Starting phenix.real_space_refine on Wed Nov 19 16:35:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5zx5_6975/11_2025/5zx5_6975.cif Found real_map, /net/cci-nas-00/data/ceres_data/5zx5_6975/11_2025/5zx5_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 { model { file = "/net/cci-nas-00/data/ceres_data/5zx5_6975/11_2025/5zx5_6975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5zx5_6975/11_2025/5zx5_6975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5zx5_6975/11_2025/5zx5_6975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5zx5_6975/11_2025/5zx5_6975.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'TRP:plan': 2, 'GLU:plan': 17, 'ARG:plan': 9, 'HIS:plan': 1, 'PHE:plan': 3, 'TYR:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 5} 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: {'TRP:plan': 2, 'GLU:plan': 17, 'ARG:plan': 9, 'HIS:plan': 1, 'PHE:plan': 3, 'TYR:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 5} 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: {'TRP:plan': 2, 'GLU:plan': 17, 'ARG:plan': 9, 'HIS:plan': 1, 'PHE:plan': 3, 'TYR:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 5} 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: {'TRP:plan': 2, 'GLU:plan': 17, 'ARG:plan': 9, 'HIS:plan': 1, 'PHE:plan': 3, 'TYR:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 5} 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: 6.30, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 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: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 8 sheets defined 67.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 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: 4.45 Time building geometry restraints manager: 2.97 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: 0.00 - 2.86: 33528 2.86 - 5.71: 1544 5.71 - 8.57: 274 8.57 - 11.43: 46 11.43 - 14.28: 24 Bond angle restraints: 35416 Sorted by residual: angle pdb=" N LEU A 298 " pdb=" CA LEU A 298 " pdb=" C LEU A 298 " ideal model delta sigma weight residual 111.28 125.33 -14.05 1.09e+00 8.42e-01 1.66e+02 angle pdb=" N GLU B 476 " pdb=" CA GLU B 476 " pdb=" C GLU B 476 " ideal model delta sigma weight residual 110.52 96.24 14.28 1.48e+00 4.57e-01 9.31e+01 angle pdb=" N GLU D 476 " pdb=" CA GLU D 476 " pdb=" C GLU D 476 " ideal model delta sigma weight residual 110.52 96.27 14.25 1.48e+00 4.57e-01 9.27e+01 angle pdb=" N GLU C 476 " pdb=" CA GLU C 476 " pdb=" C GLU C 476 " ideal model delta sigma weight residual 110.52 96.30 14.22 1.48e+00 4.57e-01 9.24e+01 angle pdb=" N GLU A 476 " pdb=" CA GLU A 476 " pdb=" C GLU A 476 " ideal model delta sigma weight residual 110.55 98.84 11.71 1.35e+00 5.49e-01 7.52e+01 ... (remaining 35411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 15359 22.47 - 44.93: 464 44.93 - 67.40: 72 67.40 - 89.86: 5 89.86 - 112.33: 12 Dihedral angle restraints: 15912 sinusoidal: 6344 harmonic: 9568 Sorted by residual: dihedral pdb=" CA ILE C 297 " pdb=" C ILE C 297 " pdb=" N LEU C 298 " pdb=" CA LEU C 298 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE D 297 " pdb=" C ILE D 297 " pdb=" N LEU D 298 " pdb=" CA LEU D 298 " ideal model delta harmonic sigma weight residual 180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE B 297 " pdb=" C ILE B 297 " pdb=" N LEU B 298 " pdb=" CA LEU B 298 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 15909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3845 0.120 - 0.241: 278 0.241 - 0.361: 42 0.361 - 0.482: 14 0.482 - 0.602: 1 Chirality restraints: 4180 Sorted by residual: chirality pdb=" CA LEU A 298 " pdb=" N LEU A 298 " pdb=" C LEU A 298 " pdb=" CB LEU A 298 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" CBH Y01 B1302 " pdb=" CAT Y01 B1302 " pdb=" CAZ Y01 B1302 " pdb=" CBF Y01 B1302 " both_signs ideal model delta sigma weight residual False -2.85 -2.41 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CBH Y01 A1303 " pdb=" CAT Y01 A1303 " pdb=" CAZ Y01 A1303 " pdb=" CBF Y01 A1303 " both_signs ideal model delta sigma weight residual False -2.85 -2.41 -0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 4177 not shown) Planarity restraints: 4312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 858 " -0.031 2.00e-02 2.50e+03 3.05e-02 1.62e+01 pdb=" CG PHE A 858 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 858 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 858 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 858 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 858 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 858 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 858 " -0.031 2.00e-02 2.50e+03 3.05e-02 1.62e+01 pdb=" CG PHE D 858 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE D 858 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE D 858 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 858 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 858 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE D 858 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 858 " 0.031 2.00e-02 2.50e+03 3.05e-02 1.62e+01 pdb=" CG PHE B 858 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 858 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE B 858 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 858 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 858 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE B 858 " -0.005 2.00e-02 2.50e+03 ... (remaining 4309 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7087 2.80 - 3.32: 23325 3.32 - 3.85: 39763 3.85 - 4.37: 49074 4.37 - 4.90: 81733 Nonbonded interactions: 200982 Sorted by model distance: nonbonded pdb=" OG1 THR B 895 " pdb=" O PRO B1130 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR C 895 " pdb=" O PRO C1130 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR D 895 " pdb=" O PRO D1130 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR A 895 " pdb=" O PRO A1130 " model vdw 2.270 3.040 nonbonded pdb=" O GLU D 775 " pdb=" CD1 TYR D 776 " model vdw 2.294 3.340 ... (remaining 200977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 1302) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 6 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.820 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- 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= 0.668 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 : 11.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.019 0.002 ARG D 942 TYR 0.067 0.004 TYR A 870 PHE 0.068 0.005 PHE D 858 TRP 0.033 0.004 TRP A 417 HIS 0.019 0.003 HIS C1137 Details of bonding type rmsd covalent geometry : bond 0.01560 (26016) covalent geometry : angle 1.40523 (35416) hydrogen bonds : bond 0.18120 ( 1266) hydrogen bonds : angle 9.72062 ( 3774) *********************** 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 to be fit. rotamer outliers: 53 poor density : 681 time to evaluate : 0.965 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: 0.1986 time to fit residues: 217.9561 Evaluate side-chains 437 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 415 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS A 295 ASN A 426 HIS A 432 GLN A 491 HIS A 700 GLN A 718 ASN A 789 GLN A 885 GLN A1090 ASN A1123 HIS A1137 HIS A1210 GLN B 276 HIS B 295 ASN B 426 HIS B 432 GLN B 491 HIS B 700 GLN B 718 ASN B 756 ASN B 789 GLN B 885 GLN B1090 ASN B1123 HIS B1137 HIS B1210 GLN C 276 HIS C 295 ASN C 426 HIS C 432 GLN C 491 HIS C 700 GLN C 718 ASN C 789 GLN C 885 GLN C1090 ASN C1123 HIS C1137 HIS C1210 GLN D 276 HIS D 295 ASN D 426 HIS D 432 GLN D 491 HIS D 700 GLN D 718 ASN D 756 ASN D 789 GLN D 885 GLN D1090 ASN D1123 HIS D1137 HIS D1210 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.147949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115458 restraints weight = 31603.283| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.91 r_work: 0.2953 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2464 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= 0.160 Angle : 0.722 10.219 35416 Z= 0.361 Chirality : 0.044 0.243 4180 Planarity : 0.005 0.051 4312 Dihedral : 9.337 76.526 4327 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 3.52 % Allowed : 9.24 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.13), residues: 3136 helix: -1.70 (0.10), residues: 2108 sheet: None (None), residues: 0 loop : -1.99 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 525 TYR 0.015 0.002 TYR A 870 PHE 0.029 0.002 PHE C 858 TRP 0.015 0.001 TRP B1111 HIS 0.007 0.001 HIS A1137 Details of bonding type rmsd covalent geometry : bond 0.00348 (26016) covalent geometry : angle 0.72230 (35416) hydrogen bonds : bond 0.04071 ( 1266) hydrogen bonds : angle 5.20675 ( 3774) *********************** 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 630 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 542 time to evaluate : 1.043 Fit side-chains REVERT: A 662 MET cc_start: 0.8947 (mtm) cc_final: 0.8252 (mtp) REVERT: A 664 TYR cc_start: 0.8766 (t80) cc_final: 0.8468 (t80) REVERT: A 703 THR cc_start: 0.8855 (p) cc_final: 0.8409 (t) REVERT: A 707 LYS cc_start: 0.9049 (mttt) cc_final: 0.8783 (mttp) REVERT: A 748 MET cc_start: 0.8783 (mtt) cc_final: 0.8552 (mtm) REVERT: A 984 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8189 (mp10) REVERT: A 1085 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: A 1088 MET cc_start: 0.9332 (mmm) cc_final: 0.8969 (mmm) REVERT: A 1089 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.8969 (t) REVERT: A 1159 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8159 (tttm) REVERT: A 1166 ASP cc_start: 0.8512 (m-30) cc_final: 0.7763 (m-30) REVERT: A 1168 LYS cc_start: 0.8434 (mttm) cc_final: 0.8125 (mtmt) REVERT: A 1171 HIS cc_start: 0.8640 (t-90) cc_final: 0.8186 (t70) REVERT: B 662 MET cc_start: 0.8931 (mtm) cc_final: 0.8229 (mtp) REVERT: B 664 TYR cc_start: 0.8773 (t80) cc_final: 0.8475 (t80) REVERT: B 703 THR cc_start: 0.8865 (p) cc_final: 0.8425 (t) REVERT: B 707 LYS cc_start: 0.9066 (mttt) cc_final: 0.8804 (mttp) REVERT: B 748 MET cc_start: 0.8789 (mtt) cc_final: 0.8554 (mtm) REVERT: B 1085 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: B 1088 MET cc_start: 0.9322 (mmm) cc_final: 0.8970 (mmm) REVERT: B 1089 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.8965 (t) REVERT: B 1166 ASP cc_start: 0.8496 (m-30) cc_final: 0.7745 (m-30) REVERT: B 1168 LYS cc_start: 0.8436 (mttm) cc_final: 0.8127 (mtmt) REVERT: B 1171 HIS cc_start: 0.8640 (t-90) cc_final: 0.8203 (t70) REVERT: B 1206 GLN cc_start: 0.8251 (pt0) cc_final: 0.8049 (pt0) REVERT: C 662 MET cc_start: 0.8938 (mtm) cc_final: 0.8234 (mtp) REVERT: C 664 TYR cc_start: 0.8757 (t80) cc_final: 0.8459 (t80) REVERT: C 697 SER cc_start: 0.9166 (p) cc_final: 0.8965 (m) REVERT: C 703 THR cc_start: 0.8852 (p) cc_final: 0.8412 (t) REVERT: C 707 LYS cc_start: 0.9056 (mttt) cc_final: 0.8789 (mttp) REVERT: C 748 MET cc_start: 0.8773 (mtt) cc_final: 0.8539 (mtm) REVERT: C 984 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8200 (mp10) REVERT: C 1085 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: C 1088 MET cc_start: 0.9327 (mmm) cc_final: 0.8977 (mmm) REVERT: C 1089 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.8973 (t) REVERT: C 1166 ASP cc_start: 0.8502 (m-30) cc_final: 0.7752 (m-30) REVERT: C 1168 LYS cc_start: 0.8455 (mttm) cc_final: 0.8142 (mtmt) REVERT: C 1171 HIS cc_start: 0.8637 (t-90) cc_final: 0.8187 (t70) REVERT: D 662 MET cc_start: 0.8958 (mtm) cc_final: 0.8258 (mtp) REVERT: D 664 TYR cc_start: 0.8776 (t80) cc_final: 0.8478 (t80) REVERT: D 703 THR cc_start: 0.8827 (p) cc_final: 0.8498 (t) REVERT: D 748 MET cc_start: 0.8769 (mtt) cc_final: 0.8532 (mtm) REVERT: D 1085 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: D 1088 MET cc_start: 0.9339 (mmm) cc_final: 0.8984 (mmm) REVERT: D 1089 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.8969 (t) REVERT: D 1159 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8159 (tttm) REVERT: D 1166 ASP cc_start: 0.8481 (m-30) cc_final: 0.7758 (m-30) REVERT: D 1168 LYS cc_start: 0.8421 (mttm) cc_final: 0.8106 (mtmt) REVERT: D 1171 HIS cc_start: 0.8633 (t-90) cc_final: 0.8167 (t70) outliers start: 88 outliers final: 38 residues processed: 610 average time/residue: 0.1707 time to fit residues: 166.9300 Evaluate side-chains 499 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 453 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1085 TYR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 THR Chi-restraints excluded: chain D residue 756 ASN Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1089 VAL Chi-restraints excluded: chain D residue 1097 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 283 optimal weight: 0.3980 chunk 174 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 139 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN A 787 GLN A 956 HIS B 366 GLN B 756 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS C 366 GLN C 787 GLN C 956 HIS D 366 GLN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 956 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111227 restraints weight = 31855.153| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.14 r_work: 0.2869 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26016 Z= 0.187 Angle : 0.689 10.476 35416 Z= 0.344 Chirality : 0.044 0.270 4180 Planarity : 0.005 0.049 4312 Dihedral : 8.370 59.900 4317 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.52 % Rotamer: Outliers : 2.84 % Allowed : 12.36 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.14), residues: 3136 helix: -0.85 (0.11), residues: 2164 sheet: None (None), residues: 0 loop : -1.82 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 525 TYR 0.018 0.002 TYR D 776 PHE 0.016 0.001 PHE B 858 TRP 0.010 0.001 TRP A 857 HIS 0.006 0.001 HIS B 850 Details of bonding type rmsd covalent geometry : bond 0.00453 (26016) covalent geometry : angle 0.68879 (35416) hydrogen bonds : bond 0.03729 ( 1266) hydrogen bonds : angle 4.64675 ( 3774) *********************** 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 533 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 462 time to evaluate : 1.028 Fit side-chains REVERT: A 413 LEU cc_start: 0.8326 (mt) cc_final: 0.7994 (tp) REVERT: A 626 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8664 (tp) REVERT: A 662 MET cc_start: 0.8978 (mtm) cc_final: 0.8503 (mtp) REVERT: A 664 TYR cc_start: 0.8780 (t80) cc_final: 0.8500 (t80) REVERT: A 695 GLU cc_start: 0.8628 (tp30) cc_final: 0.8270 (tp30) REVERT: A 703 THR cc_start: 0.8882 (p) cc_final: 0.8429 (t) REVERT: A 704 MET cc_start: 0.9152 (mmm) cc_final: 0.8777 (mmt) REVERT: A 707 LYS cc_start: 0.9140 (mttt) cc_final: 0.8846 (mttp) REVERT: A 748 MET cc_start: 0.8731 (mtt) cc_final: 0.8502 (mtm) REVERT: A 782 MET cc_start: 0.8818 (mmm) cc_final: 0.8586 (mmm) REVERT: A 984 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8307 (mp10) REVERT: A 1085 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: A 1088 MET cc_start: 0.9340 (mmm) cc_final: 0.9049 (mmm) REVERT: A 1159 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8131 (tttm) REVERT: A 1166 ASP cc_start: 0.8339 (m-30) cc_final: 0.7731 (m-30) REVERT: A 1168 LYS cc_start: 0.8486 (mttm) cc_final: 0.8191 (mtmt) REVERT: A 1171 HIS cc_start: 0.8609 (t-90) cc_final: 0.8184 (t70) REVERT: B 413 LEU cc_start: 0.8293 (mt) cc_final: 0.7954 (tp) REVERT: B 626 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8652 (tp) REVERT: B 662 MET cc_start: 0.8948 (mtm) cc_final: 0.8470 (mtp) REVERT: B 664 TYR cc_start: 0.8779 (t80) cc_final: 0.8501 (t80) REVERT: B 695 GLU cc_start: 0.8656 (tp30) cc_final: 0.8286 (tp30) REVERT: B 703 THR cc_start: 0.8892 (p) cc_final: 0.8433 (t) REVERT: B 704 MET cc_start: 0.9150 (mmm) cc_final: 0.8772 (mmt) REVERT: B 707 LYS cc_start: 0.9149 (mttt) cc_final: 0.8851 (mttp) REVERT: B 748 MET cc_start: 0.8728 (mtt) cc_final: 0.8484 (mtm) REVERT: B 782 MET cc_start: 0.8857 (mmm) cc_final: 0.8606 (mmm) REVERT: B 1085 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: B 1088 MET cc_start: 0.9359 (mmm) cc_final: 0.9081 (mmm) REVERT: B 1166 ASP cc_start: 0.8344 (m-30) cc_final: 0.7734 (m-30) REVERT: B 1168 LYS cc_start: 0.8493 (mttm) cc_final: 0.8191 (mtmt) REVERT: B 1171 HIS cc_start: 0.8625 (t-90) cc_final: 0.8186 (t70) REVERT: C 413 LEU cc_start: 0.8290 (mt) cc_final: 0.7953 (tp) REVERT: C 626 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8653 (tp) REVERT: C 662 MET cc_start: 0.8972 (mtm) cc_final: 0.8495 (mtp) REVERT: C 664 TYR cc_start: 0.8786 (t80) cc_final: 0.8507 (t80) REVERT: C 695 GLU cc_start: 0.8651 (tp30) cc_final: 0.8282 (tp30) REVERT: C 703 THR cc_start: 0.8878 (p) cc_final: 0.8421 (t) REVERT: C 704 MET cc_start: 0.9136 (mmm) cc_final: 0.8764 (mmt) REVERT: C 707 LYS cc_start: 0.9135 (mttt) cc_final: 0.8841 (mttp) REVERT: C 748 MET cc_start: 0.8727 (mtt) cc_final: 0.8491 (mtm) REVERT: C 782 MET cc_start: 0.8836 (mmm) cc_final: 0.8614 (mmm) REVERT: C 984 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8283 (mp10) REVERT: C 1085 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: C 1088 MET cc_start: 0.9354 (mmm) cc_final: 0.9072 (mmm) REVERT: C 1166 ASP cc_start: 0.8337 (m-30) cc_final: 0.7731 (m-30) REVERT: C 1168 LYS cc_start: 0.8500 (mttm) cc_final: 0.8195 (mtmt) REVERT: C 1171 HIS cc_start: 0.8623 (t-90) cc_final: 0.8181 (t70) REVERT: D 413 LEU cc_start: 0.8303 (mt) cc_final: 0.7967 (tp) REVERT: D 626 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8647 (tp) REVERT: D 662 MET cc_start: 0.8984 (mtm) cc_final: 0.8508 (mtp) REVERT: D 664 TYR cc_start: 0.8792 (t80) cc_final: 0.8511 (t80) REVERT: D 695 GLU cc_start: 0.8637 (tp30) cc_final: 0.8278 (tp30) REVERT: D 748 MET cc_start: 0.8721 (mtt) cc_final: 0.8479 (mtm) REVERT: D 782 MET cc_start: 0.8842 (mmm) cc_final: 0.8595 (mmm) REVERT: D 1085 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: D 1088 MET cc_start: 0.9341 (mmm) cc_final: 0.9052 (mmm) REVERT: D 1159 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8156 (tttm) REVERT: D 1166 ASP cc_start: 0.8317 (m-30) cc_final: 0.7726 (m-30) REVERT: D 1168 LYS cc_start: 0.8487 (mttm) cc_final: 0.8190 (mtmt) REVERT: D 1171 HIS cc_start: 0.8607 (t-90) cc_final: 0.8151 (t70) outliers start: 71 outliers final: 46 residues processed: 517 average time/residue: 0.1740 time to fit residues: 143.6058 Evaluate side-chains 489 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 435 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 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 412 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 774 LEU 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 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 477 LEU 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 858 PHE Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 710 THR Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1097 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 150 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 316 optimal weight: 0.0030 chunk 297 optimal weight: 8.9990 chunk 68 optimal weight: 0.0970 chunk 171 optimal weight: 8.9990 chunk 302 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 787 GLN D 756 ASN D 787 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116364 restraints weight = 31447.244| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.98 r_work: 0.2941 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26016 Z= 0.117 Angle : 0.615 10.474 35416 Z= 0.305 Chirality : 0.041 0.268 4180 Planarity : 0.004 0.043 4312 Dihedral : 7.861 59.972 4317 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.00 % Favored : 96.88 % Rotamer: Outliers : 2.88 % Allowed : 13.08 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3136 helix: -0.13 (0.11), residues: 2152 sheet: None (None), residues: 0 loop : -1.72 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 274 TYR 0.015 0.001 TYR A 896 PHE 0.018 0.001 PHE A 858 TRP 0.008 0.001 TRP A1111 HIS 0.004 0.001 HIS C 850 Details of bonding type rmsd covalent geometry : bond 0.00268 (26016) covalent geometry : angle 0.61513 (35416) hydrogen bonds : bond 0.03244 ( 1266) hydrogen bonds : angle 4.28273 ( 3774) *********************** 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 568 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 496 time to evaluate : 0.968 Fit side-chains REVERT: A 626 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8745 (tp) REVERT: A 662 MET cc_start: 0.9026 (mtm) cc_final: 0.8558 (mtp) REVERT: A 664 TYR cc_start: 0.8786 (t80) cc_final: 0.8486 (t80) REVERT: A 707 LYS cc_start: 0.9113 (mttt) cc_final: 0.8826 (mttp) REVERT: A 782 MET cc_start: 0.8768 (mmm) cc_final: 0.8532 (mmm) REVERT: A 1085 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: A 1088 MET cc_start: 0.9323 (mmm) cc_final: 0.9094 (mmm) REVERT: A 1159 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8159 (tttm) REVERT: A 1166 ASP cc_start: 0.8442 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1168 LYS cc_start: 0.8482 (mttm) cc_final: 0.8192 (mtmt) REVERT: A 1171 HIS cc_start: 0.8496 (t-90) cc_final: 0.8100 (t70) REVERT: B 626 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8742 (tp) REVERT: B 662 MET cc_start: 0.8998 (mtm) cc_final: 0.8525 (mtp) REVERT: B 664 TYR cc_start: 0.8787 (t80) cc_final: 0.8484 (t80) REVERT: B 707 LYS cc_start: 0.9126 (mttt) cc_final: 0.8832 (mttp) REVERT: B 748 MET cc_start: 0.8680 (mtt) cc_final: 0.8471 (mtm) REVERT: B 759 TYR cc_start: 0.8703 (p90) cc_final: 0.8417 (p90) REVERT: B 1085 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: B 1088 MET cc_start: 0.9343 (mmm) cc_final: 0.9118 (mmm) REVERT: B 1166 ASP cc_start: 0.8440 (m-30) cc_final: 0.7803 (m-30) REVERT: B 1168 LYS cc_start: 0.8480 (mttm) cc_final: 0.8190 (mtmt) REVERT: B 1171 HIS cc_start: 0.8504 (t-90) cc_final: 0.8121 (t70) REVERT: C 626 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8748 (tp) REVERT: C 662 MET cc_start: 0.9013 (mtm) cc_final: 0.8543 (mtp) REVERT: C 664 TYR cc_start: 0.8781 (t80) cc_final: 0.8486 (t80) REVERT: C 707 LYS cc_start: 0.9119 (mttt) cc_final: 0.8833 (mttp) REVERT: C 748 MET cc_start: 0.8680 (mtt) cc_final: 0.8475 (mtm) REVERT: C 782 MET cc_start: 0.8781 (mmm) cc_final: 0.8557 (mmm) REVERT: C 984 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8267 (mp10) REVERT: C 1085 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: C 1088 MET cc_start: 0.9338 (mmm) cc_final: 0.9110 (mmm) REVERT: C 1166 ASP cc_start: 0.8427 (m-30) cc_final: 0.7791 (m-30) REVERT: C 1168 LYS cc_start: 0.8488 (mttm) cc_final: 0.8195 (mtmt) REVERT: C 1171 HIS cc_start: 0.8515 (t-90) cc_final: 0.8120 (t70) REVERT: D 626 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8734 (tp) REVERT: D 662 MET cc_start: 0.9026 (mtm) cc_final: 0.8550 (mtp) REVERT: D 664 TYR cc_start: 0.8797 (t80) cc_final: 0.8499 (t80) REVERT: D 748 MET cc_start: 0.8664 (mtt) cc_final: 0.8457 (mtm) REVERT: D 1085 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: D 1088 MET cc_start: 0.9319 (mmm) cc_final: 0.9098 (mmm) REVERT: D 1159 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8236 (tttm) REVERT: D 1166 ASP cc_start: 0.8418 (m-30) cc_final: 0.7827 (m-30) REVERT: D 1168 LYS cc_start: 0.8473 (mttm) cc_final: 0.8181 (mtmt) REVERT: D 1171 HIS cc_start: 0.8509 (t-90) cc_final: 0.8066 (t70) outliers start: 72 outliers final: 48 residues processed: 552 average time/residue: 0.1734 time to fit residues: 152.9689 Evaluate side-chains 502 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 446 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 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 858 PHE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 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 161 ILE Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 477 LEU 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 901 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 477 LEU 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 858 PHE Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 756 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU 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 27 optimal weight: 4.9990 chunk 254 optimal weight: 0.1980 chunk 294 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 ASN ** D 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.144043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111707 restraints weight = 31681.918| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.01 r_work: 0.2824 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 26016 Z= 0.300 Angle : 0.731 10.064 35416 Z= 0.364 Chirality : 0.048 0.260 4180 Planarity : 0.005 0.048 4312 Dihedral : 8.074 59.251 4316 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 3.44 % Allowed : 14.80 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.15), residues: 3136 helix: -0.25 (0.11), residues: 2176 sheet: None (None), residues: 0 loop : -1.74 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 617 TYR 0.027 0.002 TYR A 870 PHE 0.018 0.002 PHE A 858 TRP 0.010 0.002 TRP A 747 HIS 0.007 0.001 HIS D 644 Details of bonding type rmsd covalent geometry : bond 0.00733 (26016) covalent geometry : angle 0.73126 (35416) hydrogen bonds : bond 0.03860 ( 1266) hydrogen bonds : angle 4.40252 ( 3774) *********************** 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 556 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 470 time to evaluate : 0.968 Fit side-chains REVERT: A 616 LYS cc_start: 0.8687 (pttp) cc_final: 0.7826 (mttt) REVERT: A 626 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8770 (tp) REVERT: A 662 MET cc_start: 0.9074 (mtm) cc_final: 0.8672 (mtp) REVERT: A 664 TYR cc_start: 0.8813 (t80) cc_final: 0.8512 (t80) REVERT: A 703 THR cc_start: 0.8970 (p) cc_final: 0.8657 (t) REVERT: A 993 ILE cc_start: 0.9062 (mt) cc_final: 0.8858 (mm) REVERT: A 1065 ILE cc_start: 0.8421 (mm) cc_final: 0.8177 (mt) REVERT: A 1159 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8257 (tttm) REVERT: A 1166 ASP cc_start: 0.8487 (m-30) cc_final: 0.7870 (m-30) REVERT: A 1168 LYS cc_start: 0.8616 (mttm) cc_final: 0.8356 (mtmt) REVERT: A 1171 HIS cc_start: 0.8559 (t-90) cc_final: 0.8145 (t70) REVERT: B 616 LYS cc_start: 0.8686 (pttp) cc_final: 0.7832 (mttt) REVERT: B 626 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8774 (tp) REVERT: B 662 MET cc_start: 0.9053 (mtm) cc_final: 0.8642 (mtp) REVERT: B 664 TYR cc_start: 0.8807 (t80) cc_final: 0.8497 (t80) REVERT: B 703 THR cc_start: 0.8962 (p) cc_final: 0.8649 (t) REVERT: B 748 MET cc_start: 0.8772 (mtt) cc_final: 0.8508 (mtm) REVERT: B 993 ILE cc_start: 0.9046 (mt) cc_final: 0.8836 (mm) REVERT: B 1065 ILE cc_start: 0.8422 (mm) cc_final: 0.8177 (mt) REVERT: B 1166 ASP cc_start: 0.8481 (m-30) cc_final: 0.7838 (m-30) REVERT: B 1168 LYS cc_start: 0.8605 (mttm) cc_final: 0.8340 (mtmt) REVERT: B 1171 HIS cc_start: 0.8560 (t-90) cc_final: 0.8144 (t70) REVERT: C 616 LYS cc_start: 0.8683 (pttp) cc_final: 0.7825 (mttt) REVERT: C 626 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8770 (tp) REVERT: C 662 MET cc_start: 0.9048 (mtm) cc_final: 0.8650 (mtp) REVERT: C 664 TYR cc_start: 0.8821 (t80) cc_final: 0.8519 (t80) REVERT: C 703 THR cc_start: 0.8965 (p) cc_final: 0.8654 (t) REVERT: C 748 MET cc_start: 0.8768 (mtt) cc_final: 0.8510 (mtm) REVERT: C 993 ILE cc_start: 0.9052 (mt) cc_final: 0.8846 (mm) REVERT: C 1065 ILE cc_start: 0.8433 (mm) cc_final: 0.8190 (mt) REVERT: C 1166 ASP cc_start: 0.8465 (m-30) cc_final: 0.7825 (m-30) REVERT: C 1168 LYS cc_start: 0.8607 (mttm) cc_final: 0.8341 (mtmt) REVERT: C 1171 HIS cc_start: 0.8569 (t-90) cc_final: 0.8151 (t70) REVERT: D 616 LYS cc_start: 0.8687 (pttp) cc_final: 0.7829 (mttt) REVERT: D 626 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8767 (tp) REVERT: D 662 MET cc_start: 0.9069 (mtm) cc_final: 0.8668 (mtp) REVERT: D 664 TYR cc_start: 0.8820 (t80) cc_final: 0.8518 (t80) REVERT: D 748 MET cc_start: 0.8758 (mtt) cc_final: 0.8498 (mtm) REVERT: D 993 ILE cc_start: 0.9050 (mt) cc_final: 0.8831 (mm) REVERT: D 1065 ILE cc_start: 0.8421 (mm) cc_final: 0.8180 (mt) REVERT: D 1159 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8252 (tttm) REVERT: D 1166 ASP cc_start: 0.8465 (m-30) cc_final: 0.7819 (m-30) REVERT: D 1168 LYS cc_start: 0.8606 (mttm) cc_final: 0.8342 (mtmt) REVERT: D 1171 HIS cc_start: 0.8546 (t-90) cc_final: 0.8110 (t70) outliers start: 86 outliers final: 64 residues processed: 538 average time/residue: 0.1705 time to fit residues: 147.9848 Evaluate side-chains 497 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 429 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1053 ILE 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 155 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1053 ILE 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 155 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 661 SER 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 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 1097 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 0.4980 chunk 127 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 42 optimal weight: 0.0770 chunk 179 optimal weight: 3.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119080 restraints weight = 31237.725| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.89 r_work: 0.2899 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26016 Z= 0.125 Angle : 0.604 10.244 35416 Z= 0.300 Chirality : 0.042 0.251 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.742 59.762 4316 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.44 % Favored : 96.43 % Rotamer: Outliers : 3.44 % Allowed : 15.16 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3136 helix: 0.28 (0.11), residues: 2156 sheet: None (None), residues: 0 loop : -1.64 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 617 TYR 0.013 0.001 TYR D 776 PHE 0.021 0.001 PHE B 858 TRP 0.009 0.001 TRP B 758 HIS 0.003 0.001 HIS D 644 Details of bonding type rmsd covalent geometry : bond 0.00293 (26016) covalent geometry : angle 0.60410 (35416) hydrogen bonds : bond 0.03186 ( 1266) hydrogen bonds : angle 4.14137 ( 3774) *********************** 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 537 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 451 time to evaluate : 1.013 Fit side-chains REVERT: A 616 LYS cc_start: 0.8584 (pttp) cc_final: 0.7572 (mttt) REVERT: A 626 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8773 (tp) REVERT: A 662 MET cc_start: 0.9041 (mtm) cc_final: 0.8598 (mtp) REVERT: A 664 TYR cc_start: 0.8770 (t80) cc_final: 0.8451 (t80) REVERT: A 782 MET cc_start: 0.8834 (mmm) cc_final: 0.8585 (mmm) REVERT: A 869 LEU cc_start: 0.8957 (mt) cc_final: 0.8723 (mt) REVERT: A 1065 ILE cc_start: 0.8325 (mm) cc_final: 0.8077 (mt) REVERT: A 1085 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: A 1159 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8179 (tttm) REVERT: A 1166 ASP cc_start: 0.8445 (m-30) cc_final: 0.7813 (m-30) REVERT: A 1168 LYS cc_start: 0.8503 (mttm) cc_final: 0.8212 (mtmt) REVERT: A 1171 HIS cc_start: 0.8479 (t-90) cc_final: 0.8070 (t70) REVERT: B 616 LYS cc_start: 0.8575 (pttp) cc_final: 0.7568 (mttt) REVERT: B 626 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8774 (tp) REVERT: B 662 MET cc_start: 0.9029 (mtm) cc_final: 0.8564 (mtp) REVERT: B 664 TYR cc_start: 0.8754 (t80) cc_final: 0.8433 (t80) REVERT: B 748 MET cc_start: 0.8698 (mtt) cc_final: 0.8440 (mtm) REVERT: B 779 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7810 (tttt) REVERT: B 869 LEU cc_start: 0.8958 (mt) cc_final: 0.8722 (mt) REVERT: B 1065 ILE cc_start: 0.8322 (mm) cc_final: 0.8074 (mt) REVERT: B 1085 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: B 1166 ASP cc_start: 0.8446 (m-30) cc_final: 0.7815 (m-30) REVERT: B 1168 LYS cc_start: 0.8496 (mttm) cc_final: 0.8202 (mtmt) REVERT: B 1171 HIS cc_start: 0.8489 (t-90) cc_final: 0.8079 (t70) REVERT: C 616 LYS cc_start: 0.8584 (pttp) cc_final: 0.7568 (mttt) REVERT: C 626 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 662 MET cc_start: 0.9042 (mtm) cc_final: 0.8601 (mtp) REVERT: C 664 TYR cc_start: 0.8763 (t80) cc_final: 0.8443 (t80) REVERT: C 748 MET cc_start: 0.8689 (mtt) cc_final: 0.8427 (mtm) REVERT: C 779 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7807 (tttt) REVERT: C 782 MET cc_start: 0.8846 (mmm) cc_final: 0.8613 (mmm) REVERT: C 869 LEU cc_start: 0.8950 (mt) cc_final: 0.8715 (mt) REVERT: C 1065 ILE cc_start: 0.8335 (mm) cc_final: 0.8088 (mt) REVERT: C 1085 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: C 1166 ASP cc_start: 0.8440 (m-30) cc_final: 0.7809 (m-30) REVERT: C 1168 LYS cc_start: 0.8505 (mttm) cc_final: 0.8211 (mtmt) REVERT: C 1171 HIS cc_start: 0.8490 (t-90) cc_final: 0.8081 (t70) REVERT: D 616 LYS cc_start: 0.8580 (pttp) cc_final: 0.7569 (mttt) REVERT: D 626 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8761 (tp) REVERT: D 662 MET cc_start: 0.9044 (mtm) cc_final: 0.8597 (mtp) REVERT: D 664 TYR cc_start: 0.8772 (t80) cc_final: 0.8451 (t80) REVERT: D 748 MET cc_start: 0.8670 (mtt) cc_final: 0.8406 (mtm) REVERT: D 779 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7805 (tttt) REVERT: D 869 LEU cc_start: 0.8959 (mt) cc_final: 0.8725 (mt) REVERT: D 1065 ILE cc_start: 0.8325 (mm) cc_final: 0.8079 (mt) REVERT: D 1085 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: D 1159 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8171 (tttm) REVERT: D 1166 ASP cc_start: 0.8433 (m-30) cc_final: 0.7767 (m-30) REVERT: D 1171 HIS cc_start: 0.8481 (t-90) cc_final: 0.8032 (t70) outliers start: 86 outliers final: 54 residues processed: 513 average time/residue: 0.1668 time to fit residues: 138.1636 Evaluate side-chains 500 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 438 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 774 LEU 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 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 412 ILE Chi-restraints excluded: chain B residue 421 ASP 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 737 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 421 ASP 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 774 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 421 ASP 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 756 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 215 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 271 optimal weight: 0.6980 chunk 304 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.116005 restraints weight = 31514.493| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.15 r_work: 0.2896 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3629 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= 0.119 Angle : 0.601 10.370 35416 Z= 0.296 Chirality : 0.042 0.228 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.531 59.430 4316 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 3.16 % Allowed : 15.48 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3136 helix: 0.57 (0.12), residues: 2152 sheet: None (None), residues: 0 loop : -1.60 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 274 TYR 0.014 0.001 TYR D 776 PHE 0.021 0.001 PHE C 858 TRP 0.009 0.001 TRP A 747 HIS 0.004 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00282 (26016) covalent geometry : angle 0.60094 (35416) hydrogen bonds : bond 0.03090 ( 1266) hydrogen bonds : angle 4.01188 ( 3774) *********************** 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 537 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 458 time to evaluate : 0.819 Fit side-chains REVERT: A 160 LEU cc_start: 0.8299 (pp) cc_final: 0.8068 (tt) REVERT: A 616 LYS cc_start: 0.8541 (pttp) cc_final: 0.7532 (mttt) REVERT: A 626 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8722 (tp) REVERT: A 662 MET cc_start: 0.9026 (mtm) cc_final: 0.8537 (mtp) REVERT: A 664 TYR cc_start: 0.8697 (t80) cc_final: 0.8344 (t80) REVERT: A 779 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7696 (tttt) REVERT: A 782 MET cc_start: 0.8796 (mmm) cc_final: 0.8567 (mmm) REVERT: A 922 ASP cc_start: 0.8128 (t0) cc_final: 0.7926 (t0) REVERT: A 1085 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: A 1159 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8054 (tttm) REVERT: A 1166 ASP cc_start: 0.8458 (m-30) cc_final: 0.7836 (m-30) REVERT: A 1168 LYS cc_start: 0.8455 (mttm) cc_final: 0.8186 (mtmt) REVERT: A 1171 HIS cc_start: 0.8470 (t-90) cc_final: 0.8063 (t70) REVERT: B 160 LEU cc_start: 0.8219 (pp) cc_final: 0.7977 (tt) REVERT: B 616 LYS cc_start: 0.8515 (pttp) cc_final: 0.7471 (mttt) REVERT: B 626 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8724 (tp) REVERT: B 662 MET cc_start: 0.9009 (mtm) cc_final: 0.8516 (mtp) REVERT: B 664 TYR cc_start: 0.8691 (t80) cc_final: 0.8339 (t80) REVERT: B 707 LYS cc_start: 0.9005 (mttt) cc_final: 0.8638 (mttp) REVERT: B 748 MET cc_start: 0.8661 (mtt) cc_final: 0.8383 (mtm) REVERT: B 779 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7848 (tttt) REVERT: B 1085 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: B 1166 ASP cc_start: 0.8454 (m-30) cc_final: 0.7807 (m-30) REVERT: B 1168 LYS cc_start: 0.8440 (mttm) cc_final: 0.8161 (mtmt) REVERT: B 1171 HIS cc_start: 0.8467 (t-90) cc_final: 0.8058 (t70) REVERT: C 160 LEU cc_start: 0.8229 (pp) cc_final: 0.7983 (tt) REVERT: C 616 LYS cc_start: 0.8518 (pttp) cc_final: 0.7466 (mttt) REVERT: C 626 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8726 (tp) REVERT: C 662 MET cc_start: 0.9014 (mtm) cc_final: 0.8530 (mtp) REVERT: C 664 TYR cc_start: 0.8698 (t80) cc_final: 0.8344 (t80) REVERT: C 707 LYS cc_start: 0.8986 (mttt) cc_final: 0.8625 (mttp) REVERT: C 748 MET cc_start: 0.8649 (mtt) cc_final: 0.8368 (mtm) REVERT: C 779 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7698 (tttt) REVERT: C 782 MET cc_start: 0.8817 (mmm) cc_final: 0.8588 (mmm) REVERT: C 922 ASP cc_start: 0.8102 (t0) cc_final: 0.7900 (t0) REVERT: C 1053 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7918 (mt) REVERT: C 1085 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: C 1166 ASP cc_start: 0.8442 (m-30) cc_final: 0.7792 (m-30) REVERT: C 1168 LYS cc_start: 0.8443 (mttm) cc_final: 0.8164 (mtmt) REVERT: C 1171 HIS cc_start: 0.8481 (t-90) cc_final: 0.8073 (t70) REVERT: D 160 LEU cc_start: 0.8255 (pp) cc_final: 0.8008 (tt) REVERT: D 616 LYS cc_start: 0.8524 (pttp) cc_final: 0.7474 (mttt) REVERT: D 626 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8706 (tp) REVERT: D 662 MET cc_start: 0.9020 (mtm) cc_final: 0.8532 (mtp) REVERT: D 664 TYR cc_start: 0.8703 (t80) cc_final: 0.8351 (t80) REVERT: D 704 MET cc_start: 0.9009 (mmm) cc_final: 0.8638 (mmt) REVERT: D 748 MET cc_start: 0.8634 (mtt) cc_final: 0.8355 (mtm) REVERT: D 779 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7851 (tttt) REVERT: D 1053 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7927 (mt) REVERT: D 1085 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: D 1159 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8057 (tttm) REVERT: D 1166 ASP cc_start: 0.8426 (m-30) cc_final: 0.7783 (m-30) REVERT: D 1171 HIS cc_start: 0.8467 (t-90) cc_final: 0.8023 (t70) outliers start: 79 outliers final: 60 residues processed: 515 average time/residue: 0.1632 time to fit residues: 135.5754 Evaluate side-chains 506 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 436 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 737 THR 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 1055 VAL Chi-restraints excluded: chain A residue 1056 CYS 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 412 ILE Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 756 ASN 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 901 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1056 CYS 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 412 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 737 THR 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 982 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1056 CYS 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 412 ILE Chi-restraints excluded: chain D residue 421 ASP 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 737 THR Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU 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 1053 ILE Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1056 CYS 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 55 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 295 optimal weight: 8.9990 chunk 302 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.149666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117152 restraints weight = 31439.241| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.94 r_work: 0.2919 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26016 Z= 0.131 Angle : 0.599 10.209 35416 Z= 0.296 Chirality : 0.042 0.229 4180 Planarity : 0.004 0.046 4312 Dihedral : 7.396 59.835 4312 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.88 % Allowed : 16.36 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3136 helix: 0.67 (0.12), residues: 2156 sheet: None (None), residues: 0 loop : -1.62 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 274 TYR 0.014 0.001 TYR A 776 PHE 0.020 0.001 PHE C 858 TRP 0.009 0.001 TRP A 747 HIS 0.004 0.001 HIS B 850 Details of bonding type rmsd covalent geometry : bond 0.00317 (26016) covalent geometry : angle 0.59908 (35416) hydrogen bonds : bond 0.03033 ( 1266) hydrogen bonds : angle 3.94444 ( 3774) *********************** 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 535 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 463 time to evaluate : 1.014 Fit side-chains REVERT: A 160 LEU cc_start: 0.8410 (pp) cc_final: 0.8187 (tt) REVERT: A 616 LYS cc_start: 0.8592 (pttp) cc_final: 0.7581 (mttt) REVERT: A 626 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8791 (tp) REVERT: A 662 MET cc_start: 0.9051 (mtm) cc_final: 0.8619 (mtp) REVERT: A 664 TYR cc_start: 0.8730 (t80) cc_final: 0.8365 (t80) REVERT: A 779 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7800 (tttt) REVERT: A 782 MET cc_start: 0.8830 (mmm) cc_final: 0.8576 (mmm) REVERT: A 992 MET cc_start: 0.8585 (mtt) cc_final: 0.8330 (mtt) REVERT: A 1053 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 1085 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: A 1159 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8182 (tttm) REVERT: A 1166 ASP cc_start: 0.8475 (m-30) cc_final: 0.7821 (m-30) REVERT: A 1168 LYS cc_start: 0.8549 (mttm) cc_final: 0.8286 (mtmt) REVERT: A 1171 HIS cc_start: 0.8485 (t-90) cc_final: 0.8102 (t70) REVERT: B 160 LEU cc_start: 0.8381 (pp) cc_final: 0.8134 (tt) REVERT: B 616 LYS cc_start: 0.8565 (pttp) cc_final: 0.7624 (mttt) REVERT: B 626 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8801 (tp) REVERT: B 662 MET cc_start: 0.9037 (mtm) cc_final: 0.8598 (mtp) REVERT: B 664 TYR cc_start: 0.8726 (t80) cc_final: 0.8359 (t80) REVERT: B 748 MET cc_start: 0.8706 (mtt) cc_final: 0.8451 (mtm) REVERT: B 779 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7794 (tttt) REVERT: B 992 MET cc_start: 0.8559 (mtt) cc_final: 0.8295 (mtt) REVERT: B 1053 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8042 (mt) REVERT: B 1085 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: B 1166 ASP cc_start: 0.8478 (m-30) cc_final: 0.7815 (m-30) REVERT: B 1171 HIS cc_start: 0.8498 (t-90) cc_final: 0.8111 (t70) REVERT: C 160 LEU cc_start: 0.8394 (pp) cc_final: 0.8144 (tt) REVERT: C 616 LYS cc_start: 0.8564 (pttp) cc_final: 0.7617 (mttt) REVERT: C 626 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8808 (tp) REVERT: C 662 MET cc_start: 0.9039 (mtm) cc_final: 0.8614 (mtp) REVERT: C 664 TYR cc_start: 0.8740 (t80) cc_final: 0.8374 (t80) REVERT: C 748 MET cc_start: 0.8702 (mtt) cc_final: 0.8457 (mtm) REVERT: C 779 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7796 (tttt) REVERT: C 922 ASP cc_start: 0.8198 (t0) cc_final: 0.7994 (t0) REVERT: C 992 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8306 (mtt) REVERT: C 1053 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8044 (mt) REVERT: C 1085 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: C 1166 ASP cc_start: 0.8461 (m-30) cc_final: 0.7798 (m-30) REVERT: C 1168 LYS cc_start: 0.8536 (mttm) cc_final: 0.8269 (mtmt) REVERT: C 1171 HIS cc_start: 0.8504 (t-90) cc_final: 0.8116 (t70) REVERT: D 160 LEU cc_start: 0.8413 (pp) cc_final: 0.8162 (tt) REVERT: D 626 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8791 (tp) REVERT: D 662 MET cc_start: 0.9050 (mtm) cc_final: 0.8617 (mtp) REVERT: D 664 TYR cc_start: 0.8745 (t80) cc_final: 0.8380 (t80) REVERT: D 704 MET cc_start: 0.9022 (mmm) cc_final: 0.8688 (mmt) REVERT: D 748 MET cc_start: 0.8692 (mtt) cc_final: 0.8444 (mtm) REVERT: D 779 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7796 (tttt) REVERT: D 1053 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8044 (mt) REVERT: D 1085 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7455 (m-80) REVERT: D 1159 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8152 (tttm) REVERT: D 1166 ASP cc_start: 0.8450 (m-30) cc_final: 0.7774 (m-30) REVERT: D 1171 HIS cc_start: 0.8493 (t-90) cc_final: 0.8070 (t70) outliers start: 72 outliers final: 52 residues processed: 517 average time/residue: 0.1645 time to fit residues: 137.9300 Evaluate side-chains 510 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 445 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 737 THR 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 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 412 ILE Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 458 LEU 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 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 412 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 737 THR 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 982 VAL Chi-restraints excluded: chain C residue 992 MET 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 412 ILE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 458 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 303 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 278 optimal weight: 0.0270 chunk 40 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 113 optimal weight: 0.0370 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116719 restraints weight = 31597.532| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.98 r_work: 0.2936 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26016 Z= 0.115 Angle : 0.586 9.494 35416 Z= 0.290 Chirality : 0.041 0.238 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.139 59.448 4310 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.88 % Allowed : 15.92 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3136 helix: 0.86 (0.12), residues: 2156 sheet: None (None), residues: 0 loop : -1.50 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 274 TYR 0.013 0.001 TYR B 776 PHE 0.020 0.001 PHE C 858 TRP 0.009 0.001 TRP A 747 HIS 0.004 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00274 (26016) covalent geometry : angle 0.58636 (35416) hydrogen bonds : bond 0.02893 ( 1266) hydrogen bonds : angle 3.82130 ( 3774) *********************** 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 544 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 472 time to evaluate : 1.018 Fit side-chains REVERT: A 626 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8807 (tp) REVERT: A 662 MET cc_start: 0.9055 (mtm) cc_final: 0.8600 (mtp) REVERT: A 664 TYR cc_start: 0.8716 (t80) cc_final: 0.8329 (t80) REVERT: A 779 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7791 (tttt) REVERT: A 992 MET cc_start: 0.8537 (mtt) cc_final: 0.8291 (mtt) REVERT: A 1051 TYR cc_start: 0.8609 (m-80) cc_final: 0.8367 (m-80) REVERT: A 1053 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7947 (mt) REVERT: A 1085 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: A 1159 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8178 (tttm) REVERT: A 1166 ASP cc_start: 0.8407 (m-30) cc_final: 0.7743 (m-30) REVERT: A 1171 HIS cc_start: 0.8496 (t-90) cc_final: 0.8114 (t70) REVERT: B 160 LEU cc_start: 0.8454 (pp) cc_final: 0.8241 (tt) REVERT: B 616 LYS cc_start: 0.8571 (pttp) cc_final: 0.7559 (mttt) REVERT: B 626 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8822 (tp) REVERT: B 662 MET cc_start: 0.9042 (mtm) cc_final: 0.8584 (mtp) REVERT: B 664 TYR cc_start: 0.8717 (t80) cc_final: 0.8333 (t80) REVERT: B 748 MET cc_start: 0.8724 (mtt) cc_final: 0.8454 (mtm) REVERT: B 779 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7774 (tttt) REVERT: B 992 MET cc_start: 0.8504 (mtt) cc_final: 0.8285 (mtt) REVERT: B 1051 TYR cc_start: 0.8609 (m-80) cc_final: 0.8372 (m-80) REVERT: B 1053 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7938 (mt) REVERT: B 1085 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: B 1166 ASP cc_start: 0.8425 (m-30) cc_final: 0.7774 (m-30) REVERT: B 1171 HIS cc_start: 0.8504 (t-90) cc_final: 0.8138 (t70) REVERT: C 160 LEU cc_start: 0.8460 (pp) cc_final: 0.8247 (tt) REVERT: C 626 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8810 (tp) REVERT: C 662 MET cc_start: 0.9043 (mtm) cc_final: 0.8591 (mtp) REVERT: C 664 TYR cc_start: 0.8731 (t80) cc_final: 0.8343 (t80) REVERT: C 748 MET cc_start: 0.8694 (mtt) cc_final: 0.8493 (mtm) REVERT: C 779 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7649 (tttt) REVERT: C 922 ASP cc_start: 0.8178 (t0) cc_final: 0.7950 (t0) REVERT: C 992 MET cc_start: 0.8505 (mtt) cc_final: 0.8251 (mtt) REVERT: C 1085 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: C 1166 ASP cc_start: 0.8401 (m-30) cc_final: 0.7733 (m-30) REVERT: C 1171 HIS cc_start: 0.8522 (t-90) cc_final: 0.8139 (t70) REVERT: D 160 LEU cc_start: 0.8469 (pp) cc_final: 0.8255 (tt) REVERT: D 626 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8801 (tp) REVERT: D 662 MET cc_start: 0.9060 (mtm) cc_final: 0.8599 (mtp) REVERT: D 664 TYR cc_start: 0.8733 (t80) cc_final: 0.8349 (t80) REVERT: D 748 MET cc_start: 0.8683 (mtt) cc_final: 0.8451 (mtm) REVERT: D 779 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7773 (tttt) REVERT: D 1085 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: D 1159 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8170 (tttm) REVERT: D 1166 ASP cc_start: 0.8446 (m-30) cc_final: 0.7772 (m-30) REVERT: D 1171 HIS cc_start: 0.8492 (t-90) cc_final: 0.8079 (t70) outliers start: 72 outliers final: 51 residues processed: 528 average time/residue: 0.1627 time to fit residues: 139.5789 Evaluate side-chains 505 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 444 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 737 THR 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 1053 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1056 CYS 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 412 ILE 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 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 1056 CYS 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 412 ILE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 737 THR 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 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1056 CYS 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 412 ILE 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 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 1056 CYS 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 156 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 73 optimal weight: 0.0040 chunk 96 optimal weight: 4.9990 chunk 186 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 chunk 323 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 252 optimal weight: 0.4980 chunk 290 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 681 GLN B 154 GLN B 681 GLN B 756 ASN C 154 GLN C 681 GLN D 154 GLN D 681 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.156476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123762 restraints weight = 30908.942| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.62 r_work: 0.3138 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26016 Z= 0.111 Angle : 0.590 9.660 35416 Z= 0.289 Chirality : 0.041 0.246 4180 Planarity : 0.004 0.047 4312 Dihedral : 6.995 59.904 4308 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.44 % Allowed : 17.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3136 helix: 1.01 (0.12), residues: 2156 sheet: None (None), residues: 0 loop : -1.43 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 274 TYR 0.012 0.001 TYR D 965 PHE 0.020 0.001 PHE B 858 TRP 0.014 0.001 TRP C1030 HIS 0.003 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00261 (26016) covalent geometry : angle 0.58986 (35416) hydrogen bonds : bond 0.02862 ( 1266) hydrogen bonds : angle 3.75057 ( 3774) ********************** 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 554 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 493 time to evaluate : 1.654 Fit side-chains REVERT: A 154 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7961 (pp30) REVERT: A 626 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 662 MET cc_start: 0.8993 (mtm) cc_final: 0.8520 (mtp) REVERT: A 664 TYR cc_start: 0.8646 (t80) cc_final: 0.8245 (t80) REVERT: A 779 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7756 (tttt) REVERT: A 992 MET cc_start: 0.8452 (mtt) cc_final: 0.8243 (mtt) REVERT: A 1051 TYR cc_start: 0.8539 (m-80) cc_final: 0.8291 (m-80) REVERT: A 1053 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 1085 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: A 1159 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8139 (tttm) REVERT: A 1166 ASP cc_start: 0.8395 (m-30) cc_final: 0.7736 (m-30) REVERT: A 1171 HIS cc_start: 0.8482 (t-90) cc_final: 0.8151 (t70) REVERT: B 154 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7947 (pp30) REVERT: B 274 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.7754 (mmp80) REVERT: B 626 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8780 (tp) REVERT: B 662 MET cc_start: 0.8980 (mtm) cc_final: 0.8507 (mtp) REVERT: B 664 TYR cc_start: 0.8649 (t80) cc_final: 0.8247 (t80) REVERT: B 748 MET cc_start: 0.8611 (mtt) cc_final: 0.8369 (mtm) REVERT: B 779 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7721 (tttt) REVERT: B 992 MET cc_start: 0.8430 (mtt) cc_final: 0.8219 (mtt) REVERT: B 1051 TYR cc_start: 0.8543 (m-80) cc_final: 0.8298 (m-80) REVERT: B 1053 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7884 (mt) REVERT: B 1085 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: B 1166 ASP cc_start: 0.8404 (m-30) cc_final: 0.7722 (m-30) REVERT: B 1171 HIS cc_start: 0.8505 (t-90) cc_final: 0.8168 (t70) REVERT: C 154 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7950 (pp30) REVERT: C 160 LEU cc_start: 0.8534 (pp) cc_final: 0.8333 (tt) REVERT: C 626 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8784 (tp) REVERT: C 662 MET cc_start: 0.8989 (mtm) cc_final: 0.8514 (mtp) REVERT: C 664 TYR cc_start: 0.8665 (t80) cc_final: 0.8261 (t80) REVERT: C 748 MET cc_start: 0.8593 (mtt) cc_final: 0.8385 (mtm) REVERT: C 779 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7630 (tttt) REVERT: C 992 MET cc_start: 0.8429 (mtt) cc_final: 0.8164 (mtt) REVERT: C 1051 TYR cc_start: 0.8533 (m-80) cc_final: 0.8308 (m-80) REVERT: C 1085 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: C 1166 ASP cc_start: 0.8404 (m-30) cc_final: 0.7739 (m-30) REVERT: C 1171 HIS cc_start: 0.8511 (t-90) cc_final: 0.8179 (t70) REVERT: D 154 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7949 (pp30) REVERT: D 274 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.7755 (mmp80) REVERT: D 626 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8758 (tp) REVERT: D 662 MET cc_start: 0.8992 (mtm) cc_final: 0.8515 (mtp) REVERT: D 664 TYR cc_start: 0.8652 (t80) cc_final: 0.8254 (t80) REVERT: D 748 MET cc_start: 0.8576 (mtt) cc_final: 0.8349 (mtm) REVERT: D 779 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7738 (tttt) REVERT: D 1085 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: D 1159 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8180 (tttm) REVERT: D 1166 ASP cc_start: 0.8374 (m-30) cc_final: 0.7672 (m-30) REVERT: D 1171 HIS cc_start: 0.8415 (t-90) cc_final: 0.8010 (t70) REVERT: D 1194 GLU cc_start: 0.7633 (mp0) cc_final: 0.7432 (mp0) outliers start: 61 outliers final: 47 residues processed: 534 average time/residue: 0.1661 time to fit residues: 143.3046 Evaluate side-chains 534 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 473 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1056 CYS 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 154 GLN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 858 PHE 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 1056 CYS 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 154 GLN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1056 CYS 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 154 GLN Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 858 PHE 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 1056 CYS 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 91 optimal weight: 0.4980 chunk 154 optimal weight: 8.9990 chunk 219 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 304 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 317 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 chunk 35 optimal weight: 0.0770 chunk 312 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 681 GLN B 154 GLN B 681 GLN C 154 GLN C 681 GLN D 154 GLN D 681 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117834 restraints weight = 31421.964| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.02 r_work: 0.2973 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4045 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= 0.116 Angle : 0.593 9.454 35416 Z= 0.290 Chirality : 0.041 0.192 4180 Planarity : 0.004 0.046 4312 Dihedral : 7.035 59.641 4308 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.60 % Allowed : 17.56 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3136 helix: 1.05 (0.12), residues: 2156 sheet: None (None), residues: 0 loop : -1.39 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 274 TYR 0.013 0.001 TYR A 965 PHE 0.020 0.001 PHE B 858 TRP 0.023 0.001 TRP A1030 HIS 0.004 0.001 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00276 (26016) covalent geometry : angle 0.59292 (35416) hydrogen bonds : bond 0.02857 ( 1266) hydrogen bonds : angle 3.73772 ( 3774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7226.19 seconds wall clock time: 124 minutes 1.84 seconds (7441.84 seconds total)