Starting phenix.real_space_refine on Mon Feb 19 18:30:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/02_2024/5zx5_6975.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/02_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_6975/02_2024/5zx5_6975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/02_2024/5zx5_6975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/02_2024/5zx5_6975.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zx5_6975/02_2024/5zx5_6975.pdb" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 13.10, per 1000 atoms: 0.51 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: 9.47 Conformation dependent library (CDL) restraints added in 4.6 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: 2.97 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: 7.97 Time building geometry restraints manager: 10.15 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 2.440 nonbonded pdb=" OG1 THR C 895 " pdb=" O PRO C1130 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR D 895 " pdb=" O PRO D1130 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR A 895 " pdb=" O PRO A1130 " model vdw 2.270 2.440 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 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.040 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 64.680 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.140 ------------------------------------------------------------------------------- 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 : 3.160 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: 0.3994 time to fit residues: 436.3740 Evaluate side-chains 437 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 415 time to evaluate : 2.898 ------------------------------------------------------------------------------- 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: 7.9990 chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 253 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 426 HIS A 432 GLN A 491 HIS A 700 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 GLN D 885 GLN D 956 HIS D1090 ASN D1123 HIS D1137 HIS D1210 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2393 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= 0.384 Angle : 0.777 10.352 35416 Z= 0.389 Chirality : 0.047 0.247 4180 Planarity : 0.006 0.051 4312 Dihedral : 9.480 76.785 4327 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 3.76 % Allowed : 10.00 % Favored : 86.24 % 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: -3.09 (0.13), residues: 3136 helix: -1.82 (0.10), residues: 2132 sheet: None (None), residues: 0 loop : -2.18 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1111 HIS 0.008 0.001 HIS A1137 PHE 0.029 0.002 PHE B 858 TYR 0.025 0.002 TYR A 870 ARG 0.007 0.001 ARG B 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 612 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 518 time to evaluate : 2.696 Fit side-chains REVERT: A 413 LEU cc_start: 0.8609 (mt) cc_final: 0.8213 (tp) REVERT: A 616 LYS cc_start: 0.8585 (pttp) cc_final: 0.8080 (mttt) REVERT: A 662 MET cc_start: 0.8711 (mtm) cc_final: 0.8199 (mtp) REVERT: A 703 THR cc_start: 0.8911 (p) cc_final: 0.8632 (t) REVERT: A 748 MET cc_start: 0.8145 (mtt) cc_final: 0.7836 (mtm) REVERT: A 1065 ILE cc_start: 0.8108 (mm) cc_final: 0.7900 (mt) REVERT: A 1085 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.6439 (m-80) REVERT: A 1109 ILE cc_start: 0.8485 (mt) cc_final: 0.8172 (mm) REVERT: A 1159 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8105 (tttm) REVERT: A 1166 ASP cc_start: 0.8192 (m-30) cc_final: 0.7319 (m-30) REVERT: A 1168 LYS cc_start: 0.8227 (mttm) cc_final: 0.7965 (mtmt) REVERT: A 1171 HIS cc_start: 0.8397 (t-90) cc_final: 0.7920 (t70) REVERT: B 413 LEU cc_start: 0.8608 (mt) cc_final: 0.8209 (tp) REVERT: B 616 LYS cc_start: 0.8588 (pttp) cc_final: 0.8081 (mttt) REVERT: B 662 MET cc_start: 0.8709 (mtm) cc_final: 0.8199 (mtp) REVERT: B 703 THR cc_start: 0.8907 (p) cc_final: 0.8631 (t) REVERT: B 748 MET cc_start: 0.8152 (mtt) cc_final: 0.7829 (mtm) REVERT: B 1065 ILE cc_start: 0.8102 (mm) cc_final: 0.7894 (mt) REVERT: B 1085 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6436 (m-80) REVERT: B 1109 ILE cc_start: 0.8480 (mt) cc_final: 0.8170 (mm) REVERT: B 1166 ASP cc_start: 0.8206 (m-30) cc_final: 0.7331 (m-30) REVERT: B 1168 LYS cc_start: 0.8231 (mttm) cc_final: 0.7964 (mtmt) REVERT: B 1171 HIS cc_start: 0.8402 (t-90) cc_final: 0.7930 (t70) REVERT: C 413 LEU cc_start: 0.8609 (mt) cc_final: 0.8209 (tp) REVERT: C 616 LYS cc_start: 0.8589 (pttp) cc_final: 0.8081 (mttt) REVERT: C 662 MET cc_start: 0.8711 (mtm) cc_final: 0.8197 (mtp) REVERT: C 703 THR cc_start: 0.8907 (p) cc_final: 0.8631 (t) REVERT: C 748 MET cc_start: 0.8152 (mtt) cc_final: 0.7845 (mtm) REVERT: C 1065 ILE cc_start: 0.8110 (mm) cc_final: 0.7904 (mt) REVERT: C 1085 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: C 1109 ILE cc_start: 0.8491 (mt) cc_final: 0.8176 (mm) REVERT: C 1166 ASP cc_start: 0.8188 (m-30) cc_final: 0.7318 (m-30) REVERT: C 1168 LYS cc_start: 0.8224 (mttm) cc_final: 0.7958 (mtmt) REVERT: C 1171 HIS cc_start: 0.8405 (t-90) cc_final: 0.7928 (t70) REVERT: D 413 LEU cc_start: 0.8609 (mt) cc_final: 0.8210 (tp) REVERT: D 616 LYS cc_start: 0.8586 (pttp) cc_final: 0.8081 (mttt) REVERT: D 662 MET cc_start: 0.8711 (mtm) cc_final: 0.8198 (mtp) REVERT: D 703 THR cc_start: 0.8885 (p) cc_final: 0.8593 (t) REVERT: D 748 MET cc_start: 0.8159 (mtt) cc_final: 0.7842 (mtm) REVERT: D 1065 ILE cc_start: 0.8102 (mm) cc_final: 0.7893 (mt) REVERT: D 1085 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6442 (m-80) REVERT: D 1109 ILE cc_start: 0.8477 (mt) cc_final: 0.8165 (mm) REVERT: D 1166 ASP cc_start: 0.8185 (m-30) cc_final: 0.7304 (m-30) REVERT: D 1168 LYS cc_start: 0.8222 (mttm) cc_final: 0.7958 (mtmt) REVERT: D 1171 HIS cc_start: 0.8401 (t-90) cc_final: 0.7924 (t70) outliers start: 94 outliers final: 50 residues processed: 600 average time/residue: 0.3428 time to fit residues: 329.0691 Evaluate side-chains 463 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 409 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 172 LEU 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 790 ASP Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 980 LEU 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 172 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 901 VAL 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 172 LEU 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 790 ASP Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 980 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 172 LEU 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 774 LEU Chi-restraints excluded: chain D residue 790 ASP 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 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: 0.9980 chunk 81 optimal weight: 20.0000 chunk 294 optimal weight: 5.9990 chunk 318 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 718 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 718 ASN B 956 HIS ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 GLN C 718 ASN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26016 Z= 0.379 Angle : 0.734 9.988 35416 Z= 0.365 Chirality : 0.046 0.292 4180 Planarity : 0.005 0.050 4312 Dihedral : 8.707 58.515 4321 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.70 % Rotamer: Outliers : 3.64 % Allowed : 12.76 % Favored : 83.60 % 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: -2.15 (0.14), residues: 3136 helix: -1.07 (0.10), residues: 2172 sheet: None (None), residues: 0 loop : -1.95 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 857 HIS 0.006 0.001 HIS B 850 PHE 0.018 0.002 PHE C 858 TYR 0.020 0.002 TYR C 870 ARG 0.005 0.000 ARG D 525 *********************** 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 540 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 449 time to evaluate : 2.729 Fit side-chains REVERT: A 413 LEU cc_start: 0.8588 (mt) cc_final: 0.8200 (tp) REVERT: A 616 LYS cc_start: 0.8426 (pttp) cc_final: 0.7836 (mttt) REVERT: A 626 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8592 (tp) REVERT: A 662 MET cc_start: 0.8692 (mtm) cc_final: 0.8401 (mtp) REVERT: A 695 GLU cc_start: 0.7975 (tp30) cc_final: 0.7682 (tp30) REVERT: A 703 THR cc_start: 0.8848 (p) cc_final: 0.8600 (t) REVERT: A 782 MET cc_start: 0.8505 (mmm) cc_final: 0.8199 (mmm) REVERT: A 1053 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7801 (mt) REVERT: A 1065 ILE cc_start: 0.8235 (mm) cc_final: 0.8024 (mt) REVERT: A 1085 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6574 (m-80) REVERT: A 1109 ILE cc_start: 0.8459 (mt) cc_final: 0.8138 (mm) REVERT: A 1159 LYS cc_start: 0.8370 (mtmm) cc_final: 0.8051 (tttm) REVERT: A 1171 HIS cc_start: 0.8396 (t-90) cc_final: 0.7933 (t70) REVERT: B 413 LEU cc_start: 0.8587 (mt) cc_final: 0.8180 (tp) REVERT: B 616 LYS cc_start: 0.8428 (pttp) cc_final: 0.7836 (mttt) REVERT: B 626 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8592 (tp) REVERT: B 662 MET cc_start: 0.8692 (mtm) cc_final: 0.8399 (mtp) REVERT: B 695 GLU cc_start: 0.7975 (tp30) cc_final: 0.7680 (tp30) REVERT: B 703 THR cc_start: 0.8846 (p) cc_final: 0.8602 (t) REVERT: B 782 MET cc_start: 0.8560 (mmm) cc_final: 0.8281 (mmm) REVERT: B 1053 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7782 (mt) REVERT: B 1065 ILE cc_start: 0.8225 (mm) cc_final: 0.8014 (mt) REVERT: B 1085 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: B 1109 ILE cc_start: 0.8455 (mt) cc_final: 0.8135 (mm) REVERT: B 1171 HIS cc_start: 0.8404 (t-90) cc_final: 0.7943 (t70) REVERT: C 413 LEU cc_start: 0.8587 (mt) cc_final: 0.8180 (tp) REVERT: C 616 LYS cc_start: 0.8428 (pttp) cc_final: 0.7836 (mttt) REVERT: C 626 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8589 (tp) REVERT: C 662 MET cc_start: 0.8693 (mtm) cc_final: 0.8398 (mtp) REVERT: C 695 GLU cc_start: 0.7975 (tp30) cc_final: 0.7687 (tp30) REVERT: C 703 THR cc_start: 0.8845 (p) cc_final: 0.8600 (t) REVERT: C 782 MET cc_start: 0.8513 (mmm) cc_final: 0.8190 (mmm) REVERT: C 1053 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7787 (mt) REVERT: C 1065 ILE cc_start: 0.8230 (mm) cc_final: 0.8023 (mt) REVERT: C 1085 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: C 1109 ILE cc_start: 0.8464 (mt) cc_final: 0.8140 (mm) REVERT: C 1171 HIS cc_start: 0.8403 (t-90) cc_final: 0.7940 (t70) REVERT: D 413 LEU cc_start: 0.8588 (mt) cc_final: 0.8181 (tp) REVERT: D 616 LYS cc_start: 0.8426 (pttp) cc_final: 0.7836 (mttt) REVERT: D 626 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8589 (tp) REVERT: D 662 MET cc_start: 0.8694 (mtm) cc_final: 0.8401 (mtp) REVERT: D 695 GLU cc_start: 0.7982 (tp30) cc_final: 0.7682 (tp30) REVERT: D 703 THR cc_start: 0.8852 (p) cc_final: 0.8578 (t) REVERT: D 782 MET cc_start: 0.8534 (mmm) cc_final: 0.8210 (mmm) REVERT: D 1053 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7779 (mt) REVERT: D 1065 ILE cc_start: 0.8224 (mm) cc_final: 0.8015 (mt) REVERT: D 1085 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: D 1109 ILE cc_start: 0.8452 (mt) cc_final: 0.8131 (mm) REVERT: D 1171 HIS cc_start: 0.8396 (t-90) cc_final: 0.7931 (t70) outliers start: 91 outliers final: 47 residues processed: 522 average time/residue: 0.3560 time to fit residues: 294.9119 Evaluate side-chains 474 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 415 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 172 LEU 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 790 ASP Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1053 ILE 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 161 ILE Chi-restraints excluded: chain B residue 172 LEU 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 790 ASP Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1053 ILE 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 161 ILE Chi-restraints excluded: chain C residue 172 LEU 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 790 ASP Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1053 ILE 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 161 ILE Chi-restraints excluded: chain D residue 172 LEU 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 774 LEU Chi-restraints excluded: chain D residue 790 ASP 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 1053 ILE 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: 0.4980 chunk 221 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 295 optimal weight: 8.9990 chunk 313 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 787 GLN B 295 ASN C 295 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26016 Z= 0.193 Angle : 0.619 10.101 35416 Z= 0.307 Chirality : 0.042 0.288 4180 Planarity : 0.004 0.045 4312 Dihedral : 8.150 59.204 4321 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.52 % Rotamer: Outliers : 3.16 % Allowed : 13.20 % Favored : 83.64 % 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: -1.28 (0.15), residues: 3136 helix: -0.35 (0.11), residues: 2168 sheet: None (None), residues: 0 loop : -1.76 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 857 HIS 0.004 0.001 HIS D 784 PHE 0.019 0.001 PHE A 858 TYR 0.017 0.001 TYR C 896 ARG 0.005 0.000 ARG D 525 *********************** REFINEMENT MACRO_CYCLE 4 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 560 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 481 time to evaluate : 2.808 Fit side-chains REVERT: A 413 LEU cc_start: 0.8519 (mt) cc_final: 0.8153 (tp) REVERT: A 616 LYS cc_start: 0.8543 (pttp) cc_final: 0.8076 (mttt) REVERT: A 626 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8578 (tp) REVERT: A 662 MET cc_start: 0.8703 (mtm) cc_final: 0.8336 (mtp) REVERT: A 748 MET cc_start: 0.8076 (mtt) cc_final: 0.7795 (mtm) REVERT: A 779 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7927 (tttt) REVERT: A 1065 ILE cc_start: 0.8158 (mm) cc_final: 0.7947 (mt) REVERT: A 1085 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: A 1109 ILE cc_start: 0.8439 (mt) cc_final: 0.8119 (mm) REVERT: A 1159 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8059 (tttm) REVERT: A 1166 ASP cc_start: 0.8074 (m-30) cc_final: 0.7329 (m-30) REVERT: A 1171 HIS cc_start: 0.8157 (t-90) cc_final: 0.7661 (t70) REVERT: B 413 LEU cc_start: 0.8514 (mt) cc_final: 0.8153 (tp) REVERT: B 616 LYS cc_start: 0.8543 (pttp) cc_final: 0.8080 (mttt) REVERT: B 626 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8579 (tp) REVERT: B 662 MET cc_start: 0.8704 (mtm) cc_final: 0.8334 (mtp) REVERT: B 748 MET cc_start: 0.8081 (mtt) cc_final: 0.7793 (mtm) REVERT: B 1065 ILE cc_start: 0.8174 (mm) cc_final: 0.7956 (mt) REVERT: B 1085 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: B 1109 ILE cc_start: 0.8434 (mt) cc_final: 0.8117 (mm) REVERT: B 1166 ASP cc_start: 0.8095 (m-30) cc_final: 0.7343 (m-30) REVERT: B 1171 HIS cc_start: 0.8165 (t-90) cc_final: 0.7671 (t70) REVERT: C 413 LEU cc_start: 0.8514 (mt) cc_final: 0.8154 (tp) REVERT: C 616 LYS cc_start: 0.8545 (pttp) cc_final: 0.8081 (mttt) REVERT: C 626 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8577 (tp) REVERT: C 662 MET cc_start: 0.8705 (mtm) cc_final: 0.8332 (mtp) REVERT: C 748 MET cc_start: 0.8088 (mtt) cc_final: 0.7805 (mtm) REVERT: C 779 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7933 (tttt) REVERT: C 1065 ILE cc_start: 0.8177 (mm) cc_final: 0.7966 (mt) REVERT: C 1085 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: C 1109 ILE cc_start: 0.8442 (mt) cc_final: 0.8126 (mm) REVERT: C 1166 ASP cc_start: 0.8081 (m-30) cc_final: 0.7332 (m-30) REVERT: C 1171 HIS cc_start: 0.8164 (t-90) cc_final: 0.7669 (t70) REVERT: D 413 LEU cc_start: 0.8516 (mt) cc_final: 0.8154 (tp) REVERT: D 616 LYS cc_start: 0.8541 (pttp) cc_final: 0.8080 (mttt) REVERT: D 626 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8574 (tp) REVERT: D 662 MET cc_start: 0.8705 (mtm) cc_final: 0.8329 (mtp) REVERT: D 748 MET cc_start: 0.8086 (mtt) cc_final: 0.7765 (mtm) REVERT: D 1065 ILE cc_start: 0.8171 (mm) cc_final: 0.7956 (mt) REVERT: D 1085 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: D 1109 ILE cc_start: 0.8435 (mt) cc_final: 0.8117 (mm) REVERT: D 1166 ASP cc_start: 0.8078 (m-30) cc_final: 0.7359 (m-30) REVERT: D 1171 HIS cc_start: 0.8149 (t-90) cc_final: 0.7667 (t70) outliers start: 79 outliers final: 63 residues processed: 536 average time/residue: 0.3390 time to fit residues: 292.1709 Evaluate side-chains 510 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 439 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 515 VAL 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 790 ASP Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 LEU 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 160 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 858 PHE 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 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 160 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 515 VAL 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 790 ASP Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 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 160 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 515 VAL 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 774 LEU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 858 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 233 optimal weight: 0.5980 chunk 129 optimal weight: 0.0770 chunk 267 optimal weight: 0.6980 chunk 216 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 281 optimal weight: 0.0870 chunk 79 optimal weight: 0.8980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26016 Z= 0.170 Angle : 0.590 10.669 35416 Z= 0.291 Chirality : 0.041 0.260 4180 Planarity : 0.004 0.046 4312 Dihedral : 7.692 59.095 4321 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.57 % Favored : 96.30 % Rotamer: Outliers : 3.56 % Allowed : 13.72 % Favored : 82.72 % 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: -0.58 (0.15), residues: 3136 helix: 0.23 (0.11), residues: 2156 sheet: None (None), residues: 0 loop : -1.63 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 857 HIS 0.004 0.001 HIS C 850 PHE 0.018 0.001 PHE A 858 TYR 0.019 0.001 TYR D 776 ARG 0.004 0.000 ARG D 525 *********************** REFINEMENT MACRO_CYCLE 5 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: 89 poor density : 458 time to evaluate : 3.112 Fit side-chains REVERT: A 413 LEU cc_start: 0.8485 (mt) cc_final: 0.8116 (tp) REVERT: A 616 LYS cc_start: 0.8550 (pttp) cc_final: 0.8069 (mttt) REVERT: A 626 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8646 (tp) REVERT: A 662 MET cc_start: 0.8705 (mtm) cc_final: 0.8353 (mtp) REVERT: A 748 MET cc_start: 0.8033 (mtt) cc_final: 0.7704 (mtm) REVERT: A 779 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7917 (tttt) REVERT: A 1085 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 1109 ILE cc_start: 0.8493 (mt) cc_final: 0.8190 (mm) REVERT: A 1159 LYS cc_start: 0.8311 (mtmm) cc_final: 0.8015 (tttm) REVERT: A 1166 ASP cc_start: 0.8021 (m-30) cc_final: 0.7332 (m-30) REVERT: A 1171 HIS cc_start: 0.8069 (t-90) cc_final: 0.7611 (t70) REVERT: B 413 LEU cc_start: 0.8498 (mt) cc_final: 0.8138 (tp) REVERT: B 616 LYS cc_start: 0.8554 (pttp) cc_final: 0.8070 (mttt) REVERT: B 626 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 662 MET cc_start: 0.8705 (mtm) cc_final: 0.8350 (mtp) REVERT: B 748 MET cc_start: 0.8040 (mtt) cc_final: 0.7751 (mtm) REVERT: B 922 ASP cc_start: 0.8029 (t0) cc_final: 0.7829 (t0) REVERT: B 1085 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: B 1109 ILE cc_start: 0.8486 (mt) cc_final: 0.8189 (mm) REVERT: B 1166 ASP cc_start: 0.8043 (m-30) cc_final: 0.7348 (m-30) REVERT: B 1171 HIS cc_start: 0.8080 (t-90) cc_final: 0.7618 (t70) REVERT: C 413 LEU cc_start: 0.8500 (mt) cc_final: 0.8143 (tp) REVERT: C 616 LYS cc_start: 0.8552 (pttp) cc_final: 0.8071 (mttt) REVERT: C 626 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8647 (tp) REVERT: C 662 MET cc_start: 0.8708 (mtm) cc_final: 0.8351 (mtp) REVERT: C 748 MET cc_start: 0.8043 (mtt) cc_final: 0.7747 (mtm) REVERT: C 779 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7920 (tttt) REVERT: C 1085 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6572 (m-80) REVERT: C 1109 ILE cc_start: 0.8493 (mt) cc_final: 0.8193 (mm) REVERT: C 1166 ASP cc_start: 0.8026 (m-30) cc_final: 0.7338 (m-30) REVERT: C 1171 HIS cc_start: 0.8076 (t-90) cc_final: 0.7620 (t70) REVERT: D 413 LEU cc_start: 0.8501 (mt) cc_final: 0.8144 (tp) REVERT: D 616 LYS cc_start: 0.8553 (pttp) cc_final: 0.8071 (mttt) REVERT: D 626 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8644 (tp) REVERT: D 662 MET cc_start: 0.8704 (mtm) cc_final: 0.8345 (mtp) REVERT: D 748 MET cc_start: 0.8056 (mtt) cc_final: 0.7751 (mtm) REVERT: D 1085 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: D 1109 ILE cc_start: 0.8481 (mt) cc_final: 0.8172 (mm) REVERT: D 1166 ASP cc_start: 0.8073 (m-30) cc_final: 0.7385 (m-30) REVERT: D 1171 HIS cc_start: 0.8090 (t-90) cc_final: 0.7617 (t70) outliers start: 89 outliers final: 65 residues processed: 525 average time/residue: 0.3236 time to fit residues: 276.8973 Evaluate side-chains 506 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 433 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 LEU 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 A residue 1123 HIS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 858 PHE 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 1055 VAL Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1123 HIS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 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 1123 HIS Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 858 PHE 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 Chi-restraints excluded: chain D residue 1123 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26016 Z= 0.247 Angle : 0.608 10.102 35416 Z= 0.301 Chirality : 0.043 0.240 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.544 59.103 4316 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 3.80 % Allowed : 14.12 % Favored : 82.08 % 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: -0.40 (0.15), residues: 3136 helix: 0.36 (0.11), residues: 2164 sheet: None (None), residues: 0 loop : -1.56 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 857 HIS 0.004 0.001 HIS D 850 PHE 0.018 0.001 PHE A 858 TYR 0.014 0.001 TYR D 965 ARG 0.003 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 6 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 550 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 455 time to evaluate : 3.157 Fit side-chains REVERT: A 413 LEU cc_start: 0.8553 (mt) cc_final: 0.8159 (tp) REVERT: A 478 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.5704 (t80) REVERT: A 616 LYS cc_start: 0.8480 (pttp) cc_final: 0.7923 (mttt) REVERT: A 626 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8664 (tp) REVERT: A 662 MET cc_start: 0.8730 (mtm) cc_final: 0.8414 (mtp) REVERT: A 748 MET cc_start: 0.8023 (mtt) cc_final: 0.7737 (mtm) REVERT: A 779 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7922 (tttt) REVERT: A 922 ASP cc_start: 0.8077 (t0) cc_final: 0.7858 (t0) REVERT: A 1053 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7634 (mt) REVERT: A 1085 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: A 1109 ILE cc_start: 0.8491 (mt) cc_final: 0.8170 (mm) REVERT: A 1159 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8043 (tttm) REVERT: A 1166 ASP cc_start: 0.8009 (m-30) cc_final: 0.7361 (m-30) REVERT: A 1171 HIS cc_start: 0.8080 (t-90) cc_final: 0.7620 (t70) REVERT: B 413 LEU cc_start: 0.8552 (mt) cc_final: 0.8184 (tp) REVERT: B 478 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.5595 (t80) REVERT: B 616 LYS cc_start: 0.8485 (pttp) cc_final: 0.7904 (mttt) REVERT: B 626 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8666 (tp) REVERT: B 662 MET cc_start: 0.8730 (mtm) cc_final: 0.8412 (mtp) REVERT: B 748 MET cc_start: 0.8040 (mtt) cc_final: 0.7761 (mtm) REVERT: B 1053 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7615 (mt) REVERT: B 1085 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.6572 (m-80) REVERT: B 1109 ILE cc_start: 0.8487 (mt) cc_final: 0.8172 (mm) REVERT: B 1166 ASP cc_start: 0.8041 (m-30) cc_final: 0.7337 (m-30) REVERT: B 1171 HIS cc_start: 0.8084 (t-90) cc_final: 0.7625 (t70) REVERT: C 413 LEU cc_start: 0.8557 (mt) cc_final: 0.8188 (tp) REVERT: C 478 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.5594 (t80) REVERT: C 616 LYS cc_start: 0.8483 (pttp) cc_final: 0.7906 (mttt) REVERT: C 626 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8663 (tp) REVERT: C 662 MET cc_start: 0.8732 (mtm) cc_final: 0.8412 (mtp) REVERT: C 748 MET cc_start: 0.8058 (mtt) cc_final: 0.7774 (mtm) REVERT: C 779 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7933 (tttt) REVERT: C 1053 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7624 (mt) REVERT: C 1085 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: C 1109 ILE cc_start: 0.8493 (mt) cc_final: 0.8178 (mm) REVERT: C 1166 ASP cc_start: 0.8021 (m-30) cc_final: 0.7350 (m-30) REVERT: C 1171 HIS cc_start: 0.8088 (t-90) cc_final: 0.7633 (t70) REVERT: D 413 LEU cc_start: 0.8557 (mt) cc_final: 0.8188 (tp) REVERT: D 478 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.5595 (t80) REVERT: D 616 LYS cc_start: 0.8482 (pttp) cc_final: 0.7904 (mttt) REVERT: D 626 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8661 (tp) REVERT: D 662 MET cc_start: 0.8729 (mtm) cc_final: 0.8408 (mtp) REVERT: D 748 MET cc_start: 0.8045 (mtt) cc_final: 0.7762 (mtm) REVERT: D 1053 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7613 (mt) REVERT: D 1085 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: D 1109 ILE cc_start: 0.8478 (mt) cc_final: 0.8165 (mm) REVERT: D 1166 ASP cc_start: 0.8094 (m-30) cc_final: 0.7398 (m-30) REVERT: D 1171 HIS cc_start: 0.8081 (t-90) cc_final: 0.7621 (t70) outliers start: 95 outliers final: 67 residues processed: 526 average time/residue: 0.3335 time to fit residues: 286.4929 Evaluate side-chains 517 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 434 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 900 LYS Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1053 ILE 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 A residue 1123 HIS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 858 PHE 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 1053 ILE 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 1123 HIS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1053 ILE 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 1123 HIS Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 900 LYS 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 1053 ILE Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1097 ASN Chi-restraints excluded: chain D residue 1123 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 312 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26016 Z= 0.187 Angle : 0.583 9.930 35416 Z= 0.288 Chirality : 0.041 0.226 4180 Planarity : 0.004 0.048 4312 Dihedral : 7.348 59.759 4316 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % Rotamer: Outliers : 3.56 % Allowed : 14.60 % Favored : 81.84 % 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: -0.14 (0.15), residues: 3136 helix: 0.57 (0.11), residues: 2160 sheet: None (None), residues: 0 loop : -1.47 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 857 HIS 0.003 0.001 HIS C 850 PHE 0.018 0.001 PHE A 858 TYR 0.013 0.001 TYR C 965 ARG 0.003 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 7 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 538 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 449 time to evaluate : 2.834 Fit side-chains REVERT: A 413 LEU cc_start: 0.8524 (mt) cc_final: 0.8141 (tp) REVERT: A 478 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.5863 (t80) REVERT: A 616 LYS cc_start: 0.8600 (pttp) cc_final: 0.8148 (mttt) REVERT: A 626 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 662 MET cc_start: 0.8729 (mtm) cc_final: 0.8408 (mtp) REVERT: A 748 MET cc_start: 0.7986 (mtt) cc_final: 0.7683 (mtm) REVERT: A 1053 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7575 (mt) REVERT: A 1085 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: A 1109 ILE cc_start: 0.8490 (mt) cc_final: 0.8184 (mm) REVERT: A 1159 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8009 (tttm) REVERT: A 1166 ASP cc_start: 0.8035 (m-30) cc_final: 0.7337 (m-30) REVERT: A 1171 HIS cc_start: 0.8083 (t-90) cc_final: 0.7652 (t70) REVERT: B 413 LEU cc_start: 0.8533 (mt) cc_final: 0.8162 (tp) REVERT: B 478 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.5817 (t80) REVERT: B 616 LYS cc_start: 0.8599 (pttp) cc_final: 0.8150 (mttt) REVERT: B 626 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8677 (tp) REVERT: B 662 MET cc_start: 0.8729 (mtm) cc_final: 0.8408 (mtp) REVERT: B 707 LYS cc_start: 0.9029 (mttt) cc_final: 0.8827 (mttp) REVERT: B 748 MET cc_start: 0.8040 (mtt) cc_final: 0.7739 (mtm) REVERT: B 1053 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 1085 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: B 1109 ILE cc_start: 0.8490 (mt) cc_final: 0.8194 (mm) REVERT: B 1166 ASP cc_start: 0.8016 (m-30) cc_final: 0.7308 (m-30) REVERT: B 1171 HIS cc_start: 0.8054 (t-90) cc_final: 0.7618 (t70) REVERT: C 413 LEU cc_start: 0.8538 (mt) cc_final: 0.8163 (tp) REVERT: C 478 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.5817 (t80) REVERT: C 616 LYS cc_start: 0.8600 (pttp) cc_final: 0.8151 (mttt) REVERT: C 626 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8673 (tp) REVERT: C 662 MET cc_start: 0.8730 (mtm) cc_final: 0.8407 (mtp) REVERT: C 748 MET cc_start: 0.8020 (mtt) cc_final: 0.7725 (mtm) REVERT: C 779 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7833 (tttt) REVERT: C 922 ASP cc_start: 0.7989 (t0) cc_final: 0.7788 (t0) REVERT: C 1053 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7555 (mt) REVERT: C 1085 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: C 1109 ILE cc_start: 0.8492 (mt) cc_final: 0.8197 (mm) REVERT: C 1166 ASP cc_start: 0.8051 (m-30) cc_final: 0.7352 (m-30) REVERT: C 1171 HIS cc_start: 0.8095 (t-90) cc_final: 0.7663 (t70) REVERT: D 413 LEU cc_start: 0.8542 (mt) cc_final: 0.8167 (tp) REVERT: D 478 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.5817 (t80) REVERT: D 616 LYS cc_start: 0.8598 (pttp) cc_final: 0.8150 (mttt) REVERT: D 626 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8673 (tp) REVERT: D 662 MET cc_start: 0.8730 (mtm) cc_final: 0.8403 (mtp) REVERT: D 748 MET cc_start: 0.8030 (mtt) cc_final: 0.7746 (mtm) REVERT: D 1053 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7553 (mt) REVERT: D 1085 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: D 1109 ILE cc_start: 0.8492 (mt) cc_final: 0.8190 (mm) REVERT: D 1166 ASP cc_start: 0.8072 (m-30) cc_final: 0.7363 (m-30) REVERT: D 1171 HIS cc_start: 0.8058 (t-90) cc_final: 0.7612 (t70) outliers start: 89 outliers final: 69 residues processed: 514 average time/residue: 0.3262 time to fit residues: 273.8126 Evaluate side-chains 510 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 425 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1053 ILE 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 A residue 1123 HIS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 881 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 1053 ILE 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 1123 HIS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1053 ILE 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 1123 HIS Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 881 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 1053 ILE Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1097 ASN Chi-restraints excluded: chain D residue 1123 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 94 optimal weight: 0.0980 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 154 optimal weight: 0.0070 chunk 29 optimal weight: 0.4980 chunk 245 optimal weight: 20.0000 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26016 Z= 0.161 Angle : 0.568 9.735 35416 Z= 0.280 Chirality : 0.041 0.226 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.129 59.820 4316 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.64 % Allowed : 14.52 % Favored : 81.84 % 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: 0.15 (0.16), residues: 3136 helix: 0.79 (0.12), residues: 2164 sheet: None (None), residues: 0 loop : -1.39 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1111 HIS 0.004 0.000 HIS D 850 PHE 0.018 0.001 PHE A 858 TYR 0.013 0.001 TYR B 965 ARG 0.007 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 8 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 553 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 462 time to evaluate : 3.123 Fit side-chains REVERT: A 413 LEU cc_start: 0.8513 (mt) cc_final: 0.8118 (tp) REVERT: A 478 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.5905 (t80) REVERT: A 616 LYS cc_start: 0.8610 (pttp) cc_final: 0.8162 (mttt) REVERT: A 626 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8682 (tp) REVERT: A 662 MET cc_start: 0.8725 (mtm) cc_final: 0.8378 (mtp) REVERT: A 748 MET cc_start: 0.7991 (mtt) cc_final: 0.7714 (mtm) REVERT: A 878 MET cc_start: 0.8667 (ttm) cc_final: 0.8397 (ttm) REVERT: A 1053 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 1085 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: A 1109 ILE cc_start: 0.8486 (mt) cc_final: 0.8194 (mm) REVERT: A 1159 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7986 (tttm) REVERT: A 1166 ASP cc_start: 0.7977 (m-30) cc_final: 0.7276 (m-30) REVERT: A 1171 HIS cc_start: 0.8080 (t-90) cc_final: 0.7685 (t70) REVERT: B 274 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7986 (mmp80) REVERT: B 478 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.5914 (t80) REVERT: B 626 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8683 (tp) REVERT: B 662 MET cc_start: 0.8727 (mtm) cc_final: 0.8397 (mtp) REVERT: B 707 LYS cc_start: 0.8997 (mttt) cc_final: 0.8772 (mttp) REVERT: B 748 MET cc_start: 0.8017 (mtt) cc_final: 0.7730 (mtm) REVERT: B 1053 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7466 (mt) REVERT: B 1085 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: B 1109 ILE cc_start: 0.8466 (mt) cc_final: 0.8167 (mm) REVERT: B 1166 ASP cc_start: 0.7944 (m-30) cc_final: 0.7245 (m-30) REVERT: B 1171 HIS cc_start: 0.8033 (t-90) cc_final: 0.7598 (t70) REVERT: C 274 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7983 (mmp80) REVERT: C 478 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.5911 (t80) REVERT: C 616 LYS cc_start: 0.8608 (pttp) cc_final: 0.8161 (mttt) REVERT: C 626 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8679 (tp) REVERT: C 662 MET cc_start: 0.8729 (mtm) cc_final: 0.8394 (mtp) REVERT: C 748 MET cc_start: 0.8010 (mtt) cc_final: 0.7732 (mtm) REVERT: C 779 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7813 (tttt) REVERT: C 922 ASP cc_start: 0.7956 (t0) cc_final: 0.7755 (t0) REVERT: C 1053 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7464 (mt) REVERT: C 1085 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: C 1109 ILE cc_start: 0.8470 (mt) cc_final: 0.8174 (mm) REVERT: C 1166 ASP cc_start: 0.7987 (m-30) cc_final: 0.7292 (m-30) REVERT: C 1171 HIS cc_start: 0.8089 (t-90) cc_final: 0.7695 (t70) REVERT: D 274 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7986 (mmp80) REVERT: D 478 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.5916 (t80) REVERT: D 626 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8681 (tp) REVERT: D 662 MET cc_start: 0.8727 (mtm) cc_final: 0.8396 (mtp) REVERT: D 704 MET cc_start: 0.8073 (mmm) cc_final: 0.7851 (mmt) REVERT: D 748 MET cc_start: 0.8013 (mtt) cc_final: 0.7717 (mtm) REVERT: D 1053 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7465 (mt) REVERT: D 1085 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: D 1109 ILE cc_start: 0.8496 (mt) cc_final: 0.8183 (mm) REVERT: D 1166 ASP cc_start: 0.7988 (m-30) cc_final: 0.7253 (m-30) REVERT: D 1171 HIS cc_start: 0.8069 (t-90) cc_final: 0.7642 (t70) outliers start: 91 outliers final: 66 residues processed: 528 average time/residue: 0.3309 time to fit residues: 284.0728 Evaluate side-chains 516 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 434 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1053 ILE 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 A residue 1123 HIS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1053 ILE 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 1123 HIS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1053 ILE 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 1123 HIS Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 881 LEU 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 1053 ILE Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1097 ASN Chi-restraints excluded: chain D residue 1123 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.1980 chunk 299 optimal weight: 1.9990 chunk 272 optimal weight: 0.4980 chunk 291 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 228 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 275 optimal weight: 0.8980 chunk 289 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN A 681 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26016 Z= 0.168 Angle : 0.585 9.737 35416 Z= 0.286 Chirality : 0.042 0.239 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.046 59.738 4316 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.40 % Allowed : 15.00 % Favored : 81.60 % 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: 0.27 (0.16), residues: 3136 helix: 0.87 (0.12), residues: 2168 sheet: None (None), residues: 0 loop : -1.34 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1030 HIS 0.004 0.001 HIS D 850 PHE 0.018 0.001 PHE A 858 TYR 0.016 0.001 TYR B 664 ARG 0.007 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 9 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 548 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 463 time to evaluate : 2.878 Fit side-chains REVERT: A 413 LEU cc_start: 0.8517 (mt) cc_final: 0.8135 (tp) REVERT: A 478 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.5963 (t80) REVERT: A 616 LYS cc_start: 0.8681 (pttp) cc_final: 0.8169 (mttt) REVERT: A 626 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8698 (tp) REVERT: A 662 MET cc_start: 0.8719 (mtm) cc_final: 0.8387 (mtp) REVERT: A 748 MET cc_start: 0.7987 (mtt) cc_final: 0.7685 (mtm) REVERT: A 878 MET cc_start: 0.8684 (ttm) cc_final: 0.8409 (ttm) REVERT: A 1051 TYR cc_start: 0.8186 (m-80) cc_final: 0.7860 (m-80) REVERT: A 1053 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7471 (mt) REVERT: A 1085 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: A 1109 ILE cc_start: 0.8502 (mt) cc_final: 0.8206 (mm) REVERT: A 1159 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7953 (tttm) REVERT: A 1166 ASP cc_start: 0.7987 (m-30) cc_final: 0.7274 (m-30) REVERT: A 1171 HIS cc_start: 0.8088 (t-90) cc_final: 0.7697 (t70) REVERT: B 478 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.5911 (t80) REVERT: B 626 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8683 (tp) REVERT: B 662 MET cc_start: 0.8723 (mtm) cc_final: 0.8387 (mtp) REVERT: B 707 LYS cc_start: 0.8987 (mttt) cc_final: 0.8753 (mttp) REVERT: B 748 MET cc_start: 0.8013 (mtt) cc_final: 0.7708 (mtm) REVERT: B 878 MET cc_start: 0.8685 (ttm) cc_final: 0.8400 (ttm) REVERT: B 1051 TYR cc_start: 0.8195 (m-80) cc_final: 0.7860 (m-80) REVERT: B 1053 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7456 (mt) REVERT: B 1085 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6497 (m-80) REVERT: B 1109 ILE cc_start: 0.8500 (mt) cc_final: 0.8198 (mm) REVERT: B 1166 ASP cc_start: 0.7969 (m-30) cc_final: 0.7254 (m-30) REVERT: B 1171 HIS cc_start: 0.8034 (t-90) cc_final: 0.7608 (t70) REVERT: C 478 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.5907 (t80) REVERT: C 616 LYS cc_start: 0.8619 (pttp) cc_final: 0.8168 (mttt) REVERT: C 626 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8681 (tp) REVERT: C 662 MET cc_start: 0.8722 (mtm) cc_final: 0.8386 (mtp) REVERT: C 748 MET cc_start: 0.8015 (mtt) cc_final: 0.7723 (mtm) REVERT: C 779 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7826 (tttt) REVERT: C 878 MET cc_start: 0.8674 (ttm) cc_final: 0.8398 (ttm) REVERT: C 1051 TYR cc_start: 0.8171 (m-80) cc_final: 0.7848 (m-80) REVERT: C 1053 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7458 (mt) REVERT: C 1085 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: C 1109 ILE cc_start: 0.8502 (mt) cc_final: 0.8197 (mm) REVERT: C 1166 ASP cc_start: 0.7997 (m-30) cc_final: 0.7292 (m-30) REVERT: C 1171 HIS cc_start: 0.8092 (t-90) cc_final: 0.7701 (t70) REVERT: D 274 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.8000 (mmp80) REVERT: D 478 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.5912 (t80) REVERT: D 626 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8680 (tp) REVERT: D 662 MET cc_start: 0.8723 (mtm) cc_final: 0.8389 (mtp) REVERT: D 748 MET cc_start: 0.8038 (mtt) cc_final: 0.7746 (mtm) REVERT: D 878 MET cc_start: 0.8706 (ttm) cc_final: 0.8434 (ttm) REVERT: D 1051 TYR cc_start: 0.8210 (m-80) cc_final: 0.7874 (m-80) REVERT: D 1053 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7457 (mt) REVERT: D 1085 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: D 1109 ILE cc_start: 0.8499 (mt) cc_final: 0.8194 (mm) REVERT: D 1166 ASP cc_start: 0.8005 (m-30) cc_final: 0.7263 (m-30) REVERT: D 1171 HIS cc_start: 0.8081 (t-90) cc_final: 0.7642 (t70) outliers start: 85 outliers final: 64 residues processed: 523 average time/residue: 0.3471 time to fit residues: 294.0946 Evaluate side-chains 521 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 441 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1053 ILE 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 A residue 1123 HIS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1053 ILE 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 1123 HIS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1053 ILE 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 1123 HIS Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 881 LEU 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 1053 ILE Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1097 ASN Chi-restraints excluded: chain D residue 1123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.8980 chunk 307 optimal weight: 0.0070 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 0.4980 chunk 213 optimal weight: 6.9990 chunk 322 optimal weight: 0.8980 chunk 297 optimal weight: 8.9990 chunk 257 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 681 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 681 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN D 681 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26016 Z= 0.172 Angle : 0.584 9.697 35416 Z= 0.285 Chirality : 0.042 0.248 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.061 59.960 4316 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.08 % Allowed : 16.20 % Favored : 80.72 % 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: 0.31 (0.15), residues: 3136 helix: 0.92 (0.12), residues: 2160 sheet: None (None), residues: 0 loop : -1.36 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1030 HIS 0.004 0.001 HIS B 850 PHE 0.018 0.001 PHE A 858 TYR 0.014 0.001 TYR C 776 ARG 0.007 0.000 ARG A 274 ********************** REFINEMENT MACRO_CYCLE 10 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 535 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 458 time to evaluate : 2.741 Fit side-chains REVERT: A 274 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7916 (mmp80) REVERT: A 413 LEU cc_start: 0.8535 (mt) cc_final: 0.8164 (tp) REVERT: A 478 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.6000 (t80) REVERT: A 616 LYS cc_start: 0.8663 (pttp) cc_final: 0.7996 (mttt) REVERT: A 626 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 662 MET cc_start: 0.8720 (mtm) cc_final: 0.8392 (mtp) REVERT: A 748 MET cc_start: 0.7972 (mtt) cc_final: 0.7661 (mtm) REVERT: A 878 MET cc_start: 0.8710 (ttm) cc_final: 0.8439 (ttm) REVERT: A 1051 TYR cc_start: 0.8157 (m-80) cc_final: 0.7825 (m-80) REVERT: A 1053 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7461 (mt) REVERT: A 1085 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: A 1109 ILE cc_start: 0.8507 (mt) cc_final: 0.8215 (mm) REVERT: A 1159 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7975 (tttm) REVERT: A 1166 ASP cc_start: 0.7975 (m-30) cc_final: 0.7305 (m-30) REVERT: A 1171 HIS cc_start: 0.8096 (t-90) cc_final: 0.7708 (t70) REVERT: B 478 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6295 (t80) REVERT: B 616 LYS cc_start: 0.8686 (pttp) cc_final: 0.8178 (mttt) REVERT: B 626 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8696 (tp) REVERT: B 662 MET cc_start: 0.8722 (mtm) cc_final: 0.8393 (mtp) REVERT: B 707 LYS cc_start: 0.8986 (mttt) cc_final: 0.8762 (mttp) REVERT: B 748 MET cc_start: 0.8005 (mtt) cc_final: 0.7698 (mtm) REVERT: B 878 MET cc_start: 0.8697 (ttm) cc_final: 0.8414 (ttm) REVERT: B 1051 TYR cc_start: 0.8162 (m-80) cc_final: 0.7827 (m-80) REVERT: B 1053 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7447 (mt) REVERT: B 1085 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: B 1166 ASP cc_start: 0.7968 (m-30) cc_final: 0.7253 (m-30) REVERT: B 1171 HIS cc_start: 0.8035 (t-90) cc_final: 0.7569 (t70) REVERT: C 478 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.6293 (t80) REVERT: C 616 LYS cc_start: 0.8688 (pttp) cc_final: 0.8179 (mttt) REVERT: C 626 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8693 (tp) REVERT: C 662 MET cc_start: 0.8723 (mtm) cc_final: 0.8392 (mtp) REVERT: C 748 MET cc_start: 0.8012 (mtt) cc_final: 0.7735 (mtm) REVERT: C 779 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7820 (tttt) REVERT: C 878 MET cc_start: 0.8692 (ttm) cc_final: 0.8416 (ttm) REVERT: C 1051 TYR cc_start: 0.8144 (m-80) cc_final: 0.7812 (m-80) REVERT: C 1053 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7449 (mt) REVERT: C 1085 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: C 1166 ASP cc_start: 0.7989 (m-30) cc_final: 0.7294 (m-30) REVERT: C 1171 HIS cc_start: 0.8105 (t-90) cc_final: 0.7703 (t70) REVERT: D 274 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7993 (mmp80) REVERT: D 478 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6296 (t80) REVERT: D 626 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8693 (tp) REVERT: D 662 MET cc_start: 0.8727 (mtm) cc_final: 0.8395 (mtp) REVERT: D 748 MET cc_start: 0.8029 (mtt) cc_final: 0.7713 (mtm) REVERT: D 878 MET cc_start: 0.8737 (ttm) cc_final: 0.8471 (ttm) REVERT: D 1051 TYR cc_start: 0.8181 (m-80) cc_final: 0.7840 (m-80) REVERT: D 1053 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7450 (mt) REVERT: D 1085 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: D 1165 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7384 (tm-30) REVERT: D 1166 ASP cc_start: 0.8002 (m-30) cc_final: 0.7071 (m-30) REVERT: D 1171 HIS cc_start: 0.8084 (t-90) cc_final: 0.7646 (t70) outliers start: 77 outliers final: 58 residues processed: 509 average time/residue: 0.3458 time to fit residues: 284.2798 Evaluate side-chains 513 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 439 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1085 TYR Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1123 HIS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 943 PHE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1123 HIS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1123 HIS Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 858 PHE Chi-restraints excluded: chain D residue 881 LEU 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 1053 ILE Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1097 ASN Chi-restraints excluded: chain D residue 1123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.0980 chunk 273 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 237 optimal weight: 5.9990 chunk 37 optimal weight: 0.0020 chunk 71 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117022 restraints weight = 31440.072| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.88 r_work: 0.2947 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26016 Z= 0.176 Angle : 0.598 11.301 35416 Z= 0.289 Chirality : 0.042 0.245 4180 Planarity : 0.004 0.048 4312 Dihedral : 6.954 59.681 4312 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.12 % Allowed : 16.36 % Favored : 80.52 % 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: 0.44 (0.16), residues: 3136 helix: 1.02 (0.12), residues: 2156 sheet: None (None), residues: 0 loop : -1.28 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1030 HIS 0.003 0.001 HIS D 850 PHE 0.019 0.001 PHE A 858 TYR 0.013 0.001 TYR D 965 ARG 0.007 0.000 ARG A 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6200.01 seconds wall clock time: 112 minutes 13.84 seconds (6733.84 seconds total)