Starting phenix.real_space_refine on Sun Sep 13 20:26:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5zx5_6975/09_2026/5zx5_6975.cif Found real_map, /net/cci-nas-00/data/ceres_data/5zx5_6975/09_2026/5zx5_6975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5zx5_6975/09_2026/5zx5_6975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5zx5_6975/09_2026/5zx5_6975.map" model { file = "/net/cci-nas-00/data/ceres_data/5zx5_6975/09_2026/5zx5_6975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5zx5_6975/09_2026/5zx5_6975.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5zx5_6975/09_2026/5zx5_6975.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5zx5_6975/09_2026/5zx5_6975.cif" } 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-2.2.1-6174/lib/python3.11/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: 5.75, per 1000 atoms: 0.23 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: 2.13 Conformation dependent library (CDL) restraints added in 1.0 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: 0.79 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: 4.31 Time building geometry restraints manager: 2.88 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 - 21.47: 14693 21.47 - 42.94: 442 42.94 - 64.41: 73 64.41 - 85.88: 4 85.88 - 107.35: 4 Dihedral angle restraints: 15216 sinusoidal: 5648 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 15213 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.720 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 11.530 107.351 8976 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/Z covalent geometry : bond 0.01560 / 0.67 (26016) covalent geometry : angle 1.40523 / 0.75 (35416) hydrogen bonds : bond 0.18120 / 12.34 ( 1266) hydrogen bonds : angle 9.72062 / 6.77 ( 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 : 0.639 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: 0.8061 (mmmt) REVERT: B 662 MET cc_start: 0.8707 (mtm) cc_final: 0.8288 (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: 0.8141 (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: 0.8057 (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: 0.1851 time to fit residues: 205.8519 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 : 0.929 ------------------------------------------------------------------------------- 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... A 276 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 432 GLN A 491 HIS A 700 GLN A 718 ASN A 787 GLN A 789 GLN A 885 GLN A1090 ASN A1123 HIS A1137 HIS A1210 GLN B 276 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 432 GLN B 491 HIS B 700 GLN B 718 ASN B 756 ASN B 787 GLN B 789 GLN B 885 GLN B1090 ASN B1123 HIS B1137 HIS B1210 GLN C 276 HIS ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS C 432 GLN C 491 HIS C 700 GLN C 718 ASN C 789 GLN C 885 GLN 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: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.148822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115199 restraints weight = 31437.145| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.89 r_work: 0.2949 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26016 Z= 0.156 Angle : 0.722 10.491 35416 Z= 0.364 Chirality : 0.044 0.255 4180 Planarity : 0.005 0.052 4312 Dihedral : 8.797 102.836 3631 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 3.48 % Allowed : 9.48 % Favored : 87.04 % 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: -2.94 (0.13), residues: 3136 helix: -1.74 (0.10), residues: 2128 sheet: None (None), residues: 0 loop : -2.05 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 525 TYR 0.017 0.001 TYR A 870 PHE 0.027 0.001 PHE C 858 TRP 0.014 0.001 TRP B1111 HIS 0.007 0.001 HIS A1137 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (26016) covalent geometry : angle 0.72170 / 0.36 (35416) hydrogen bonds : bond 0.04241 / 2.92 ( 1266) hydrogen bonds : angle 5.30316 / 3.69 ( 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 615 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 528 time to evaluate : 0.954 Fit side-chains REVERT: A 662 MET cc_start: 0.8954 (mtm) cc_final: 0.8265 (mtp) REVERT: A 664 TYR cc_start: 0.8778 (t80) cc_final: 0.8483 (t80) REVERT: A 703 THR cc_start: 0.8878 (p) cc_final: 0.8524 (t) REVERT: A 748 MET cc_start: 0.8792 (mtt) cc_final: 0.8562 (mtm) REVERT: A 984 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8191 (mp10) REVERT: A 1085 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: A 1088 MET cc_start: 0.9331 (mmm) cc_final: 0.8976 (mmm) REVERT: A 1089 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.8980 (t) REVERT: A 1159 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8176 (tttm) REVERT: A 1166 ASP cc_start: 0.8523 (m-30) cc_final: 0.7820 (m-30) REVERT: A 1168 LYS cc_start: 0.8460 (mttm) cc_final: 0.8147 (mtmt) REVERT: A 1171 HIS cc_start: 0.8660 (t-90) cc_final: 0.8220 (t70) REVERT: B 662 MET cc_start: 0.8938 (mtm) cc_final: 0.8241 (mtp) REVERT: B 664 TYR cc_start: 0.8783 (t80) cc_final: 0.8488 (t80) REVERT: B 703 THR cc_start: 0.8887 (p) cc_final: 0.8438 (t) REVERT: B 707 LYS cc_start: 0.9117 (mttt) cc_final: 0.8857 (mttp) REVERT: B 748 MET cc_start: 0.8800 (mtt) cc_final: 0.8564 (mtm) REVERT: B 1085 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: B 1088 MET cc_start: 0.9324 (mmm) cc_final: 0.8970 (mmm) REVERT: B 1089 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.8976 (t) REVERT: B 1166 ASP cc_start: 0.8513 (m-30) cc_final: 0.7770 (m-30) REVERT: B 1168 LYS cc_start: 0.8467 (mttm) cc_final: 0.8152 (mtmt) REVERT: B 1171 HIS cc_start: 0.8657 (t-90) cc_final: 0.8226 (t70) REVERT: C 662 MET cc_start: 0.8944 (mtm) cc_final: 0.8248 (mtp) REVERT: C 664 TYR cc_start: 0.8774 (t80) cc_final: 0.8479 (t80) REVERT: C 703 THR cc_start: 0.8877 (p) cc_final: 0.8430 (t) REVERT: C 707 LYS cc_start: 0.9106 (mttt) cc_final: 0.8851 (mttp) REVERT: C 748 MET cc_start: 0.8788 (mtt) cc_final: 0.8555 (mtm) REVERT: C 984 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8204 (mp10) REVERT: C 1085 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: C 1088 MET cc_start: 0.9325 (mmm) cc_final: 0.8965 (mmm) REVERT: C 1089 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.8976 (t) REVERT: C 1166 ASP cc_start: 0.8513 (m-30) cc_final: 0.7776 (m-30) REVERT: C 1168 LYS cc_start: 0.8480 (mttm) cc_final: 0.8163 (mtmt) REVERT: C 1171 HIS cc_start: 0.8649 (t-90) cc_final: 0.8214 (t70) REVERT: D 662 MET cc_start: 0.8965 (mtm) cc_final: 0.8275 (mtp) REVERT: D 664 TYR cc_start: 0.8794 (t80) cc_final: 0.8499 (t80) REVERT: D 703 THR cc_start: 0.8859 (p) cc_final: 0.8495 (t) REVERT: D 748 MET cc_start: 0.8784 (mtt) cc_final: 0.8548 (mtm) REVERT: D 1085 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: D 1088 MET cc_start: 0.9338 (mmm) cc_final: 0.8992 (mmm) REVERT: D 1089 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.8979 (t) REVERT: D 1159 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8170 (tttm) REVERT: D 1166 ASP cc_start: 0.8496 (m-30) cc_final: 0.7783 (m-30) REVERT: D 1168 LYS cc_start: 0.8456 (mttm) cc_final: 0.8138 (mtmt) REVERT: D 1171 HIS cc_start: 0.8642 (t-90) cc_final: 0.8199 (t70) outliers start: 87 outliers final: 37 residues processed: 599 average time/residue: 0.1677 time to fit residues: 162.7108 Evaluate side-chains 484 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 439 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 515 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1085 TYR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 710 THR Chi-restraints excluded: chain D residue 756 ASN Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1085 TYR Chi-restraints excluded: chain D residue 1089 VAL Chi-restraints excluded: chain D residue 1097 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN A 366 GLN A 956 HIS B 295 ASN B 366 GLN B 956 HIS C 295 ASN C 366 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3580 r_free = 0.3580 target = 0.143412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111267 restraints weight = 32030.268| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.11 r_work: 0.2826 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 26016 Z= 0.283 Angle : 0.755 10.753 35416 Z= 0.380 Chirality : 0.048 0.263 4180 Planarity : 0.005 0.052 4312 Dihedral : 8.544 102.178 3621 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 3.44 % Allowed : 12.20 % Favored : 84.36 % 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: -2.13 (0.14), residues: 3136 helix: -1.06 (0.10), residues: 2164 sheet: None (None), residues: 0 loop : -1.92 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 634 TYR 0.027 0.002 TYR B 870 PHE 0.019 0.002 PHE B 858 TRP 0.011 0.002 TRP A 857 HIS 0.006 0.001 HIS B 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.28 (26016) covalent geometry : angle 0.75545 / 0.38 (35416) hydrogen bonds : bond 0.04139 / 2.85 ( 1266) hydrogen bonds : angle 4.80706 / 3.35 ( 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 552 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 466 time to evaluate : 0.950 Fit side-chains REVERT: A 413 LEU cc_start: 0.8490 (mt) cc_final: 0.8126 (tp) REVERT: A 616 LYS cc_start: 0.8636 (pttp) cc_final: 0.7913 (mttt) REVERT: A 626 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8723 (tp) REVERT: A 662 MET cc_start: 0.9063 (mtm) cc_final: 0.8629 (mtp) REVERT: A 664 TYR cc_start: 0.8842 (t80) cc_final: 0.8343 (t80) REVERT: A 695 GLU cc_start: 0.8706 (tp30) cc_final: 0.8349 (tp30) REVERT: A 703 THR cc_start: 0.8953 (p) cc_final: 0.8666 (t) REVERT: A 706 MET cc_start: 0.9073 (mtp) cc_final: 0.8862 (mtt) REVERT: A 748 MET cc_start: 0.8793 (mtt) cc_final: 0.8553 (mtm) REVERT: A 984 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8368 (mp10) REVERT: A 993 ILE cc_start: 0.9006 (mt) cc_final: 0.8775 (mm) REVERT: A 1053 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8282 (mt) REVERT: A 1065 ILE cc_start: 0.8449 (mm) cc_final: 0.8201 (mt) REVERT: A 1159 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8215 (tttm) REVERT: A 1166 ASP cc_start: 0.8457 (m-30) cc_final: 0.7801 (m-30) REVERT: A 1168 LYS cc_start: 0.8602 (mttm) cc_final: 0.8349 (mtmt) REVERT: A 1171 HIS cc_start: 0.8683 (t-90) cc_final: 0.8241 (t70) REVERT: B 413 LEU cc_start: 0.8491 (mt) cc_final: 0.8122 (tp) REVERT: B 616 LYS cc_start: 0.8631 (pttp) cc_final: 0.7919 (mttt) REVERT: B 626 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8715 (tp) REVERT: B 662 MET cc_start: 0.9024 (mtm) cc_final: 0.8592 (mtp) REVERT: B 664 TYR cc_start: 0.8836 (t80) cc_final: 0.8337 (t80) REVERT: B 695 GLU cc_start: 0.8713 (tp30) cc_final: 0.8357 (tp30) REVERT: B 703 THR cc_start: 0.8955 (p) cc_final: 0.8667 (t) REVERT: B 706 MET cc_start: 0.9089 (mtp) cc_final: 0.8878 (mtt) REVERT: B 748 MET cc_start: 0.8795 (mtt) cc_final: 0.8546 (mtm) REVERT: B 993 ILE cc_start: 0.8994 (mt) cc_final: 0.8759 (mm) REVERT: B 1053 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8258 (mt) REVERT: B 1065 ILE cc_start: 0.8447 (mm) cc_final: 0.8198 (mt) REVERT: B 1166 ASP cc_start: 0.8453 (m-30) cc_final: 0.7792 (m-30) REVERT: B 1168 LYS cc_start: 0.8601 (mttm) cc_final: 0.8346 (mtmt) REVERT: B 1171 HIS cc_start: 0.8674 (t-90) cc_final: 0.8238 (t70) REVERT: C 413 LEU cc_start: 0.8480 (mt) cc_final: 0.8111 (tp) REVERT: C 616 LYS cc_start: 0.8635 (pttp) cc_final: 0.7922 (mttt) REVERT: C 626 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8721 (tp) REVERT: C 662 MET cc_start: 0.9033 (mtm) cc_final: 0.8602 (mtp) REVERT: C 664 TYR cc_start: 0.8835 (t80) cc_final: 0.8338 (t80) REVERT: C 695 GLU cc_start: 0.8707 (tp30) cc_final: 0.8352 (tp30) REVERT: C 703 THR cc_start: 0.8951 (p) cc_final: 0.8669 (t) REVERT: C 706 MET cc_start: 0.9077 (mtp) cc_final: 0.8867 (mtt) REVERT: C 748 MET cc_start: 0.8801 (mtt) cc_final: 0.8558 (mtm) REVERT: C 984 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8345 (mp10) REVERT: C 993 ILE cc_start: 0.8974 (mt) cc_final: 0.8736 (mm) REVERT: C 1053 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 1065 ILE cc_start: 0.8452 (mm) cc_final: 0.8206 (mt) REVERT: C 1085 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: C 1166 ASP cc_start: 0.8451 (m-30) cc_final: 0.7798 (m-30) REVERT: C 1168 LYS cc_start: 0.8604 (mttm) cc_final: 0.8348 (mtmt) REVERT: C 1171 HIS cc_start: 0.8679 (t-90) cc_final: 0.8235 (t70) REVERT: D 413 LEU cc_start: 0.8493 (mt) cc_final: 0.8127 (tp) REVERT: D 616 LYS cc_start: 0.8644 (pttp) cc_final: 0.7925 (mttt) REVERT: D 626 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8700 (tp) REVERT: D 662 MET cc_start: 0.9054 (mtm) cc_final: 0.8621 (mtp) REVERT: D 664 TYR cc_start: 0.8852 (t80) cc_final: 0.8353 (t80) REVERT: D 695 GLU cc_start: 0.8714 (tp30) cc_final: 0.8355 (tp30) REVERT: D 703 THR cc_start: 0.8928 (p) cc_final: 0.8605 (t) REVERT: D 748 MET cc_start: 0.8795 (mtt) cc_final: 0.8548 (mtm) REVERT: D 993 ILE cc_start: 0.9004 (mt) cc_final: 0.8762 (mm) REVERT: D 1053 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8268 (mt) REVERT: D 1065 ILE cc_start: 0.8429 (mm) cc_final: 0.8184 (mt) REVERT: D 1159 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8273 (tttm) REVERT: D 1166 ASP cc_start: 0.8432 (m-30) cc_final: 0.7759 (m-30) REVERT: D 1168 LYS cc_start: 0.8595 (mttm) cc_final: 0.8337 (mtmt) REVERT: D 1171 HIS cc_start: 0.8675 (t-90) cc_final: 0.8221 (t70) outliers start: 86 outliers final: 46 residues processed: 539 average time/residue: 0.1720 time to fit residues: 148.4654 Evaluate side-chains 480 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 425 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 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 161 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 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 161 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain C residue 1097 ASN Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 710 THR Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1055 VAL 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: 0.3980 chunk 317 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 316 optimal weight: 0.0370 chunk 297 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 302 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 756 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 ASN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.148108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116218 restraints weight = 31491.991| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.13 r_work: 0.2912 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26016 Z= 0.121 Angle : 0.625 10.075 35416 Z= 0.311 Chirality : 0.042 0.283 4180 Planarity : 0.004 0.044 4312 Dihedral : 8.250 102.401 3621 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.94 % Rotamer: Outliers : 2.76 % Allowed : 13.24 % Favored : 84.00 % 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: -1.28 (0.15), residues: 3136 helix: -0.35 (0.11), residues: 2164 sheet: None (None), residues: 0 loop : -1.78 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 274 TYR 0.017 0.001 TYR D 896 PHE 0.021 0.001 PHE A 858 TRP 0.009 0.001 TRP A1111 HIS 0.004 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (26016) covalent geometry : angle 0.62497 / 0.31 (35416) hydrogen bonds : bond 0.03377 / 2.33 ( 1266) hydrogen bonds : angle 4.39147 / 3.05 ( 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 557 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 488 time to evaluate : 0.949 Fit side-chains REVERT: A 413 LEU cc_start: 0.8410 (mt) cc_final: 0.8059 (tp) REVERT: A 616 LYS cc_start: 0.8580 (pttp) cc_final: 0.7859 (mttt) REVERT: A 626 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8755 (tp) REVERT: A 662 MET cc_start: 0.9026 (mtm) cc_final: 0.8521 (mtp) REVERT: A 664 TYR cc_start: 0.8799 (t80) cc_final: 0.8525 (t80) REVERT: A 707 LYS cc_start: 0.9203 (mttt) cc_final: 0.8940 (mttp) REVERT: A 748 MET cc_start: 0.8743 (mtt) cc_final: 0.8509 (mtm) REVERT: A 1085 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: A 1159 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8183 (tttm) REVERT: A 1166 ASP cc_start: 0.8484 (m-30) cc_final: 0.7853 (m-30) REVERT: A 1168 LYS cc_start: 0.8567 (mttm) cc_final: 0.8277 (mtmt) REVERT: A 1171 HIS cc_start: 0.8575 (t-90) cc_final: 0.8151 (t70) REVERT: A 1212 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8385 (ttmm) REVERT: B 413 LEU cc_start: 0.8409 (mt) cc_final: 0.8051 (tp) REVERT: B 616 LYS cc_start: 0.8594 (pttp) cc_final: 0.7869 (mttt) REVERT: B 626 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8744 (tp) REVERT: B 662 MET cc_start: 0.9001 (mtm) cc_final: 0.8489 (mtp) REVERT: B 664 TYR cc_start: 0.8799 (t80) cc_final: 0.8517 (t80) REVERT: B 707 LYS cc_start: 0.9217 (mttt) cc_final: 0.8952 (mttp) REVERT: B 748 MET cc_start: 0.8750 (mtt) cc_final: 0.8508 (mtm) REVERT: B 1085 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: B 1166 ASP cc_start: 0.8481 (m-30) cc_final: 0.7854 (m-30) REVERT: B 1168 LYS cc_start: 0.8563 (mttm) cc_final: 0.8272 (mtmt) REVERT: B 1171 HIS cc_start: 0.8564 (t-90) cc_final: 0.8140 (t70) REVERT: B 1212 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8419 (ttmm) REVERT: C 413 LEU cc_start: 0.8409 (mt) cc_final: 0.8051 (tp) REVERT: C 616 LYS cc_start: 0.8596 (pttp) cc_final: 0.7874 (mttt) REVERT: C 626 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8745 (tp) REVERT: C 662 MET cc_start: 0.9008 (mtm) cc_final: 0.8501 (mtp) REVERT: C 664 TYR cc_start: 0.8807 (t80) cc_final: 0.8535 (t80) REVERT: C 707 LYS cc_start: 0.9206 (mttt) cc_final: 0.8946 (mttp) REVERT: C 748 MET cc_start: 0.8739 (mtt) cc_final: 0.8500 (mtm) REVERT: C 984 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8288 (mp10) REVERT: C 1085 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: C 1166 ASP cc_start: 0.8474 (m-30) cc_final: 0.7843 (m-30) REVERT: C 1168 LYS cc_start: 0.8573 (mttm) cc_final: 0.8279 (mtmt) REVERT: C 1171 HIS cc_start: 0.8570 (t-90) cc_final: 0.8143 (t70) REVERT: C 1212 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8408 (ttmm) REVERT: D 413 LEU cc_start: 0.8419 (mt) cc_final: 0.8061 (tp) REVERT: D 616 LYS cc_start: 0.8597 (pttp) cc_final: 0.7872 (mttt) REVERT: D 626 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8744 (tp) REVERT: D 662 MET cc_start: 0.9033 (mtm) cc_final: 0.8526 (mtp) REVERT: D 664 TYR cc_start: 0.8821 (t80) cc_final: 0.8546 (t80) REVERT: D 748 MET cc_start: 0.8740 (mtt) cc_final: 0.8507 (mtm) REVERT: D 1085 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: D 1159 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8201 (tttm) REVERT: D 1166 ASP cc_start: 0.8468 (m-30) cc_final: 0.7859 (m-30) REVERT: D 1168 LYS cc_start: 0.8564 (mttm) cc_final: 0.8317 (mtmt) REVERT: D 1171 HIS cc_start: 0.8571 (t-90) cc_final: 0.8124 (t70) outliers start: 69 outliers final: 55 residues processed: 537 average time/residue: 0.1723 time to fit residues: 147.8437 Evaluate side-chains 507 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 444 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 421 ASP 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 1056 CYS 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 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 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 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 1056 CYS 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 710 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 27 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107045 restraints weight = 32021.575| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.04 r_work: 0.2798 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 26016 Z= 0.325 Angle : 0.758 10.354 35416 Z= 0.378 Chirality : 0.049 0.288 4180 Planarity : 0.005 0.047 4312 Dihedral : 8.413 100.160 3621 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.50 % Rotamer: Outliers : 3.60 % Allowed : 14.36 % Favored : 82.04 % 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: -1.33 (0.15), residues: 3136 helix: -0.41 (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 0.005 0.001 ARG B 634 TYR 0.026 0.002 TYR C 870 PHE 0.019 0.002 PHE D 858 TRP 0.010 0.002 TRP D 857 HIS 0.007 0.002 HIS D 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.32 (26016) covalent geometry : angle 0.75847 / 0.38 (35416) hydrogen bonds : bond 0.04057 / 2.79 ( 1266) hydrogen bonds : angle 4.46590 / 3.11 ( 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 544 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 454 time to evaluate : 0.997 Fit side-chains REVERT: A 413 LEU cc_start: 0.8455 (mt) cc_final: 0.8068 (tp) REVERT: A 616 LYS cc_start: 0.8469 (pttp) cc_final: 0.7623 (mttt) REVERT: A 626 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8741 (tp) REVERT: A 662 MET cc_start: 0.9024 (mtm) cc_final: 0.8607 (mtp) REVERT: A 664 TYR cc_start: 0.8811 (t80) cc_final: 0.8562 (t80) REVERT: A 703 THR cc_start: 0.8918 (p) cc_final: 0.8627 (t) REVERT: A 922 ASP cc_start: 0.8147 (t0) cc_final: 0.7945 (t0) REVERT: A 965 TYR cc_start: 0.8023 (t80) cc_final: 0.7537 (t80) REVERT: A 993 ILE cc_start: 0.8989 (mt) cc_final: 0.8769 (mm) REVERT: A 1053 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 1065 ILE cc_start: 0.8462 (mm) cc_final: 0.8207 (mt) REVERT: A 1159 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8189 (tttm) REVERT: A 1166 ASP cc_start: 0.8508 (m-30) cc_final: 0.7842 (m-30) REVERT: A 1168 LYS cc_start: 0.8602 (mttm) cc_final: 0.8336 (mtmt) REVERT: A 1171 HIS cc_start: 0.8563 (t-90) cc_final: 0.8127 (t70) REVERT: B 413 LEU cc_start: 0.8428 (mt) cc_final: 0.8045 (tp) REVERT: B 456 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8440 (ttmm) REVERT: B 616 LYS cc_start: 0.8469 (pttp) cc_final: 0.7625 (mttt) REVERT: B 626 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8735 (tp) REVERT: B 662 MET cc_start: 0.9007 (mtm) cc_final: 0.8604 (mtp) REVERT: B 664 TYR cc_start: 0.8812 (t80) cc_final: 0.8565 (t80) REVERT: B 703 THR cc_start: 0.8919 (p) cc_final: 0.8630 (t) REVERT: B 965 TYR cc_start: 0.8031 (t80) cc_final: 0.7547 (t80) REVERT: B 993 ILE cc_start: 0.8987 (mt) cc_final: 0.8764 (mm) REVERT: B 1009 LEU cc_start: 0.8804 (mp) cc_final: 0.8590 (mt) REVERT: B 1035 ASP cc_start: 0.8645 (t0) cc_final: 0.8406 (t0) REVERT: B 1053 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8245 (mt) REVERT: B 1065 ILE cc_start: 0.8465 (mm) cc_final: 0.8207 (mt) REVERT: B 1166 ASP cc_start: 0.8498 (m-30) cc_final: 0.7837 (m-30) REVERT: B 1168 LYS cc_start: 0.8596 (mttm) cc_final: 0.8326 (mtmt) REVERT: B 1171 HIS cc_start: 0.8573 (t-90) cc_final: 0.8137 (t70) REVERT: C 413 LEU cc_start: 0.8432 (mt) cc_final: 0.8048 (tp) REVERT: C 456 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8424 (ttmm) REVERT: C 616 LYS cc_start: 0.8477 (pttp) cc_final: 0.7632 (mttt) REVERT: C 626 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8734 (tp) REVERT: C 662 MET cc_start: 0.9016 (mtm) cc_final: 0.8615 (mtp) REVERT: C 664 TYR cc_start: 0.8821 (t80) cc_final: 0.8575 (t80) REVERT: C 703 THR cc_start: 0.8914 (p) cc_final: 0.8625 (t) REVERT: C 922 ASP cc_start: 0.8071 (t0) cc_final: 0.7831 (t0) REVERT: C 965 TYR cc_start: 0.8027 (t80) cc_final: 0.7546 (t80) REVERT: C 984 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8336 (mp10) REVERT: C 993 ILE cc_start: 0.8978 (mt) cc_final: 0.8757 (mm) REVERT: C 1035 ASP cc_start: 0.8641 (t0) cc_final: 0.8403 (t0) REVERT: C 1053 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8262 (mt) REVERT: C 1065 ILE cc_start: 0.8472 (mm) cc_final: 0.8216 (mt) REVERT: C 1166 ASP cc_start: 0.8489 (m-30) cc_final: 0.7833 (m-30) REVERT: C 1168 LYS cc_start: 0.8597 (mttm) cc_final: 0.8327 (mtmt) REVERT: C 1171 HIS cc_start: 0.8572 (t-90) cc_final: 0.8134 (t70) REVERT: D 413 LEU cc_start: 0.8438 (mt) cc_final: 0.8056 (tp) REVERT: D 456 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8455 (ttmm) REVERT: D 616 LYS cc_start: 0.8475 (pttp) cc_final: 0.7633 (mttt) REVERT: D 626 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8722 (tp) REVERT: D 662 MET cc_start: 0.9030 (mtm) cc_final: 0.8626 (mtp) REVERT: D 664 TYR cc_start: 0.8823 (t80) cc_final: 0.8573 (t80) REVERT: D 922 ASP cc_start: 0.8041 (t0) cc_final: 0.7836 (t0) REVERT: D 965 TYR cc_start: 0.8053 (t80) cc_final: 0.7571 (t80) REVERT: D 993 ILE cc_start: 0.8964 (mt) cc_final: 0.8731 (mm) REVERT: D 1053 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8260 (mt) REVERT: D 1065 ILE cc_start: 0.8456 (mm) cc_final: 0.8201 (mt) REVERT: D 1159 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8204 (tttm) REVERT: D 1166 ASP cc_start: 0.8479 (m-30) cc_final: 0.7801 (m-30) REVERT: D 1168 LYS cc_start: 0.8593 (mttm) cc_final: 0.8323 (mtmt) REVERT: D 1171 HIS cc_start: 0.8555 (t-90) cc_final: 0.8119 (t70) outliers start: 90 outliers final: 67 residues processed: 529 average time/residue: 0.1683 time to fit residues: 144.1014 Evaluate side-chains 516 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 441 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 421 ASP 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 858 PHE Chi-restraints excluded: chain A residue 900 LYS Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 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 695 GLU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 858 PHE Chi-restraints excluded: chain B residue 900 LYS 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 695 GLU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 858 PHE Chi-restraints excluded: chain C residue 900 LYS 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 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 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: 6.9990 chunk 26 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 127 optimal weight: 0.5980 chunk 156 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114006 restraints weight = 31668.824| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.06 r_work: 0.2890 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3476 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= 0.128 Angle : 0.608 9.534 35416 Z= 0.300 Chirality : 0.042 0.301 4180 Planarity : 0.004 0.048 4312 Dihedral : 8.151 103.363 3621 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 15.20 % Favored : 82.00 % 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: -0.67 (0.15), residues: 3136 helix: 0.15 (0.11), residues: 2164 sheet: None (None), residues: 0 loop : -1.65 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 274 TYR 0.014 0.001 TYR D 776 PHE 0.019 0.001 PHE D 858 TRP 0.009 0.001 TRP A 628 HIS 0.004 0.001 HIS C 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (26016) covalent geometry : angle 0.60833 / 0.30 (35416) hydrogen bonds : bond 0.03230 / 2.23 ( 1266) hydrogen bonds : angle 4.12547 / 2.87 ( 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 543 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 473 time to evaluate : 1.020 Fit side-chains REVERT: A 616 LYS cc_start: 0.8439 (pttp) cc_final: 0.7587 (mttt) REVERT: A 617 ARG cc_start: 0.8602 (mpt180) cc_final: 0.8358 (mpt180) REVERT: A 626 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 662 MET cc_start: 0.9059 (mtm) cc_final: 0.8621 (mtp) REVERT: A 664 TYR cc_start: 0.8787 (t80) cc_final: 0.8488 (t80) REVERT: A 748 MET cc_start: 0.8740 (mtt) cc_final: 0.8348 (mtm) REVERT: A 1065 ILE cc_start: 0.8384 (mm) cc_final: 0.8122 (mt) REVERT: A 1085 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: A 1159 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8187 (tttm) REVERT: A 1166 ASP cc_start: 0.8484 (m-30) cc_final: 0.7850 (m-30) REVERT: A 1168 LYS cc_start: 0.8578 (mttm) cc_final: 0.8326 (mtmt) REVERT: A 1171 HIS cc_start: 0.8521 (t-90) cc_final: 0.8110 (t70) REVERT: B 456 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8558 (ttmm) REVERT: B 616 LYS cc_start: 0.8446 (pttp) cc_final: 0.7638 (mttt) REVERT: B 617 ARG cc_start: 0.8597 (mpt180) cc_final: 0.8355 (mpt180) REVERT: B 626 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8785 (tp) REVERT: B 662 MET cc_start: 0.9036 (mtm) cc_final: 0.8598 (mtp) REVERT: B 664 TYR cc_start: 0.8799 (t80) cc_final: 0.8502 (t80) REVERT: B 748 MET cc_start: 0.8749 (mtt) cc_final: 0.8362 (mtm) REVERT: B 779 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7860 (tttt) REVERT: B 1065 ILE cc_start: 0.8378 (mm) cc_final: 0.8118 (mt) REVERT: B 1085 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: B 1166 ASP cc_start: 0.8483 (m-30) cc_final: 0.7858 (m-30) REVERT: B 1168 LYS cc_start: 0.8565 (mttm) cc_final: 0.8310 (mtmt) REVERT: B 1171 HIS cc_start: 0.8525 (t-90) cc_final: 0.8113 (t70) REVERT: C 456 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8545 (ttmm) REVERT: C 616 LYS cc_start: 0.8452 (pttp) cc_final: 0.7635 (mttt) REVERT: C 617 ARG cc_start: 0.8620 (mpt180) cc_final: 0.8379 (mpt180) REVERT: C 626 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8788 (tp) REVERT: C 662 MET cc_start: 0.9047 (mtm) cc_final: 0.8612 (mtp) REVERT: C 664 TYR cc_start: 0.8794 (t80) cc_final: 0.8496 (t80) REVERT: C 748 MET cc_start: 0.8739 (mtt) cc_final: 0.8359 (mtm) REVERT: C 984 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8286 (mp10) REVERT: C 1065 ILE cc_start: 0.8400 (mm) cc_final: 0.8139 (mt) REVERT: C 1085 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: C 1166 ASP cc_start: 0.8477 (m-30) cc_final: 0.7854 (m-30) REVERT: C 1168 LYS cc_start: 0.8585 (mttm) cc_final: 0.8329 (mtmt) REVERT: C 1171 HIS cc_start: 0.8528 (t-90) cc_final: 0.8117 (t70) REVERT: D 456 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8564 (ttmm) REVERT: D 616 LYS cc_start: 0.8457 (pttp) cc_final: 0.7649 (mttt) REVERT: D 617 ARG cc_start: 0.8620 (mpt180) cc_final: 0.8382 (mpt180) REVERT: D 626 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8781 (tp) REVERT: D 662 MET cc_start: 0.9059 (mtm) cc_final: 0.8620 (mtp) REVERT: D 664 TYR cc_start: 0.8801 (t80) cc_final: 0.8498 (t80) REVERT: D 748 MET cc_start: 0.8731 (mtt) cc_final: 0.8359 (mtm) REVERT: D 779 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7858 (tttt) REVERT: D 1065 ILE cc_start: 0.8386 (mm) cc_final: 0.8126 (mt) REVERT: D 1085 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: D 1159 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8205 (tttm) REVERT: D 1166 ASP cc_start: 0.8467 (m-30) cc_final: 0.7805 (m-30) REVERT: D 1168 LYS cc_start: 0.8577 (mttm) cc_final: 0.8324 (mtmt) REVERT: D 1171 HIS cc_start: 0.8519 (t-90) cc_final: 0.8103 (t70) outliers start: 70 outliers final: 53 residues processed: 520 average time/residue: 0.1705 time to fit residues: 142.4482 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 160 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 421 ASP 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 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 737 THR 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 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 774 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 215 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 238 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119955 restraints weight = 31048.301| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.69 r_work: 0.2923 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3631 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= 0.124 Angle : 0.607 9.651 35416 Z= 0.297 Chirality : 0.042 0.297 4180 Planarity : 0.004 0.048 4312 Dihedral : 7.870 103.736 3616 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.11 % Rotamer: Outliers : 3.16 % Allowed : 15.12 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.15), residues: 3136 helix: 0.49 (0.11), residues: 2152 sheet: None (None), residues: 0 loop : -1.66 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 274 TYR 0.014 0.001 TYR D 965 PHE 0.018 0.001 PHE A 858 TRP 0.009 0.001 TRP A 628 HIS 0.004 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (26016) covalent geometry : angle 0.60674 / 0.30 (35416) hydrogen bonds : bond 0.03136 / 2.17 ( 1266) hydrogen bonds : angle 3.98032 / 2.77 ( 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 553 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 474 time to evaluate : 1.022 Fit side-chains REVERT: A 478 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.5787 (t80) REVERT: A 616 LYS cc_start: 0.8427 (pttp) cc_final: 0.7645 (mttt) REVERT: A 626 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8712 (tp) REVERT: A 662 MET cc_start: 0.8984 (mtm) cc_final: 0.8559 (mtp) REVERT: A 664 TYR cc_start: 0.8700 (t80) cc_final: 0.8353 (t80) REVERT: A 748 MET cc_start: 0.8677 (mtt) cc_final: 0.8287 (mtm) REVERT: A 779 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7866 (tttt) REVERT: A 991 MET cc_start: 0.8674 (mmp) cc_final: 0.8472 (mmp) REVERT: A 1035 ASP cc_start: 0.8440 (t0) cc_final: 0.8237 (t0) REVERT: A 1065 ILE cc_start: 0.8267 (mm) cc_final: 0.8023 (mt) REVERT: A 1085 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: A 1159 LYS cc_start: 0.8518 (mtmm) cc_final: 0.7967 (tttm) REVERT: A 1166 ASP cc_start: 0.8446 (m-30) cc_final: 0.7794 (m-30) REVERT: A 1168 LYS cc_start: 0.8474 (mttm) cc_final: 0.8255 (mtmt) REVERT: A 1171 HIS cc_start: 0.8442 (t-90) cc_final: 0.8033 (t70) REVERT: B 478 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.5747 (t80) REVERT: B 616 LYS cc_start: 0.8454 (pttp) cc_final: 0.7641 (mttt) REVERT: B 617 ARG cc_start: 0.8512 (mpt180) cc_final: 0.8304 (mpt180) REVERT: B 626 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8711 (tp) REVERT: B 662 MET cc_start: 0.8958 (mtm) cc_final: 0.8533 (mtp) REVERT: B 664 TYR cc_start: 0.8704 (t80) cc_final: 0.8357 (t80) REVERT: B 748 MET cc_start: 0.8694 (mtt) cc_final: 0.8311 (mtm) REVERT: B 779 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7804 (tttt) REVERT: B 1065 ILE cc_start: 0.8267 (mm) cc_final: 0.8025 (mt) REVERT: B 1085 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: B 1166 ASP cc_start: 0.8436 (m-30) cc_final: 0.7783 (m-30) REVERT: B 1168 LYS cc_start: 0.8455 (mttm) cc_final: 0.8231 (mtmt) REVERT: B 1171 HIS cc_start: 0.8443 (t-90) cc_final: 0.8035 (t70) REVERT: C 456 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8453 (ttmm) REVERT: C 478 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.5738 (t80) REVERT: C 616 LYS cc_start: 0.8457 (pttp) cc_final: 0.7639 (mttt) REVERT: C 617 ARG cc_start: 0.8522 (mpt180) cc_final: 0.8313 (mpt180) REVERT: C 626 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8715 (tp) REVERT: C 662 MET cc_start: 0.8973 (mtm) cc_final: 0.8552 (mtp) REVERT: C 664 TYR cc_start: 0.8706 (t80) cc_final: 0.8359 (t80) REVERT: C 748 MET cc_start: 0.8667 (mtt) cc_final: 0.8283 (mtm) REVERT: C 779 LYS cc_start: 0.8295 (mmtt) cc_final: 0.7869 (tttt) REVERT: C 922 ASP cc_start: 0.8127 (t0) cc_final: 0.7917 (t0) REVERT: C 984 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8229 (mp10) REVERT: C 1065 ILE cc_start: 0.8282 (mm) cc_final: 0.8041 (mt) REVERT: C 1085 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: C 1166 ASP cc_start: 0.8436 (m-30) cc_final: 0.7787 (m-30) REVERT: C 1168 LYS cc_start: 0.8469 (mttm) cc_final: 0.8243 (mtmt) REVERT: C 1171 HIS cc_start: 0.8452 (t-90) cc_final: 0.8042 (t70) REVERT: D 456 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8465 (ttmm) REVERT: D 478 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.5745 (t80) REVERT: D 616 LYS cc_start: 0.8457 (pttp) cc_final: 0.7640 (mttt) REVERT: D 617 ARG cc_start: 0.8517 (mpt180) cc_final: 0.8312 (mpt180) REVERT: D 626 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8698 (tp) REVERT: D 662 MET cc_start: 0.8984 (mtm) cc_final: 0.8557 (mtp) REVERT: D 664 TYR cc_start: 0.8706 (t80) cc_final: 0.8358 (t80) REVERT: D 748 MET cc_start: 0.8630 (mtt) cc_final: 0.8239 (mtm) REVERT: D 779 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7802 (tttt) REVERT: D 1065 ILE cc_start: 0.8262 (mm) cc_final: 0.8020 (mt) REVERT: D 1085 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: D 1159 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8081 (tttm) REVERT: D 1166 ASP cc_start: 0.8424 (m-30) cc_final: 0.7763 (m-30) REVERT: D 1168 LYS cc_start: 0.8464 (mttm) cc_final: 0.8238 (mtmt) REVERT: D 1171 HIS cc_start: 0.8439 (t-90) cc_final: 0.8027 (t70) outliers start: 79 outliers final: 59 residues processed: 532 average time/residue: 0.1723 time to fit residues: 147.0114 Evaluate side-chains 511 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 440 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 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 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 478 TYR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 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 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 478 TYR 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 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 478 TYR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 55 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 303 optimal weight: 0.9990 chunk 295 optimal weight: 8.9990 chunk 302 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.146484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113667 restraints weight = 31727.224| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.94 r_work: 0.2885 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26016 Z= 0.142 Angle : 0.616 9.581 35416 Z= 0.301 Chirality : 0.042 0.297 4180 Planarity : 0.004 0.048 4312 Dihedral : 7.753 104.458 3612 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.08 % Allowed : 14.96 % Favored : 81.96 % 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: -0.18 (0.15), residues: 3136 helix: 0.58 (0.11), residues: 2160 sheet: None (None), residues: 0 loop : -1.62 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 274 TYR 0.015 0.001 TYR D 776 PHE 0.018 0.001 PHE A 858 TRP 0.008 0.001 TRP A 628 HIS 0.004 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (26016) covalent geometry : angle 0.61583 / 0.30 (35416) hydrogen bonds : bond 0.03132 / 2.16 ( 1266) hydrogen bonds : angle 3.94801 / 2.75 ( 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 537 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 460 time to evaluate : 1.039 Fit side-chains REVERT: A 478 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.5859 (t80) REVERT: A 616 LYS cc_start: 0.8685 (pttp) cc_final: 0.7881 (mttt) REVERT: A 626 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8744 (tp) REVERT: A 662 MET cc_start: 0.9022 (mtm) cc_final: 0.8579 (mtp) REVERT: A 664 TYR cc_start: 0.8702 (t80) cc_final: 0.8330 (t80) REVERT: A 748 MET cc_start: 0.8686 (mtt) cc_final: 0.8307 (mtm) REVERT: A 779 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7863 (tttt) REVERT: A 1065 ILE cc_start: 0.8282 (mm) cc_final: 0.8039 (mt) REVERT: A 1085 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: A 1159 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8100 (tttm) REVERT: A 1166 ASP cc_start: 0.8461 (m-30) cc_final: 0.7791 (m-30) REVERT: A 1168 LYS cc_start: 0.8502 (mttm) cc_final: 0.8246 (mtmt) REVERT: A 1171 HIS cc_start: 0.8496 (t-90) cc_final: 0.8085 (t70) REVERT: B 478 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.5847 (t80) REVERT: B 616 LYS cc_start: 0.8459 (pttp) cc_final: 0.7652 (mttt) REVERT: B 617 ARG cc_start: 0.8545 (mpt180) cc_final: 0.8326 (mpt180) REVERT: B 626 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8744 (tp) REVERT: B 662 MET cc_start: 0.8996 (mtm) cc_final: 0.8555 (mtp) REVERT: B 664 TYR cc_start: 0.8708 (t80) cc_final: 0.8344 (t80) REVERT: B 748 MET cc_start: 0.8731 (mtt) cc_final: 0.8349 (mtm) REVERT: B 779 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7795 (tttt) REVERT: B 1065 ILE cc_start: 0.8281 (mm) cc_final: 0.8038 (mt) REVERT: B 1085 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: B 1166 ASP cc_start: 0.8399 (m-30) cc_final: 0.7721 (m-30) REVERT: B 1168 LYS cc_start: 0.8483 (mttm) cc_final: 0.8224 (mtmt) REVERT: B 1171 HIS cc_start: 0.8492 (t-90) cc_final: 0.8081 (t70) REVERT: C 456 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8482 (ttmm) REVERT: C 478 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.5849 (t80) REVERT: C 616 LYS cc_start: 0.8467 (pttp) cc_final: 0.7653 (mttt) REVERT: C 617 ARG cc_start: 0.8553 (mpt180) cc_final: 0.8333 (mpt180) REVERT: C 626 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8754 (tp) REVERT: C 662 MET cc_start: 0.9012 (mtm) cc_final: 0.8574 (mtp) REVERT: C 664 TYR cc_start: 0.8709 (t80) cc_final: 0.8340 (t80) REVERT: C 748 MET cc_start: 0.8674 (mtt) cc_final: 0.8306 (mtm) REVERT: C 779 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7861 (tttt) REVERT: C 922 ASP cc_start: 0.8134 (t0) cc_final: 0.7914 (t0) REVERT: C 984 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8260 (mp10) REVERT: C 1065 ILE cc_start: 0.8286 (mm) cc_final: 0.8044 (mt) REVERT: C 1085 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: C 1166 ASP cc_start: 0.8387 (m-30) cc_final: 0.7709 (m-30) REVERT: C 1168 LYS cc_start: 0.8494 (mttm) cc_final: 0.8232 (mtmt) REVERT: C 1171 HIS cc_start: 0.8494 (t-90) cc_final: 0.8081 (t70) REVERT: D 456 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8499 (ttmm) REVERT: D 478 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.5828 (t80) REVERT: D 616 LYS cc_start: 0.8461 (pttp) cc_final: 0.7653 (mttt) REVERT: D 617 ARG cc_start: 0.8547 (mpt180) cc_final: 0.8327 (mpt180) REVERT: D 626 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8735 (tp) REVERT: D 662 MET cc_start: 0.9024 (mtm) cc_final: 0.8582 (mtp) REVERT: D 664 TYR cc_start: 0.8713 (t80) cc_final: 0.8344 (t80) REVERT: D 748 MET cc_start: 0.8690 (mtt) cc_final: 0.8301 (mtm) REVERT: D 779 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7794 (tttt) REVERT: D 1065 ILE cc_start: 0.8279 (mm) cc_final: 0.8034 (mt) REVERT: D 1085 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: D 1159 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8098 (tttm) REVERT: D 1166 ASP cc_start: 0.8439 (m-30) cc_final: 0.7761 (m-30) REVERT: D 1168 LYS cc_start: 0.8491 (mttm) cc_final: 0.8231 (mtmt) REVERT: D 1171 HIS cc_start: 0.8484 (t-90) cc_final: 0.8073 (t70) outliers start: 77 outliers final: 52 residues processed: 515 average time/residue: 0.1728 time to fit residues: 141.2341 Evaluate side-chains 501 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 437 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 421 ASP Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 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 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 478 TYR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 626 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 478 TYR 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 421 ASP Chi-restraints excluded: chain D residue 478 TYR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 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 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: 0.9980 chunk 177 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 278 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 246 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 227 optimal weight: 0.0470 chunk 270 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 787 GLN ** 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 = 0.3626 r_free = 0.3626 target = 0.147941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.115316 restraints weight = 31654.413| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.87 r_work: 0.2919 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3849 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= 0.120 Angle : 0.606 9.475 35416 Z= 0.295 Chirality : 0.041 0.299 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.596 105.158 3612 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.88 % Allowed : 15.48 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.02 (0.15), residues: 3136 helix: 0.75 (0.12), residues: 2160 sheet: None (None), residues: 0 loop : -1.57 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 902 TYR 0.013 0.001 TYR B 776 PHE 0.018 0.001 PHE A 858 TRP 0.008 0.001 TRP A 628 HIS 0.004 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (26016) covalent geometry : angle 0.60642 / 0.29 (35416) hydrogen bonds : bond 0.03006 / 2.07 ( 1266) hydrogen bonds : angle 3.86820 / 2.69 ( 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 541 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 469 time to evaluate : 0.929 Fit side-chains REVERT: A 478 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.5883 (t80) REVERT: A 616 LYS cc_start: 0.8666 (pttp) cc_final: 0.7793 (mttt) REVERT: A 626 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8729 (tp) REVERT: A 662 MET cc_start: 0.8999 (mtm) cc_final: 0.8542 (mtp) REVERT: A 664 TYR cc_start: 0.8654 (t80) cc_final: 0.8269 (t80) REVERT: A 748 MET cc_start: 0.8618 (mtt) cc_final: 0.8241 (mtm) REVERT: A 779 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7684 (tttt) REVERT: A 1065 ILE cc_start: 0.8200 (mm) cc_final: 0.7962 (mt) REVERT: A 1085 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: A 1159 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8047 (tttm) REVERT: A 1166 ASP cc_start: 0.8380 (m-30) cc_final: 0.7706 (m-30) REVERT: A 1168 LYS cc_start: 0.8430 (mttm) cc_final: 0.8195 (mtmt) REVERT: A 1171 HIS cc_start: 0.8471 (t-90) cc_final: 0.8062 (t70) REVERT: B 478 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.5854 (t80) REVERT: B 616 LYS cc_start: 0.8483 (pttp) cc_final: 0.7686 (mttt) REVERT: B 617 ARG cc_start: 0.8523 (mpt180) cc_final: 0.8287 (mpt180) REVERT: B 626 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8730 (tp) REVERT: B 662 MET cc_start: 0.8978 (mtm) cc_final: 0.8541 (mtp) REVERT: B 664 TYR cc_start: 0.8675 (t80) cc_final: 0.8291 (t80) REVERT: B 748 MET cc_start: 0.8638 (mtt) cc_final: 0.8247 (mtm) REVERT: B 779 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7617 (tttt) REVERT: B 1065 ILE cc_start: 0.8206 (mm) cc_final: 0.7971 (mt) REVERT: B 1085 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: B 1166 ASP cc_start: 0.8385 (m-30) cc_final: 0.7708 (m-30) REVERT: B 1168 LYS cc_start: 0.8449 (mttm) cc_final: 0.8225 (mtmt) REVERT: B 1171 HIS cc_start: 0.8465 (t-90) cc_final: 0.8054 (t70) REVERT: C 478 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.5867 (t80) REVERT: C 616 LYS cc_start: 0.8486 (pttp) cc_final: 0.7684 (mttt) REVERT: C 617 ARG cc_start: 0.8513 (mpt180) cc_final: 0.8275 (mpt180) REVERT: C 626 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8732 (tp) REVERT: C 662 MET cc_start: 0.8985 (mtm) cc_final: 0.8553 (mtp) REVERT: C 664 TYR cc_start: 0.8666 (t80) cc_final: 0.8284 (t80) REVERT: C 748 MET cc_start: 0.8611 (mtt) cc_final: 0.8244 (mtm) REVERT: C 779 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7835 (tttt) REVERT: C 922 ASP cc_start: 0.8096 (t0) cc_final: 0.7847 (t0) REVERT: C 984 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8209 (mp10) REVERT: C 1065 ILE cc_start: 0.8218 (mm) cc_final: 0.7983 (mt) REVERT: C 1085 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: C 1114 GLN cc_start: 0.8549 (mt0) cc_final: 0.8342 (mm-40) REVERT: C 1166 ASP cc_start: 0.8376 (m-30) cc_final: 0.7699 (m-30) REVERT: C 1168 LYS cc_start: 0.8464 (mttm) cc_final: 0.8238 (mtmt) REVERT: C 1171 HIS cc_start: 0.8469 (t-90) cc_final: 0.8060 (t70) REVERT: D 478 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.5902 (t80) REVERT: D 626 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8719 (tp) REVERT: D 662 MET cc_start: 0.9003 (mtm) cc_final: 0.8564 (mtp) REVERT: D 664 TYR cc_start: 0.8678 (t80) cc_final: 0.8292 (t80) REVERT: D 704 MET cc_start: 0.9015 (mmm) cc_final: 0.8643 (mmt) REVERT: D 748 MET cc_start: 0.8608 (mtt) cc_final: 0.8199 (mtm) REVERT: D 779 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7625 (tttt) REVERT: D 1065 ILE cc_start: 0.8203 (mm) cc_final: 0.7966 (mt) REVERT: D 1085 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: D 1114 GLN cc_start: 0.8506 (mt0) cc_final: 0.8303 (mm-40) REVERT: D 1159 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8056 (tttm) REVERT: D 1166 ASP cc_start: 0.8368 (m-30) cc_final: 0.7688 (m-30) REVERT: D 1168 LYS cc_start: 0.8429 (mttm) cc_final: 0.8186 (mtmt) REVERT: D 1171 HIS cc_start: 0.8462 (t-90) cc_final: 0.8048 (t70) outliers start: 72 outliers final: 46 residues processed: 525 average time/residue: 0.1629 time to fit residues: 138.4686 Evaluate side-chains 499 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 441 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 478 TYR 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 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 458 LEU Chi-restraints excluded: chain B residue 478 TYR 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 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 458 LEU Chi-restraints excluded: chain C residue 478 TYR 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 161 ILE Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 478 TYR 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 156 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 252 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 968 ASN B 968 ASN C 154 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 968 ASN D 154 GLN D 968 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115553 restraints weight = 31598.908| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.01 r_work: 0.2915 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3933 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= 0.126 Angle : 0.612 9.543 35416 Z= 0.297 Chirality : 0.042 0.297 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.511 105.600 3612 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.36 % Allowed : 16.56 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.15), residues: 3136 helix: 0.84 (0.12), residues: 2160 sheet: None (None), residues: 0 loop : -1.51 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 274 TYR 0.014 0.001 TYR B 776 PHE 0.018 0.001 PHE D 858 TRP 0.008 0.001 TRP A 628 HIS 0.004 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (26016) covalent geometry : angle 0.61212 / 0.30 (35416) hydrogen bonds : bond 0.02985 / 2.06 ( 1266) hydrogen bonds : angle 3.81796 / 2.65 ( 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 529 residues out of total 2908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 470 time to evaluate : 0.992 Fit side-chains REVERT: A 154 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7969 (pp30) REVERT: A 478 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.6152 (t80) REVERT: A 626 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8829 (tp) REVERT: A 662 MET cc_start: 0.9070 (mtm) cc_final: 0.8633 (mtp) REVERT: A 664 TYR cc_start: 0.8715 (t80) cc_final: 0.8197 (t80) REVERT: A 681 GLN cc_start: 0.8205 (tp40) cc_final: 0.7886 (tp40) REVERT: A 748 MET cc_start: 0.8712 (mtt) cc_final: 0.8346 (mtm) REVERT: A 779 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7757 (tttt) REVERT: A 1051 TYR cc_start: 0.8629 (m-80) cc_final: 0.8400 (m-80) REVERT: A 1085 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: A 1159 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8165 (tttm) REVERT: A 1166 ASP cc_start: 0.8415 (m-30) cc_final: 0.7760 (m-30) REVERT: A 1168 LYS cc_start: 0.8538 (mttm) cc_final: 0.8323 (mtmt) REVERT: A 1171 HIS cc_start: 0.8525 (t-90) cc_final: 0.8144 (t70) REVERT: B 478 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.6134 (t80) REVERT: B 616 LYS cc_start: 0.8533 (pttp) cc_final: 0.7776 (mttt) REVERT: B 626 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8828 (tp) REVERT: B 662 MET cc_start: 0.9041 (mtm) cc_final: 0.8604 (mtp) REVERT: B 664 TYR cc_start: 0.8743 (t80) cc_final: 0.8223 (t80) REVERT: B 681 GLN cc_start: 0.8179 (tp40) cc_final: 0.7852 (tp40) REVERT: B 748 MET cc_start: 0.8724 (mtt) cc_final: 0.8384 (mtm) REVERT: B 779 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7680 (tttt) REVERT: B 1065 ILE cc_start: 0.8293 (mm) cc_final: 0.8053 (mt) REVERT: B 1085 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: B 1166 ASP cc_start: 0.8434 (m-30) cc_final: 0.7761 (m-30) REVERT: B 1168 LYS cc_start: 0.8510 (mttm) cc_final: 0.8297 (mtmt) REVERT: B 1171 HIS cc_start: 0.8491 (t-90) cc_final: 0.8102 (t70) REVERT: C 478 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.6147 (t80) REVERT: C 616 LYS cc_start: 0.8533 (pttp) cc_final: 0.7774 (mttt) REVERT: C 626 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8827 (tp) REVERT: C 662 MET cc_start: 0.9043 (mtm) cc_final: 0.8610 (mtp) REVERT: C 664 TYR cc_start: 0.8725 (t80) cc_final: 0.8211 (t80) REVERT: C 681 GLN cc_start: 0.8189 (tp40) cc_final: 0.7863 (tp40) REVERT: C 748 MET cc_start: 0.8703 (mtt) cc_final: 0.8347 (mtm) REVERT: C 779 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7750 (tttt) REVERT: C 922 ASP cc_start: 0.8153 (t0) cc_final: 0.7916 (t0) REVERT: C 1051 TYR cc_start: 0.8620 (m-80) cc_final: 0.8396 (m-80) REVERT: C 1085 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: C 1166 ASP cc_start: 0.8417 (m-30) cc_final: 0.7759 (m-30) REVERT: C 1168 LYS cc_start: 0.8545 (mttm) cc_final: 0.8324 (mtmt) REVERT: C 1171 HIS cc_start: 0.8525 (t-90) cc_final: 0.8144 (t70) REVERT: D 154 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7967 (pp30) REVERT: D 478 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.6134 (t80) REVERT: D 626 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8820 (tp) REVERT: D 662 MET cc_start: 0.9072 (mtm) cc_final: 0.8631 (mtp) REVERT: D 664 TYR cc_start: 0.8742 (t80) cc_final: 0.8224 (t80) REVERT: D 748 MET cc_start: 0.8693 (mtt) cc_final: 0.8344 (mtm) REVERT: D 779 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7699 (tttt) REVERT: D 1051 TYR cc_start: 0.8636 (m-80) cc_final: 0.8396 (m-80) REVERT: D 1085 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: D 1159 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8161 (tttm) REVERT: D 1166 ASP cc_start: 0.8402 (m-30) cc_final: 0.7744 (m-30) REVERT: D 1168 LYS cc_start: 0.8543 (mttm) cc_final: 0.8323 (mtmt) REVERT: D 1171 HIS cc_start: 0.8525 (t-90) cc_final: 0.8129 (t70) outliers start: 59 outliers final: 42 residues processed: 510 average time/residue: 0.1684 time to fit residues: 139.7671 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 154 GLN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 478 TYR 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 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 458 LEU Chi-restraints excluded: chain B residue 478 TYR 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 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 458 LEU Chi-restraints excluded: chain C residue 478 TYR 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 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 458 LEU Chi-restraints excluded: chain D residue 478 TYR 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 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: 10.0000 chunk 154 optimal weight: 0.0000 chunk 219 optimal weight: 0.5980 chunk 224 optimal weight: 0.6980 chunk 277 optimal weight: 3.9990 chunk 304 optimal weight: 0.5980 chunk 101 optimal weight: 0.0470 chunk 317 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 312 optimal weight: 0.7980 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN C 154 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115743 restraints weight = 31564.076| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.88 r_work: 0.2949 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26016 Z= 0.108 Angle : 0.603 9.424 35416 Z= 0.293 Chirality : 0.041 0.296 4180 Planarity : 0.004 0.047 4312 Dihedral : 7.436 105.823 3608 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.48 % Allowed : 16.68 % Favored : 80.84 % 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: 0.33 (0.15), residues: 3136 helix: 0.97 (0.12), residues: 2156 sheet: None (None), residues: 0 loop : -1.41 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 274 TYR 0.012 0.001 TYR B 776 PHE 0.018 0.001 PHE A 858 TRP 0.008 0.001 TRP A 628 HIS 0.004 0.001 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (26016) covalent geometry : angle 0.60335 / 0.29 (35416) hydrogen bonds : bond 0.02912 / 2.01 ( 1266) hydrogen bonds : angle 3.77413 / 2.62 ( 3774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7046.90 seconds wall clock time: 121 minutes 2.05 seconds (7262.05 seconds total)