluate side-chains 437 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 415 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1011 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 710 THR Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 1011 LEU Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1097 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 136 optimal weight: 0.0470 chunk 83 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 253 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 294 optimal weight: 6.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 432 GLN A 491 HIS A 700 GLN A 718 ASN A 787 GLN A 789 GLN A 885 GLN A 956 HIS A1090 ASN A1123 HIS A1137 HIS A1210 GLN B 276 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 432 GLN B 491 HIS B 700 GLN B 718 ASN B 756 ASN B 787 GLN B 789 GLN B 885 GLN B 956 HIS B1090 ASN B1123 HIS B1137 HIS B1210 GLN C 276 HIS ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS C 432 GLN C 491 HIS C 700 GLN C 718 ASN C 789 GLN C 885 GLN C 956 HIS C1090 ASN C1123 HIS C1137 HIS C1210 GLN D 276 HIS ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 432 GLN D 491 HIS D 700 GLN D 718 ASN D 756 ASN D 789 GLN D 885 GLN D 956 HIS D1090 ASN D1123 HIS D1137 HIS D1210 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26016 Z= 0.236 Angle : 0.728 10.490 35416 Z= 0.365 Chirality : 0.045 0.241 4180 Planarity : 0.005 0.051 4312 Dihedral : 9.396 78.654 4327 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.10 % Rotamer: Outliers : 3.32 % Allowed : 9.52 % Favored : 87.16 % 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: -2.91 (0.13), residues: 3136 helix: -1.73 (0.10), residues: 2108 sheet: None (None), residues: 0 loop : -2.01 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1111 HIS 0.008 0.001 HIS A1137 PHE 0.029 0.002 PHE C 858 TYR 0.018 0.002 TYR A 870 ARG 0.007 0.001 ARG D 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 525 time to evaluate : 2.985 Fit side-chains REVERT: A 662 MET cc_start: 0.8678 (mtm) cc_final: 0.8094 (mtp) REVERT: A 703 THR cc_start: 0.8923 (p) cc_final: 0.8617 (t) REVERT: A 748 MET cc_start: 0.8110 (mtt) cc_final: 0.7869 (mtm) REVERT: A 1085 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: A 1088 MET cc_start: 0.9087 (mmm) cc_final: 0.8648 (mmm) REVERT: A 1089 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8859 (t) REVERT: A 1109 ILE cc_start: 0.8454 (mt) cc_final: 0.8187 (mm) REVERT: A 1159 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8093 (tttm) REVERT: A 1166 ASP cc_start: 0.8185 (m-30) cc_final: 0.7308 (m-30) REVERT: A 1168 LYS cc_start: 0.8171 (mttm) cc_final: 0.7891 (mtmt) REVERT: A 1171 HIS cc_start: 0.8270 (t-90) cc_final: 0.7770 (t70) REVERT: B 662 MET cc_start: 0.8676 (mtm) cc_final: 0.8095 (mtp) REVERT: B 703 THR cc_start: 0.8920 (p) cc_final: 0.8562 (t) REVERT: B 748 MET cc_start: 0.8117 (mtt) cc_final: 0.7858 (mtm) REVERT: B 1085 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: B 1088 MET cc_start: 0.9092 (mmm) cc_final: 0.8644 (mmm) REVERT: B 1089 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8843 (t) REVERT: B 1109 ILE cc_start: 0.8448 (mt) cc_final: 0.8184 (mm) REVERT: B 1166 ASP cc_start: 0.8199 (m-30) cc_final: 0.7286 (m-30) REVERT: B 1168 LYS cc_start: 0.8176 (mttm) cc_final: 0.7896 (mtmt) REVERT: B 1171 HIS cc_start: 0.8276 (t-90) cc_final: 0.7786 (t70) REVERT: C 662 MET cc_start: 0.8678 (mtm) cc_final: 0.8093 (mtp) REVERT: C 703 THR cc_start: 0.8917 (p) cc_final: 0.8560 (t) REVERT: C 748 MET cc_start: 0.8118 (mtt) cc_final: 0.7875 (mtm) REVERT: C 984 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7802 (mp10) REVERT: C 1085 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: C 1088 MET cc_start: 0.9091 (mmm) cc_final: 0.8641 (mmm) REVERT: C 1089 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8854 (t) REVERT: C 1109 ILE cc_start: 0.8462 (mt) cc_final: 0.8194 (mm) REVERT: C 1166 ASP cc_start: 0.8182 (m-30) cc_final: 0.7274 (m-30) REVERT: C 1168 LYS cc_start: 0.8169 (mttm) cc_final: 0.7889 (mtmt) REVERT: C 1171 HIS cc_start: 0.8280 (t-90) cc_final: 0.7783 (t70) REVERT: D 662 MET cc_start: 0.8678 (mtm) cc_final: 0.8095 (mtp) REVERT: D 703 THR cc_start: 0.8882 (p) cc_final: 0.8570 (t) REVERT: D 748 MET cc_start: 0.8124 (mtt) cc_final: 0.7875 (mtm) REVERT: D 1085 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: D 1088 MET cc_start: 0.9104 (mmm) cc_final: 0.8653 (mmm) REVERT: D 1089 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8848 (t) REVERT: D 1109 ILE cc_start: 0.8447 (mt) cc_final: 0.8183 (mm) REVERT: D 1166 ASP cc_start: 0.8175 (m-30) cc_final: 0.7318 (m-30) REVERT: D 1168 LYS cc_start: 0.8164 (mttm) cc_final: 0.7880 (mtmt) REVERT: D 1171 HIS cc_start: 0.8274 (t-90) cc_final: 0.7765 (t70) outliers start: 83 outliers final: 37 residues processed: 592 average time/residue: 0.3591 time to fit residues: 339.7194 Evaluate side-chains 497 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 452 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1085 TYR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 THR Chi-restraints excluded: chain D residue 756 ASN Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1089 VAL Chi-restraints excluded: chain D residue 1097 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 200 optimal weight: 0.0060 chunk 81 optimal weight: 20.0000 chunk 294 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 292 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN A 956 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 956 HIS ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 HIS ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 GLN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 956 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 26016 Z= 0.375 Angle : 0.737 10.547 35416 Z= 0.367 Chirality : 0.046 0.274 4180 Planarity : 0.005 0.050 4312 Dihedral : 8.548 57.735 4317 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 3.48 % Allowed : 11.96 % Favored : 84.56 % 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: -2.08 (0.14), residues: 3136 helix: -1.01 (0.10), residues: 2168 sheet: None (None), residues: 0 loop : -1.92 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 857 HIS 0.006 0.001 HIS B 850 PHE 0.018 0.002 PHE C 858 TYR 0.023 0.002 TYR B 870 ARG 0.005 0.000 ARG D 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 460 time to evaluate : 2.767 Fit side-chains REVERT: A 413 LEU cc_start: 0.8574 (mt) cc_final: 0.8199 (tp) REVERT: A 626 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8620 (tp) REVERT: A 662 MET cc_start: 0.8682 (mtm) cc_final: 0.8373 (mtp) REVERT: A 695 GLU cc_start: 0.7988 (tp30) cc_final: 0.7689 (tp30) REVERT: A 703 THR cc_start: 0.8866 (p) cc_final: 0.8590 (t) REVERT: A 748 MET cc_start: 0.8097 (mtt) cc_final: 0.7820 (mtm) REVERT: A 1085 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6382 (m-80) REVERT: A 1088 MET cc_start: 0.9028 (mmm) cc_final: 0.8740 (mmm) REVERT: A 1109 ILE cc_start: 0.8472 (mt) cc_final: 0.8165 (mm) REVERT: A 1159 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8084 (tttm) REVERT: A 1166 ASP cc_start: 0.8040 (m-30) cc_final: 0.7370 (m-30) REVERT: A 1168 LYS cc_start: 0.8207 (mttm) cc_final: 0.7989 (mtmt) REVERT: A 1171 HIS cc_start: 0.8206 (t-90) cc_final: 0.7718 (t70) REVERT: B 413 LEU cc_start: 0.8561 (mt) cc_final: 0.8183 (tp) REVERT: B 616 LYS cc_start: 0.8552 (pttp) cc_final: 0.8075 (mttt) REVERT: B 626 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8615 (tp) REVERT: B 637 MET cc_start: 0.8997 (tpp) cc_final: 0.8770 (tpp) REVERT: B 662 MET cc_start: 0.8680 (mtm) cc_final: 0.8370 (mtp) REVERT: B 695 GLU cc_start: 0.7983 (tp30) cc_final: 0.7685 (tp30) REVERT: B 703 THR cc_start: 0.8891 (p) cc_final: 0.8662 (t) REVERT: B 748 MET cc_start: 0.8104 (mtt) cc_final: 0.7802 (mtm) REVERT: B 1085 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: B 1088 MET cc_start: 0.9025 (mmm) cc_final: 0.8731 (mmm) REVERT: B 1109 ILE cc_start: 0.8465 (mt) cc_final: 0.8164 (mm) REVERT: B 1166 ASP cc_start: 0.8036 (m-30) cc_final: 0.7412 (m-30) REVERT: B 1168 LYS cc_start: 0.8214 (mttm) cc_final: 0.7993 (mtmt) REVERT: B 1171 HIS cc_start: 0.8221 (t-90) cc_final: 0.7726 (t70) REVERT: C 413 LEU cc_start: 0.8561 (mt) cc_final: 0.8182 (tp) REVERT: C 616 LYS cc_start: 0.8552 (pttp) cc_final: 0.8077 (mttt) REVERT: C 626 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8613 (tp) REVERT: C 637 MET cc_start: 0.8997 (tpp) cc_final: 0.8771 (tpp) REVERT: C 662 MET cc_start: 0.8681 (mtm) cc_final: 0.8368 (mtp) REVERT: C 695 GLU cc_start: 0.7985 (tp30) cc_final: 0.7693 (tp30) REVERT: C 703 THR cc_start: 0.8890 (p) cc_final: 0.8660 (t) REVERT: C 748 MET cc_start: 0.8099 (mtt) cc_final: 0.7810 (mtm) REVERT: C 1085 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: C 1088 MET cc_start: 0.9025 (mmm) cc_final: 0.8732 (mmm) REVERT: C 1109 ILE cc_start: 0.8476 (mt) cc_final: 0.8168 (mm) REVERT: C 1166 ASP cc_start: 0.8018 (m-30) cc_final: 0.7403 (m-30) REVERT: C 1168 LYS cc_start: 0.8208 (mttm) cc_final: 0.7989 (mtmt) REVERT: C 1171 HIS cc_start: 0.8219 (t-90) cc_final: 0.7723 (t70) REVERT: D 413 LEU cc_start: 0.8561 (mt) cc_final: 0.8184 (tp) REVERT: D 616 LYS cc_start: 0.8551 (pttp) cc_final: 0.8077 (mttt) REVERT: D 626 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8606 (tp) REVERT: D 637 MET cc_start: 0.8999 (tpp) cc_final: 0.8774 (tpp) REVERT: D 662 MET cc_start: 0.8728 (mtm) cc_final: 0.8393 (mtp) REVERT: D 695 GLU cc_start: 0.7991 (tp30) cc_final: 0.7690 (tp30) REVERT: D 703 THR cc_start: 0.8885 (p) cc_final: 0.8592 (t) REVERT: D 748 MET cc_start: 0.8112 (mtt) cc_final: 0.7810 (mtm) REVERT: D 1085 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: D 1088 MET cc_start: 0.9034 (mmm) cc_final: 0.8734 (mmm) REVERT: D 1109 ILE cc_start: 0.8465 (mt) cc_final: 0.8161 (mm) REVERT: D 1166 ASP cc_start: 0.8046 (m-30) cc_final: 0.7417 (m-30) REVERT: D 1168 LYS cc_start: 0.8205 (mttm) cc_final: 0.7985 (mtmt) REVERT: D 1171 HIS cc_start: 0.8214 (t-90) cc_final: 0.7714 (t70) outliers start: 87 outliers final: 46 residues processed: 533 average time/residue: 0.3603 time to fit residues: 303.2320 Evaluate side-chains 477 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 423 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1085 TYR Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 710 THR Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1097 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.0050 chunk 221 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 295 optimal weight: 7.9990 chunk 313 optimal weight: 0.5980 chunk 154 optimal weight: 0.2980 chunk 280 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 295 ASN B 756 ASN C 295 ASN C 787 GLN D 295 ASN D 756 ASN D 787 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3253 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: