Starting phenix.real_space_refine on Sat Feb 7 11:47:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o83_70216/02_2026/9o83_70216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o83_70216/02_2026/9o83_70216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o83_70216/02_2026/9o83_70216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o83_70216/02_2026/9o83_70216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o83_70216/02_2026/9o83_70216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o83_70216/02_2026/9o83_70216.map" } resolution = 3.96 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= 0.000 sd= 0.000 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 229 5.16 5 C 20767 2.51 5 N 5323 2.21 5 O 5562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31881 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7890 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 988} Chain breaks: 8 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 421 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 15, 'ARG:plan': 14, 'ASP:plan': 7, 'HIS:plan': 5, 'GLN:plan1': 12, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 293 Chain: "C" Number of atoms: 7908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7908 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 989} Chain breaks: 8 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 589 Unresolved non-hydrogen dihedrals: 413 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 15, 'ARG:plan': 11, 'ASP:plan': 7, 'HIS:plan': 5, 'GLN:plan1': 12, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 278 Chain: "B" Number of atoms: 7913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7913 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 989} Chain breaks: 8 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 407 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 15, 'ARG:plan': 11, 'ASP:plan': 8, 'HIS:plan': 5, 'GLN:plan1': 12, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 281 Chain: "D" Number of atoms: 7750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7750 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 984} Chain breaks: 8 Unresolved non-hydrogen bonds: 583 Unresolved non-hydrogen angles: 716 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 17, 'ASP:plan': 12, 'HIS:plan': 5, 'GLN:plan1': 15, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 372 Chain: "A" 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} Chain: "C" 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} Chain: "B" 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} 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: 9.68, per 1000 atoms: 0.30 Number of scatterers: 31881 At special positions: 0 Unit cell: (151.984, 152.81, 153.636, 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 229 16.00 O 5562 8.00 N 5323 7.00 C 20767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1061 " distance=2.03 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1061 " distance=2.03 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1061 " distance=2.03 Simple disulfide: pdb=" SG CYS D1044 " - pdb=" SG CYS D1061 " distance=2.03 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: 4.43 Conformation dependent library (CDL) restraints added in 1.5 seconds 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7772 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 8 sheets defined 66.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 removed outlier: 4.137A pdb=" N PHE A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.571A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 182 removed outlier: 4.159A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 206 removed outlier: 3.816A pdb=" N HIS A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.583A pdb=" N GLN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.945A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.641A pdb=" N ASP A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 368 Processing helix chain 'A' and resid 371 through 388 removed outlier: 4.259A pdb=" N LYS A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 removed outlier: 4.072A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 430 Processing helix chain 'A' and resid 433 through 441 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.729A pdb=" N LEU A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 555 through 565 Processing helix chain 'A' and resid 613 through 625 removed outlier: 4.267A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 4.199A pdb=" N PHE A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 662 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.661A pdb=" N SER A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.912A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 836 through 845 removed outlier: 4.203A pdb=" N TYR A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 872 removed outlier: 3.627A pdb=" N TYR A 868 " --> pdb=" O MET A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 902 Processing helix chain 'A' and resid 907 through 917 removed outlier: 3.709A pdb=" N GLN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 939 removed outlier: 3.770A pdb=" N VAL A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 962 removed outlier: 3.718A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 968 removed outlier: 3.815A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1009 removed outlier: 3.984A pdb=" N TYR A 976 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1025 Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 3.913A pdb=" N GLY A1033 " --> pdb=" O MET A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1081 removed outlier: 3.977A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1120 removed outlier: 4.393A pdb=" N PHE A1096 " --> pdb=" O ASN A1092 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU A1097 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1141 removed outlier: 4.383A pdb=" N ILE A1129 " --> pdb=" O PRO A1125 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE A1130 " --> pdb=" O PRO A1126 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A1136 " --> pdb=" O HIS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1192 Processing helix chain 'A' and resid 1192 through 1232 removed outlier: 3.774A pdb=" N MET A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.763A pdb=" N PHE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 removed outlier: 4.270A pdb=" N HIS C 63 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 removed outlier: 4.214A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 182 removed outlier: 3.862A pdb=" N LEU C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 206 removed outlier: 3.683A pdb=" N HIS C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.750A pdb=" N ILE C 231 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.966A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.583A pdb=" N TYR C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 404 through 415 removed outlier: 3.915A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 440 removed outlier: 4.046A pdb=" N ALA C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 465 through 476 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 501 through 513 Processing helix chain 'C' and resid 533 through 546 Processing helix chain 'C' and resid 555 through 563 Processing helix chain 'C' and resid 613 through 625 removed outlier: 4.088A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 Processing helix chain 'C' and resid 640 through 662 Processing helix chain 'C' and resid 665 through 694 removed outlier: 3.513A pdb=" N SER C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 702 Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 749 through 759 Processing helix chain 'C' and resid 763 through 767 removed outlier: 3.696A pdb=" N SER C 766 " --> pdb=" O SER C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 removed outlier: 4.304A pdb=" N LYS C 840 " --> pdb=" O PRO C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 872 removed outlier: 3.526A pdb=" N LYS C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 872 " --> pdb=" O TYR C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 902 Processing helix chain 'C' and resid 907 through 917 Processing helix chain 'C' and resid 918 through 939 removed outlier: 3.523A pdb=" N VAL C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 967 removed outlier: 3.708A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 958 " --> pdb=" O VAL C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1010 removed outlier: 4.776A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1026 removed outlier: 3.775A pdb=" N LYS C1021 " --> pdb=" O TRP C1017 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET C1026 " --> pdb=" O ASN C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1031 Processing helix chain 'C' and resid 1066 through 1081 removed outlier: 4.338A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1102 removed outlier: 3.767A pdb=" N SER C1100 " --> pdb=" O PHE C1096 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C1101 " --> pdb=" O GLU C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1120 removed outlier: 3.947A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1127 Processing helix chain 'C' and resid 1128 through 1138 Processing helix chain 'C' and resid 1139 through 1141 No H-bonds generated for 'chain 'C' and resid 1139 through 1141' Processing helix chain 'C' and resid 1163 through 1192 Processing helix chain 'C' and resid 1192 through 1232 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.684A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.602A pdb=" N LEU B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.513A pdb=" N HIS B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.743A pdb=" N GLN B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.957A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.762A pdb=" N ASP B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 367 Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.540A pdb=" N ALA B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.640A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 440 removed outlier: 3.804A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 501 through 514 Processing helix chain 'B' and resid 533 through 546 Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 555 through 566 removed outlier: 3.722A pdb=" N LEU B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 625 removed outlier: 4.302A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 Processing helix chain 'B' and resid 640 through 663 Processing helix chain 'B' and resid 665 through 692 removed outlier: 4.219A pdb=" N SER B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 703 Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 728 removed outlier: 3.901A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 741 Processing helix chain 'B' and resid 749 through 759 removed outlier: 3.976A pdb=" N LYS B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 765 removed outlier: 3.503A pdb=" N ILE B 764 " --> pdb=" O PRO B 761 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 845 removed outlier: 4.302A pdb=" N LYS B 840 " --> pdb=" O PRO B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 872 Processing helix chain 'B' and resid 879 through 902 Processing helix chain 'B' and resid 907 through 918 removed outlier: 4.499A pdb=" N GLU B 918 " --> pdb=" O VAL B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 939 removed outlier: 3.843A pdb=" N VAL B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 967 removed outlier: 3.976A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 957 " --> pdb=" O CYS B 953 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 958 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 964 " --> pdb=" O TYR B 960 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 1009 removed outlier: 4.883A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1029 removed outlier: 3.568A pdb=" N LYS B1021 " --> pdb=" O TRP B1017 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET B1026 " --> pdb=" O ASN B1022 " (cutoff:3.500A) Proline residue: B1027 - end of helix Processing helix chain 'B' and resid 1036 through 1040 removed outlier: 3.742A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1120 removed outlier: 4.395A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B1083 " --> pdb=" O ALA B1079 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE B1101 " --> pdb=" O GLU B1097 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN B1103 " --> pdb=" O LYS B1099 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLN B1104 " --> pdb=" O SER B1100 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B1113 " --> pdb=" O GLN B1109 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS B1118 " --> pdb=" O ILE B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1138 removed outlier: 4.525A pdb=" N ILE B1129 " --> pdb=" O PRO B1125 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE B1130 " --> pdb=" O PRO B1126 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1192 Processing helix chain 'B' and resid 1192 through 1231 Processing helix chain 'D' and resid 130 through 140 Processing helix chain 'D' and resid 163 through 181 removed outlier: 4.389A pdb=" N LYS D 172 " --> pdb=" O GLN D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 271 through 285 removed outlier: 4.090A pdb=" N LYS D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.963A pdb=" N ILE D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 removed outlier: 3.950A pdb=" N ILE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 367 Processing helix chain 'D' and resid 371 through 386 removed outlier: 4.219A pdb=" N ILE D 381 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 416 removed outlier: 4.175A pdb=" N LYS D 415 " --> pdb=" O THR D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 434 through 440 Processing helix chain 'D' and resid 452 through 462 removed outlier: 3.840A pdb=" N ALA D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 474 removed outlier: 3.550A pdb=" N GLU D 474 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 484 through 494 removed outlier: 3.550A pdb=" N THR D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 512 removed outlier: 4.339A pdb=" N LEU D 505 " --> pdb=" O THR D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 555 through 565 Processing helix chain 'D' and resid 613 through 625 removed outlier: 4.051A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 637 removed outlier: 3.598A pdb=" N HIS D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'D' and resid 665 through 694 removed outlier: 3.643A pdb=" N SER D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 704 Processing helix chain 'D' and resid 706 through 710 removed outlier: 3.702A pdb=" N SER D 710 " --> pdb=" O LYS D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 721 Processing helix chain 'D' and resid 723 through 729 removed outlier: 3.584A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 741 Processing helix chain 'D' and resid 752 through 760 Processing helix chain 'D' and resid 761 through 767 removed outlier: 3.924A pdb=" N LEU D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D 767 " --> pdb=" O ILE D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 845 Processing helix chain 'D' and resid 847 through 872 Processing helix chain 'D' and resid 879 through 902 Processing helix chain 'D' and resid 907 through 917 removed outlier: 3.632A pdb=" N GLN D 917 " --> pdb=" O LYS D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 940 removed outlier: 3.710A pdb=" N GLN D 940 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 968 removed outlier: 3.893A pdb=" N ASP D 947 " --> pdb=" O PRO D 943 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE D 957 " --> pdb=" O CYS D 953 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR D 958 " --> pdb=" O VAL D 954 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 1009 removed outlier: 4.659A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1025 removed outlier: 3.659A pdb=" N LYS D1021 " --> pdb=" O TRP D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1030 Processing helix chain 'D' and resid 1031 through 1033 No H-bonds generated for 'chain 'D' and resid 1031 through 1033' Processing helix chain 'D' and resid 1036 through 1040 removed outlier: 3.731A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1080 removed outlier: 3.861A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1082 through 1120 removed outlier: 4.903A pdb=" N PHE D1096 " --> pdb=" O ASN D1092 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU D1097 " --> pdb=" O ASN D1093 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D1098 " --> pdb=" O THR D1094 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER D1100 " --> pdb=" O PHE D1096 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN D1104 " --> pdb=" O SER D1100 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1124 through 1127 Processing helix chain 'D' and resid 1128 through 1145 removed outlier: 4.154A pdb=" N LEU D1140 " --> pdb=" O ILE D1136 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG D1143 " --> pdb=" O HIS D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1191 Processing helix chain 'D' and resid 1194 through 1232 removed outlier: 3.582A pdb=" N ARG D1198 " --> pdb=" O ASP D1194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 240 removed outlier: 7.850A pdb=" N PHE A 106 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR A 108 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR A 239 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU A 110 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 105 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 109 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET A 121 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU A 261 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL A 123 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASP A 263 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 125 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A 215 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 260 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY A 217 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A 262 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 219 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE A 185 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 218 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR A 187 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL A 327 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA A 301 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS A 329 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE A 303 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 40 Processing sheet with id=AA4, first strand: chain 'C' and resid 232 through 233 removed outlier: 6.109A pdb=" N ALA C 105 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR C 215 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE C 260 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY C 217 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA C 262 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA C 219 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 185 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE C 218 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR C 187 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL C 327 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA C 301 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N CYS C 329 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE C 303 " --> pdb=" O CYS C 329 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 41 Processing sheet with id=AA6, first strand: chain 'B' and resid 233 through 240 removed outlier: 6.983A pdb=" N PHE B 106 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR B 239 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU B 110 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET B 121 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N LEU B 261 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 123 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP B 263 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 125 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE B 185 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 218 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR B 187 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE B 151 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 302 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL B 327 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA B 301 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.614A pdb=" N MET D 121 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 261 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL D 123 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 215 through 216 removed outlier: 6.159A pdb=" N ILE D 185 " --> pdb=" O ILE D 216 " (cutoff:3.500A) 1950 hydrogen bonds defined for protein. 5763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5867 1.33 - 1.45: 8345 1.45 - 1.58: 18030 1.58 - 1.71: 1 1.71 - 1.84: 382 Bond restraints: 32625 Sorted by residual: bond pdb=" C PRO C1125 " pdb=" N PRO C1126 " ideal model delta sigma weight residual 1.335 1.429 -0.095 1.19e-02 7.06e+03 6.33e+01 bond pdb=" C ILE B 835 " pdb=" N PRO B 836 " ideal model delta sigma weight residual 1.337 1.411 -0.074 9.80e-03 1.04e+04 5.73e+01 bond pdb=" C PRO B1125 " pdb=" N PRO B1126 " ideal model delta sigma weight residual 1.335 1.420 -0.085 1.19e-02 7.06e+03 5.09e+01 bond pdb=" C ILE C 835 " pdb=" N PRO C 836 " ideal model delta sigma weight residual 1.334 1.393 -0.059 8.40e-03 1.42e+04 4.94e+01 bond pdb=" C PRO D 761 " pdb=" N PRO D 762 " ideal model delta sigma weight residual 1.337 1.394 -0.057 9.80e-03 1.04e+04 3.40e+01 ... (remaining 32620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 41672 2.56 - 5.12: 2260 5.12 - 7.68: 379 7.68 - 10.23: 87 10.23 - 12.79: 14 Bond angle restraints: 44412 Sorted by residual: angle pdb=" C ASN B1080 " pdb=" N ILE B1081 " pdb=" CA ILE B1081 " ideal model delta sigma weight residual 122.97 116.12 6.85 9.80e-01 1.04e+00 4.88e+01 angle pdb=" C ILE B1067 " pdb=" N VAL B1068 " pdb=" CA VAL B1068 " ideal model delta sigma weight residual 120.24 124.45 -4.21 6.30e-01 2.52e+00 4.46e+01 angle pdb=" C PRO D 102 " pdb=" N THR D 103 " pdb=" CA THR D 103 " ideal model delta sigma weight residual 122.61 132.71 -10.10 1.56e+00 4.11e-01 4.20e+01 angle pdb=" C HIS A 723 " pdb=" N ARG A 724 " pdb=" CA ARG A 724 " ideal model delta sigma weight residual 120.54 129.06 -8.52 1.35e+00 5.49e-01 3.98e+01 angle pdb=" C GLU D1174 " pdb=" N GLU D1175 " pdb=" CA GLU D1175 " ideal model delta sigma weight residual 120.31 111.77 8.54 1.52e+00 4.33e-01 3.16e+01 ... (remaining 44407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 18191 17.81 - 35.63: 1345 35.63 - 53.44: 263 53.44 - 71.26: 88 71.26 - 89.07: 26 Dihedral angle restraints: 19913 sinusoidal: 7919 harmonic: 11994 Sorted by residual: dihedral pdb=" CA MET C 121 " pdb=" C MET C 121 " pdb=" N TYR C 122 " pdb=" CA TYR C 122 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LEU A1009 " pdb=" C LEU A1009 " pdb=" N PHE A1010 " pdb=" CA PHE A1010 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ILE B1101 " pdb=" C ILE B1101 " pdb=" N SER B1102 " pdb=" CA SER B1102 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 19910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 4852 0.127 - 0.253: 284 0.253 - 0.380: 18 0.380 - 0.507: 0 0.507 - 0.634: 1 Chirality restraints: 5155 Sorted by residual: chirality pdb=" CB ILE D 45 " pdb=" CA ILE D 45 " pdb=" CG1 ILE D 45 " pdb=" CG2 ILE D 45 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA GLU D1175 " pdb=" N GLU D1175 " pdb=" C GLU D1175 " pdb=" CB GLU D1175 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB VAL C1068 " pdb=" CA VAL C1068 " pdb=" CG1 VAL C1068 " pdb=" CG2 VAL C1068 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 5152 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 854 " -0.056 2.00e-02 2.50e+03 4.91e-02 4.23e+01 pdb=" CG PHE C 854 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE C 854 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 854 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 854 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 854 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE C 854 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 854 " -0.044 2.00e-02 2.50e+03 3.96e-02 2.74e+01 pdb=" CG PHE B 854 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE B 854 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 854 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 854 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 854 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE B 854 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 761 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO A 762 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO A 762 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 762 " 0.069 5.00e-02 4.00e+02 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 11147 2.90 - 3.40: 34518 3.40 - 3.90: 53152 3.90 - 4.40: 59831 4.40 - 4.90: 96011 Nonbonded interactions: 254659 Sorted by model distance: nonbonded pdb=" O THR B 554 " pdb=" OG1 THR B 554 " model vdw 2.402 3.040 nonbonded pdb=" O MET C 699 " pdb=" OG1 THR C 703 " model vdw 2.472 3.040 nonbonded pdb=" O LEU A1158 " pdb=" C LYS A1159 " model vdw 2.485 3.270 nonbonded pdb=" O GLY A 296 " pdb=" C VAL A 297 " model vdw 2.514 3.270 nonbonded pdb=" N ASP D 229 " pdb=" OD1 ASP D 229 " model vdw 2.523 3.120 ... (remaining 254654 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 30 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 64 or resid 96 through 133 or (res \ id 134 and (name N or name CA or name C or name O or name CB )) or resid 135 thr \ ough 156 or (resid 157 through 158 and (name N or name CA or name C or name O or \ name CB )) or resid 159 through 203 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB )) or resid 205 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 276 or (resid 2 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 278 through \ 289 or resid 297 through 405 or (resid 406 and (name N or name CA or name C or \ name O or name CB )) or resid 407 through 434 or (resid 435 and (name N or name \ CA or name C or name O or name CB )) or resid 436 through 443 or (resid 444 and \ (name N or name CA or name C or name O or name CB )) or resid 445 through 446 or \ (resid 447 through 448 and (name N or name CA or name C or name O or name CB )) \ or resid 449 through 473 or (resid 474 and (name N or name CA or name C or name \ O or name CB )) or resid 475 through 480 or (resid 481 and (name N or name CA o \ r name C or name O or name CB )) or resid 482 through 489 or (resid 490 and (nam \ e N or name CA or name C or name O or name CB )) or resid 491 through 494 or (re \ sid 495 and (name N or name CA or name C or name O or name CB )) or resid 496 th \ rough 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) \ or resid 501 through 511 or (resid 512 through 513 and (name N or name CA or na \ me C or name O or name CB )) or resid 528 through 530 or (resid 531 and (name N \ or name CA or name C or name O or name CB )) or resid 532 through 535 or (resid \ 536 and (name N or name CA or name C or name O or name CB )) or resid 537 throug \ h 554 or (resid 555 through 557 and (name N or name CA or name C or name O or na \ me CB )) or resid 558 through 562 or (resid 563 through 608 and (name N or name \ CA or name C or name O or name CB )) or resid 609 through 628 or (resid 629 and \ (name N or name CA or name C or name O or name CB )) or resid 630 through 660 or \ (resid 661 and (name N or name CA or name C or name O or name CB )) or resid 66 \ 2 through 664 or (resid 665 through 667 and (name N or name CA or name C or name \ O or name CB )) or resid 668 through 743 or (resid 744 and (name N or name CA o \ r name C or name O or name CB )) or resid 745 through 746 or (resid 747 through \ 748 and (name N or name CA or name C or name O or name CB )) or resid 749 throug \ h 759 or (resid 760 and (name N or name CA or name C or name O or name CB )) or \ resid 761 through 767 or (resid 768 and (name N or name CA or name C or name O o \ r name CB )) or resid 769 through 770 or (resid 771 through 835 and (name N or n \ ame CA or name C or name O or name CB )) or resid 836 or (resid 837 and (name N \ or name CA or name C or name O or name CB )) or resid 838 or (resid 839 and (nam \ e N or name CA or name C or name O or name CB )) or resid 840 through 842 or (re \ sid 843 and (name N or name CA or name C or name O or name CB )) or resid 844 th \ rough 903 or (resid 904 and (name N or name CA or name C or name O or name CB )) \ or resid 905 through 917 or (resid 918 and (name N or name CA or name C or name \ O or name CB )) or resid 919 through 970 or (resid 971 and (name N or name CA o \ r name C or name O or name CB )) or resid 972 through 1017 or (resid 1018 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1019 through 1108 or \ (resid 1109 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 110 through 1111 or (resid 1112 and (name N or name CA or name C or name O or na \ me CB )) or resid 1113 through 1118 or (resid 1119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1120 through 1167 or (resid 1168 and (name \ N or name CA or name C or name O or name CB )) or resid 1169 through 1194 or (re \ sid 1195 and (name N or name CA or name C or name O or name CB )) or resid 1196 \ through 1211 or (resid 1212 through 1213 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1214 through 1216 or (resid 1217 through 1232 and (na \ me N or name CA or name C or name O or name CB )) or resid 1401 through 1403)) selection = (chain 'B' and (resid 30 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 64 or resid 96 through 133 or (res \ id 134 and (name N or name CA or name C or name O or name CB )) or resid 135 thr \ ough 156 or (resid 157 through 158 and (name N or name CA or name C or name O or \ name CB )) or resid 159 through 203 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB )) or resid 205 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 276 or (resid 2 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 278 through \ 289 or resid 297 through 356 or (resid 357 and (name N or name CA or name C or \ name O or name CB )) or resid 358 through 405 or (resid 406 and (name N or name \ CA or name C or name O or name CB )) or resid 407 through 434 or (resid 435 and \ (name N or name CA or name C or name O or name CB )) or resid 436 through 443 or \ (resid 444 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 5 through 446 or (resid 447 through 448 and (name N or name CA or name C or name \ O or name CB )) or resid 449 through 473 or (resid 474 and (name N or name CA o \ r name C or name O or name CB )) or resid 475 through 480 or (resid 481 and (nam \ e N or name CA or name C or name O or name CB )) or resid 482 through 489 or (re \ sid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 th \ rough 494 or (resid 495 and (name N or name CA or name C or name O or name CB )) \ or resid 496 through 499 or (resid 500 and (name N or name CA or name C or name \ O or name CB )) or resid 501 through 511 or (resid 512 through 513 and (name N \ or name CA or name C or name O or name CB )) or resid 528 through 530 or (resid \ 531 and (name N or name CA or name C or name O or name CB )) or resid 532 throug \ h 535 or (resid 536 and (name N or name CA or name C or name O or name CB )) or \ resid 537 through 556 or (resid 557 and (name N or name CA or name C or name O o \ r name CB )) or resid 558 or (resid 559 and (name N or name CA or name C or name \ O or name CB )) or resid 560 through 562 or (resid 563 through 608 and (name N \ or name CA or name C or name O or name CB )) or resid 609 through 628 or (resid \ 629 and (name N or name CA or name C or name O or name CB )) or resid 630 throug \ h 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) or \ resid 662 through 663 or (resid 664 through 667 and (name N or name CA or name C \ or name O or name CB )) or resid 668 through 742 or (resid 743 through 744 and \ (name N or name CA or name C or name O or name CB )) or resid 745 through 746 or \ (resid 747 through 748 and (name N or name CA or name C or name O or name CB )) \ or resid 749 through 759 or (resid 760 and (name N or name CA or name C or name \ O or name CB )) or resid 761 through 767 or (resid 768 and (name N or name CA o \ r name C or name O or name CB )) or resid 769 through 770 or (resid 771 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 835 and (name N or na \ me CA or name C or name O or name CB )) or resid 836 or (resid 837 and (name N o \ r name CA or name C or name O or name CB )) or resid 838 or (resid 839 and (name \ N or name CA or name C or name O or name CB )) or resid 840 through 842 or (res \ id 843 and (name N or name CA or name C or name O or name CB )) or resid 844 thr \ ough 903 or (resid 904 and (name N or name CA or name C or name O or name CB )) \ or resid 905 through 917 or (resid 918 and (name N or name CA or name C or name \ O or name CB )) or resid 919 through 970 or (resid 971 and (name N or name CA or \ name C or name O or name CB )) or resid 972 through 1017 or (resid 1018 and (na \ me N or name CA or name C or name O or name CB )) or resid 1019 through 1108 or \ (resid 1109 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 10 through 1111 or (resid 1112 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1113 through 1118 or (resid 1119 and (name N or name CA or name \ C or name O or name CB )) or resid 1120 through 1167 or (resid 1168 and (name N \ or name CA or name C or name O or name CB )) or resid 1169 through 1194 or (res \ id 1195 and (name N or name CA or name C or name O or name CB )) or resid 1196 t \ hrough 1211 or (resid 1212 through 1213 and (name N or name CA or name C or name \ O or name CB )) or resid 1214 through 1216 or (resid 1217 through 1232 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1401 through 1403)) selection = (chain 'C' and (resid 30 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 64 or resid 96 through 133 or (res \ id 134 and (name N or name CA or name C or name O or name CB )) or resid 135 thr \ ough 156 or (resid 157 through 158 and (name N or name CA or name C or name O or \ name CB )) or resid 159 through 203 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB )) or resid 205 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 276 or (resid 2 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 278 through \ 289 or resid 297 through 356 or (resid 357 and (name N or name CA or name C or \ name O or name CB )) or resid 358 through 405 or (resid 406 and (name N or name \ CA or name C or name O or name CB )) or resid 407 through 434 or (resid 435 and \ (name N or name CA or name C or name O or name CB )) or resid 436 through 443 or \ (resid 444 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 5 through 446 or (resid 447 through 448 and (name N or name CA or name C or name \ O or name CB )) or resid 449 through 473 or (resid 474 and (name N or name CA o \ r name C or name O or name CB )) or resid 475 through 480 or (resid 481 and (nam \ e N or name CA or name C or name O or name CB )) or resid 482 through 489 or (re \ sid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 th \ rough 494 or (resid 495 and (name N or name CA or name C or name O or name CB )) \ or resid 496 through 499 or (resid 500 and (name N or name CA or name C or name \ O or name CB )) or resid 501 through 511 or (resid 512 through 513 and (name N \ or name CA or name C or name O or name CB )) or resid 528 through 530 or (resid \ 531 and (name N or name CA or name C or name O or name CB )) or resid 532 throug \ h 535 or (resid 536 and (name N or name CA or name C or name O or name CB )) or \ resid 537 through 554 or (resid 555 through 557 and (name N or name CA or name C \ or name O or name CB )) or resid 558 or (resid 559 and (name N or name CA or na \ me C or name O or name CB )) or resid 560 through 562 or (resid 563 through 608 \ and (name N or name CA or name C or name O or name CB )) or resid 609 through 62 \ 8 or (resid 629 and (name N or name CA or name C or name O or name CB )) or resi \ d 630 through 660 or (resid 661 and (name N or name CA or name C or name O or na \ me CB )) or resid 662 through 663 or (resid 664 through 667 and (name N or name \ CA or name C or name O or name CB )) or resid 668 through 746 or (resid 747 thro \ ugh 748 and (name N or name CA or name C or name O or name CB )) or resid 749 th \ rough 759 or (resid 760 and (name N or name CA or name C or name O or name CB )) \ or resid 761 through 767 or (resid 768 and (name N or name CA or name C or name \ O or name CB )) or resid 769 through 770 or (resid 771 and (name N or name CA o \ r name C or name O or name CB )) or (resid 835 and (name N or name CA or name C \ or name O or name CB )) or resid 836 or (resid 837 and (name N or name CA or nam \ e C or name O or name CB )) or resid 838 or (resid 839 and (name N or name CA or \ name C or name O or name CB )) or resid 840 through 842 or (resid 843 and (name \ N or name CA or name C or name O or name CB )) or resid 844 through 903 or (res \ id 904 and (name N or name CA or name C or name O or name CB )) or resid 905 thr \ ough 917 or (resid 918 and (name N or name CA or name C or name O or name CB )) \ or resid 919 through 1017 or (resid 1018 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1019 through 1108 or (resid 1109 and (name N or name \ CA or name C or name O or name CB )) or resid 1110 through 1111 or (resid 1112 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1113 through 11 \ 18 or (resid 1119 and (name N or name CA or name C or name O or name CB )) or re \ sid 1120 through 1167 or (resid 1168 and (name N or name CA or name C or name O \ or name CB )) or resid 1169 through 1194 or (resid 1195 and (name N or name CA o \ r name C or name O or name CB )) or resid 1196 through 1211 or (resid 1212 throu \ gh 1213 and (name N or name CA or name C or name O or name CB )) or resid 1214 t \ hrough 1216 or (resid 1217 through 1232 and (name N or name CA or name C or name \ O or name CB )) or resid 1401 through 1403)) selection = (chain 'D' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 137 or (resid 138 and (name N or name CA or n \ ame C or name O or name CB )) or resid 139 through 207 or resid 213 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 342 or (resid 343 and (name N or name CA or name C o \ r name O or name CB )) or resid 344 through 356 or (resid 357 and (name N or nam \ e CA or name C or name O or name CB )) or resid 358 through 369 or (resid 370 an \ d (name N or name CA or name C or name O or name CB )) or resid 371 through 385 \ or (resid 386 through 387 and (name N or name CA or name C or name O or name CB \ )) or resid 388 through 398 or resid 403 or (resid 404 and (name N or name CA or \ name C or name O or name CB )) or resid 405 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 419 or (res \ id 420 through 421 and (name N or name CA or name C or name O or name CB )) or r \ esid 422 through 451 or (resid 452 and (name N or name CA or name C or name O or \ name CB )) or resid 453 through 488 or (resid 489 through 490 and (name N or na \ me CA or name C or name O or name CB )) or resid 491 through 498 or (resid 499 t \ hrough 500 and (name N or name CA or name C or name O or name CB )) or resid 501 \ through 509 or (resid 510 through 513 and (name N or name CA or name C or name \ O or name CB )) or resid 528 through 529 or (resid 530 through 531 and (name N o \ r name CA or name C or name O or name CB )) or resid 532 through 554 or (resid 5 \ 55 through 557 and (name N or name CA or name C or name O or name CB )) or resid \ 558 or (resid 559 and (name N or name CA or name C or name O or name CB )) or r \ esid 560 through 742 or (resid 743 through 744 and (name N or name CA or name C \ or name O or name CB )) or resid 745 or (resid 746 through 748 and (name N or na \ me CA or name C or name O or name CB )) or resid 749 through 771 or resid 835 th \ rough 934 or (resid 935 and (name N or name CA or name C or name O or name CB )) \ or resid 936 through 955 or (resid 956 and (name N or name CA or name C or name \ O or name CB )) or resid 957 through 970 or (resid 971 and (name N or name CA o \ r name C or name O or name CB )) or resid 972 through 1061 or (resid 1062 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1063 through 1132 or \ (resid 1133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 134 through 1138 or (resid 1139 and (name N or name CA or name C or name O or na \ me CB )) or resid 1140 through 1201 or (resid 1202 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1203 through 1403)) } 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 group one per residue 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: 6.170 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: 0.070 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.070 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.007 0.095 32629 Z= 0.397 Angle : 1.332 12.792 44420 Z= 0.760 Chirality : 0.068 0.634 5155 Planarity : 0.011 0.125 5523 Dihedral : 13.741 89.070 12129 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.33 % Favored : 93.65 % Rotamer: Outliers : 1.83 % Allowed : 1.17 % Favored : 97.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.03 % 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: -2.79 (0.11), residues: 4045 helix: -1.38 (0.09), residues: 2584 sheet: -1.46 (0.32), residues: 224 loop : -2.64 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 745 TYR 0.058 0.003 TYR B1181 PHE 0.111 0.004 PHE C 854 TRP 0.076 0.003 TRP A1017 HIS 0.039 0.003 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00698 (32625) covalent geometry : angle 1.33230 (44412) SS BOND : bond 0.00216 ( 4) SS BOND : angle 1.61113 ( 8) hydrogen bonds : bond 0.14070 ( 1950) hydrogen bonds : angle 7.04130 ( 5763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 850 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8499 (mt) cc_final: 0.8287 (mt) REVERT: A 175 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8271 (tp) REVERT: A 242 MET cc_start: 0.5353 (tpp) cc_final: 0.5004 (tpt) REVERT: A 270 TYR cc_start: 0.7900 (m-80) cc_final: 0.7472 (m-10) REVERT: A 304 VAL cc_start: 0.8909 (t) cc_final: 0.8579 (t) REVERT: A 329 CYS cc_start: 0.8185 (m) cc_final: 0.7591 (t) REVERT: A 471 LEU cc_start: 0.9393 (tp) cc_final: 0.9172 (tp) REVERT: A 681 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8548 (tp-100) REVERT: A 685 GLU cc_start: 0.8791 (mp0) cc_final: 0.8488 (mp0) REVERT: A 741 MET cc_start: 0.9279 (mmt) cc_final: 0.8945 (mmm) REVERT: A 864 MET cc_start: 0.8973 (mtm) cc_final: 0.8751 (mmp) REVERT: A 987 MET cc_start: 0.8800 (tpp) cc_final: 0.8510 (tmm) REVERT: A 1115 MET cc_start: 0.8868 (mmp) cc_final: 0.8587 (tpp) REVERT: A 1184 GLU cc_start: 0.8990 (tp30) cc_final: 0.8750 (tp30) REVERT: C 150 LEU cc_start: 0.9145 (tp) cc_final: 0.8873 (mm) REVERT: C 179 MET cc_start: 0.8818 (mmp) cc_final: 0.8555 (mtp) REVERT: C 242 MET cc_start: 0.8599 (ppp) cc_final: 0.8123 (ppp) REVERT: C 280 LEU cc_start: 0.9300 (mt) cc_final: 0.9029 (pp) REVERT: C 326 VAL cc_start: 0.9463 (p) cc_final: 0.9251 (t) REVERT: C 470 LYS cc_start: 0.9366 (tptp) cc_final: 0.9164 (tptp) REVERT: C 661 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8419 (tm-30) REVERT: C 673 ASN cc_start: 0.9294 (t0) cc_final: 0.9083 (t0) REVERT: C 681 GLN cc_start: 0.9022 (tp40) cc_final: 0.8455 (tp40) REVERT: C 685 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8368 (mt-10) REVERT: C 687 LEU cc_start: 0.9718 (tp) cc_final: 0.9473 (tt) REVERT: C 979 MET cc_start: 0.8884 (mpp) cc_final: 0.8668 (mmt) REVERT: C 999 MET cc_start: 0.8886 (ttp) cc_final: 0.8659 (tmm) REVERT: C 1075 TYR cc_start: 0.8730 (t80) cc_final: 0.8520 (t80) REVERT: C 1135 MET cc_start: 0.7822 (tmm) cc_final: 0.7438 (ttm) REVERT: C 1180 GLU cc_start: 0.8786 (tp30) cc_final: 0.8339 (tm-30) REVERT: C 1205 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 127 PHE cc_start: 0.8125 (p90) cc_final: 0.7398 (p90) REVERT: B 142 TRP cc_start: 0.8368 (m-10) cc_final: 0.8032 (m100) REVERT: B 170 PHE cc_start: 0.9196 (t80) cc_final: 0.8883 (t80) REVERT: B 179 MET cc_start: 0.8971 (mmm) cc_final: 0.8550 (mmt) REVERT: B 457 MET cc_start: 0.9214 (tpt) cc_final: 0.8967 (tpp) REVERT: B 490 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8712 (tp30) REVERT: B 722 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8781 (tptm) REVERT: B 747 ARG cc_start: 0.8405 (mpt180) cc_final: 0.7989 (ptt90) REVERT: B 979 MET cc_start: 0.8929 (mpp) cc_final: 0.8665 (mmp) REVERT: B 1032 TYR cc_start: 0.8670 (m-80) cc_final: 0.8253 (m-80) REVERT: B 1096 PHE cc_start: 0.7597 (m-80) cc_final: 0.7316 (m-10) REVERT: B 1168 LYS cc_start: 0.9449 (tptp) cc_final: 0.8553 (tppt) REVERT: D 121 MET cc_start: 0.8004 (mtp) cc_final: 0.7728 (ttm) REVERT: D 149 LEU cc_start: 0.9354 (tp) cc_final: 0.9153 (tt) REVERT: D 410 LEU cc_start: 0.9176 (mt) cc_final: 0.8968 (mm) REVERT: D 431 TRP cc_start: 0.8181 (m-10) cc_final: 0.7889 (m-10) REVERT: D 545 MET cc_start: 0.8553 (tpp) cc_final: 0.8149 (tpp) REVERT: D 699 MET cc_start: 0.9110 (mmm) cc_final: 0.8693 (mmm) REVERT: D 956 ILE cc_start: 0.9215 (tt) cc_final: 0.8910 (tt) REVERT: D 960 TYR cc_start: 0.8023 (m-80) cc_final: 0.6934 (m-10) outliers start: 58 outliers final: 11 residues processed: 886 average time/residue: 0.2111 time to fit residues: 301.6874 Evaluate side-chains 544 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 531 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 706 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 GLN A 480 HIS A 637 HIS A 657 HIS A1092 ASN A1112 GLN A1219 HIS C 475 ASN ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1176 GLN B 197 HIS B 480 HIS ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS D 63 HIS D 136 HIS D 197 HIS D 279 GLN D 343 HIS D 636 GLN D1080 ASN D1092 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.078298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.060335 restraints weight = 142684.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.062298 restraints weight = 73759.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063602 restraints weight = 47266.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.064442 restraints weight = 34724.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.065022 restraints weight = 28174.807| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32629 Z= 0.154 Angle : 0.734 16.559 44420 Z= 0.372 Chirality : 0.043 0.307 5155 Planarity : 0.006 0.098 5523 Dihedral : 8.094 78.473 5266 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 2.37 % Allowed : 10.03 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 (0.13), residues: 4045 helix: -0.09 (0.10), residues: 2611 sheet: -0.89 (0.35), residues: 203 loop : -2.36 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 724 TYR 0.025 0.002 TYR D 958 PHE 0.054 0.002 PHE D 854 TRP 0.038 0.002 TRP A1017 HIS 0.025 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00321 (32625) covalent geometry : angle 0.73415 (44412) SS BOND : bond 0.00463 ( 4) SS BOND : angle 0.54950 ( 8) hydrogen bonds : bond 0.05137 ( 1950) hydrogen bonds : angle 5.14911 ( 5763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 575 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8513 (mt) cc_final: 0.8310 (mt) REVERT: A 175 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8784 (tp) REVERT: A 179 MET cc_start: 0.8761 (mmm) cc_final: 0.8241 (mmm) REVERT: A 270 TYR cc_start: 0.7991 (m-80) cc_final: 0.7595 (m-10) REVERT: A 566 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: A 681 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8104 (tp-100) REVERT: A 978 MET cc_start: 0.8855 (mmm) cc_final: 0.8537 (mmm) REVERT: A 987 MET cc_start: 0.8804 (tpp) cc_final: 0.8517 (tmm) REVERT: A 999 MET cc_start: 0.8679 (mmm) cc_final: 0.8338 (mmm) REVERT: A 1030 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8572 (mmm) REVERT: A 1115 MET cc_start: 0.8793 (mmp) cc_final: 0.8499 (tpp) REVERT: A 1160 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8720 (tt) REVERT: A 1184 GLU cc_start: 0.8988 (tp30) cc_final: 0.8685 (tp30) REVERT: A 1194 ASP cc_start: 0.8007 (p0) cc_final: 0.7629 (p0) REVERT: C 104 ASP cc_start: 0.8047 (p0) cc_final: 0.7724 (m-30) REVERT: C 150 LEU cc_start: 0.9098 (tp) cc_final: 0.8838 (mm) REVERT: C 174 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9358 (mm) REVERT: C 470 LYS cc_start: 0.9445 (tptp) cc_final: 0.9209 (tptp) REVERT: C 483 LEU cc_start: 0.9195 (mm) cc_final: 0.8907 (mm) REVERT: C 628 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 681 GLN cc_start: 0.9043 (tp40) cc_final: 0.8467 (tp40) REVERT: C 685 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8366 (mt-10) REVERT: C 734 MET cc_start: 0.8914 (ttp) cc_final: 0.8696 (ptm) REVERT: C 863 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8900 (mp) REVERT: C 864 MET cc_start: 0.8956 (mmm) cc_final: 0.8712 (mmt) REVERT: C 902 MET cc_start: 0.8867 (tpp) cc_final: 0.8650 (mmm) REVERT: C 962 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.8036 (mmm-85) REVERT: C 979 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8371 (mpp) REVERT: C 1030 MET cc_start: 0.9529 (mtp) cc_final: 0.9262 (mtp) REVERT: C 1075 TYR cc_start: 0.8927 (t80) cc_final: 0.8639 (t80) REVERT: C 1115 MET cc_start: 0.8806 (tpp) cc_final: 0.8532 (tpp) REVERT: C 1119 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 127 PHE cc_start: 0.7995 (p90) cc_final: 0.7292 (p90) REVERT: B 179 MET cc_start: 0.9046 (mmm) cc_final: 0.8634 (mmp) REVERT: B 255 MET cc_start: 0.8300 (pmm) cc_final: 0.7922 (ptm) REVERT: B 457 MET cc_start: 0.9269 (tpt) cc_final: 0.8864 (tpp) REVERT: B 458 LEU cc_start: 0.9539 (tt) cc_final: 0.9199 (mt) REVERT: B 492 TYR cc_start: 0.8589 (m-80) cc_final: 0.8280 (m-80) REVERT: B 563 HIS cc_start: 0.8660 (t70) cc_final: 0.8307 (t-90) REVERT: B 566 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: B 655 MET cc_start: 0.8900 (mpp) cc_final: 0.8579 (mpp) REVERT: B 681 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8472 (tp-100) REVERT: B 685 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 722 LYS cc_start: 0.9239 (mtpp) cc_final: 0.8953 (tptm) REVERT: B 932 SER cc_start: 0.9139 (m) cc_final: 0.8817 (p) REVERT: B 984 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7645 (ttt) REVERT: B 1032 TYR cc_start: 0.8794 (m-80) cc_final: 0.8586 (m-80) REVERT: B 1096 PHE cc_start: 0.7663 (m-80) cc_final: 0.7462 (m-10) REVERT: B 1168 LYS cc_start: 0.9160 (tptp) cc_final: 0.8863 (tppt) REVERT: D 681 GLN cc_start: 0.9298 (tp-100) cc_final: 0.8789 (tp-100) REVERT: D 685 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 1202 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8064 (tm-30) outliers start: 75 outliers final: 41 residues processed: 620 average time/residue: 0.1877 time to fit residues: 195.6442 Evaluate side-chains 527 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 476 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1219 HIS Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 984 MET Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1185 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 707 LYS Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 995 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 251 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 186 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 366 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 716 GLN A1092 ASN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 ASN ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS B 867 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.076319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.058442 restraints weight = 145698.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060317 restraints weight = 75900.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061563 restraints weight = 48908.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.062391 restraints weight = 36200.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.062937 restraints weight = 29431.002| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32629 Z= 0.166 Angle : 0.682 14.873 44420 Z= 0.348 Chirality : 0.042 0.263 5155 Planarity : 0.005 0.102 5523 Dihedral : 7.528 74.958 5258 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 2.74 % Allowed : 12.71 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: -0.65 (0.13), residues: 4045 helix: 0.45 (0.10), residues: 2628 sheet: -1.04 (0.31), residues: 253 loop : -2.24 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 39 TYR 0.022 0.001 TYR D 958 PHE 0.048 0.002 PHE A 854 TRP 0.038 0.002 TRP A 915 HIS 0.011 0.001 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00360 (32625) covalent geometry : angle 0.68190 (44412) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.53396 ( 8) hydrogen bonds : bond 0.04745 ( 1950) hydrogen bonds : angle 4.86482 ( 5763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 492 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8785 (mm) cc_final: 0.8383 (mm) REVERT: A 175 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8624 (tp) REVERT: A 179 MET cc_start: 0.8807 (mmm) cc_final: 0.8314 (mmm) REVERT: A 270 TYR cc_start: 0.7982 (m-80) cc_final: 0.7669 (m-10) REVERT: A 681 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8351 (tp-100) REVERT: A 979 MET cc_start: 0.8986 (mmm) cc_final: 0.8680 (mpp) REVERT: A 987 MET cc_start: 0.8798 (tpp) cc_final: 0.8536 (tmm) REVERT: A 1115 MET cc_start: 0.8746 (mmp) cc_final: 0.8447 (tpp) REVERT: A 1165 ASP cc_start: 0.9343 (p0) cc_final: 0.8921 (p0) REVERT: A 1168 LYS cc_start: 0.9345 (mmmt) cc_final: 0.8926 (mtmm) REVERT: A 1184 GLU cc_start: 0.8995 (tp30) cc_final: 0.8707 (tp30) REVERT: A 1194 ASP cc_start: 0.8102 (p0) cc_final: 0.7717 (p0) REVERT: A 1205 GLU cc_start: 0.8263 (tp30) cc_final: 0.7639 (tp30) REVERT: C 104 ASP cc_start: 0.8052 (p0) cc_final: 0.7781 (m-30) REVERT: C 150 LEU cc_start: 0.9080 (tp) cc_final: 0.8880 (mm) REVERT: C 174 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9433 (mm) REVERT: C 479 MET cc_start: 0.8629 (mmm) cc_final: 0.8312 (mmm) REVERT: C 483 LEU cc_start: 0.9401 (mm) cc_final: 0.8819 (mm) REVERT: C 628 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7879 (tm-30) REVERT: C 681 GLN cc_start: 0.9072 (tp40) cc_final: 0.8546 (tp40) REVERT: C 685 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8335 (mt-10) REVERT: C 741 MET cc_start: 0.9155 (mmt) cc_final: 0.8854 (mmp) REVERT: C 962 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8037 (mmm-85) REVERT: C 1030 MET cc_start: 0.9533 (mtp) cc_final: 0.9227 (mtp) REVERT: C 1075 TYR cc_start: 0.9048 (t80) cc_final: 0.8798 (t80) REVERT: C 1115 MET cc_start: 0.8798 (tpp) cc_final: 0.8588 (tpp) REVERT: C 1119 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 1135 MET cc_start: 0.8165 (tmm) cc_final: 0.7948 (ppp) REVERT: C 1180 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 127 PHE cc_start: 0.7977 (p90) cc_final: 0.7270 (p90) REVERT: B 179 MET cc_start: 0.9057 (mmm) cc_final: 0.8645 (mmp) REVERT: B 457 MET cc_start: 0.9312 (tpt) cc_final: 0.8914 (tpp) REVERT: B 474 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9045 (mm-30) REVERT: B 682 LEU cc_start: 0.9512 (mt) cc_final: 0.9142 (mm) REVERT: B 685 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8363 (mt-10) REVERT: B 722 LYS cc_start: 0.9253 (mtpp) cc_final: 0.8976 (tptm) REVERT: B 932 SER cc_start: 0.9136 (m) cc_final: 0.8814 (p) REVERT: B 979 MET cc_start: 0.8793 (mmt) cc_final: 0.8391 (mmt) REVERT: B 1096 PHE cc_start: 0.7499 (m-80) cc_final: 0.7255 (m-10) REVERT: B 1168 LYS cc_start: 0.9144 (tptp) cc_final: 0.8743 (tppt) REVERT: D 186 PHE cc_start: 0.8690 (m-10) cc_final: 0.8409 (m-80) REVERT: D 642 MET cc_start: 0.9387 (tpt) cc_final: 0.8997 (tpt) REVERT: D 652 CYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8353 (t) REVERT: D 999 MET cc_start: 0.8906 (mtp) cc_final: 0.8351 (ttm) outliers start: 87 outliers final: 50 residues processed: 545 average time/residue: 0.1673 time to fit residues: 155.5089 Evaluate side-chains 504 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 450 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1185 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 707 LYS Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1175 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 86 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 399 optimal weight: 9.9990 chunk 349 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 GLN A1103 ASN A1215 ASN C 493 ASN ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN B 628 GLN B 657 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 ASN D 636 GLN D 917 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.074234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056452 restraints weight = 147188.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058250 restraints weight = 77274.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059447 restraints weight = 50115.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.060242 restraints weight = 37303.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060702 restraints weight = 30489.272| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32629 Z= 0.207 Angle : 0.684 15.106 44420 Z= 0.349 Chirality : 0.042 0.257 5155 Planarity : 0.005 0.099 5523 Dihedral : 7.142 73.217 5251 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 3.37 % Allowed : 14.41 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 (0.13), residues: 4045 helix: 0.69 (0.10), residues: 2625 sheet: -0.81 (0.33), residues: 236 loop : -2.03 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1210 TYR 0.021 0.002 TYR C 958 PHE 0.047 0.002 PHE D 854 TRP 0.048 0.002 TRP D 431 HIS 0.013 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00448 (32625) covalent geometry : angle 0.68410 (44412) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.66751 ( 8) hydrogen bonds : bond 0.04707 ( 1950) hydrogen bonds : angle 4.78339 ( 5763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 456 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8699 (mm) cc_final: 0.8172 (mm) REVERT: A 179 MET cc_start: 0.8853 (mmm) cc_final: 0.8391 (mmm) REVERT: A 255 MET cc_start: 0.7563 (pmm) cc_final: 0.6862 (ptm) REVERT: A 483 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 681 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8346 (tp40) REVERT: A 685 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: A 967 PHE cc_start: 0.8505 (m-10) cc_final: 0.8204 (m-80) REVERT: A 978 MET cc_start: 0.8800 (mmm) cc_final: 0.8450 (mmm) REVERT: A 987 MET cc_start: 0.8798 (tpp) cc_final: 0.8537 (tmm) REVERT: A 1115 MET cc_start: 0.8669 (mmp) cc_final: 0.8392 (tpp) REVERT: A 1165 ASP cc_start: 0.9335 (p0) cc_final: 0.9076 (p0) REVERT: A 1168 LYS cc_start: 0.9454 (mmmt) cc_final: 0.8944 (mtmm) REVERT: A 1194 ASP cc_start: 0.8185 (p0) cc_final: 0.7851 (p0) REVERT: C 104 ASP cc_start: 0.8037 (p0) cc_final: 0.7810 (m-30) REVERT: C 150 LEU cc_start: 0.9106 (tp) cc_final: 0.8887 (mm) REVERT: C 479 MET cc_start: 0.8704 (mmm) cc_final: 0.8479 (mmm) REVERT: C 483 LEU cc_start: 0.9287 (mm) cc_final: 0.8833 (mm) REVERT: C 681 GLN cc_start: 0.9021 (tp40) cc_final: 0.8594 (tp40) REVERT: C 685 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8377 (mt-10) REVERT: C 741 MET cc_start: 0.9184 (mmt) cc_final: 0.8914 (mmp) REVERT: C 856 THR cc_start: 0.9006 (m) cc_final: 0.8795 (p) REVERT: C 962 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7908 (mmm-85) REVERT: C 1030 MET cc_start: 0.9523 (mtp) cc_final: 0.9075 (mtp) REVERT: C 1119 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7899 (tm-30) REVERT: C 1180 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 179 MET cc_start: 0.9063 (mmm) cc_final: 0.8608 (mmp) REVERT: B 474 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9134 (mm-30) REVERT: B 682 LEU cc_start: 0.9539 (mt) cc_final: 0.9156 (mm) REVERT: B 685 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8466 (mt-10) REVERT: B 722 LYS cc_start: 0.9291 (mtpp) cc_final: 0.8994 (tptm) REVERT: B 932 SER cc_start: 0.9088 (m) cc_final: 0.8766 (p) REVERT: B 1096 PHE cc_start: 0.7509 (m-80) cc_final: 0.7271 (m-10) REVERT: B 1168 LYS cc_start: 0.9138 (tptp) cc_final: 0.8761 (tppt) REVERT: B 1209 MET cc_start: 0.8380 (ppp) cc_final: 0.8116 (tmm) REVERT: D 642 MET cc_start: 0.9408 (tpt) cc_final: 0.8932 (tpt) REVERT: D 652 CYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8422 (t) REVERT: D 978 MET cc_start: 0.9231 (mmm) cc_final: 0.9016 (mmm) REVERT: D 979 MET cc_start: 0.8897 (ttm) cc_final: 0.8671 (ttm) REVERT: D 999 MET cc_start: 0.8923 (mtp) cc_final: 0.8413 (ttm) outliers start: 107 outliers final: 74 residues processed: 527 average time/residue: 0.1724 time to fit residues: 155.8390 Evaluate side-chains 505 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 427 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 707 LYS Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 874 MET Chi-restraints excluded: chain D residue 894 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 995 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1080 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 340 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN C 955 ASN ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN B 657 HIS B 733 GLN B 917 GLN B1132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.072398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054677 restraints weight = 149040.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056456 restraints weight = 77840.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057624 restraints weight = 50487.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.058381 restraints weight = 37584.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.058904 restraints weight = 30878.430| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 32629 Z= 0.262 Angle : 0.743 15.076 44420 Z= 0.378 Chirality : 0.043 0.262 5155 Planarity : 0.005 0.101 5523 Dihedral : 7.133 78.057 5247 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.81 % Favored : 94.17 % Rotamer: Outliers : 3.88 % Allowed : 15.67 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: -0.32 (0.13), residues: 4045 helix: 0.68 (0.10), residues: 2611 sheet: -0.96 (0.33), residues: 236 loop : -1.98 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1210 TYR 0.020 0.002 TYR C 958 PHE 0.048 0.002 PHE D 854 TRP 0.025 0.002 TRP D 431 HIS 0.014 0.002 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00564 (32625) covalent geometry : angle 0.74307 (44412) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.77000 ( 8) hydrogen bonds : bond 0.04856 ( 1950) hydrogen bonds : angle 4.90779 ( 5763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 433 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8575 (mm) cc_final: 0.8038 (mm) REVERT: A 179 MET cc_start: 0.8926 (mmm) cc_final: 0.8490 (mmm) REVERT: A 242 MET cc_start: 0.6292 (tpp) cc_final: 0.5936 (tpp) REVERT: A 255 MET cc_start: 0.7556 (pmm) cc_final: 0.7283 (ptm) REVERT: A 967 PHE cc_start: 0.8605 (m-10) cc_final: 0.8249 (m-80) REVERT: A 978 MET cc_start: 0.8789 (mmm) cc_final: 0.8563 (mmm) REVERT: A 979 MET cc_start: 0.8973 (mmm) cc_final: 0.8726 (mpp) REVERT: A 987 MET cc_start: 0.8851 (tpp) cc_final: 0.8562 (tmm) REVERT: A 1115 MET cc_start: 0.8662 (mmp) cc_final: 0.8349 (tpp) REVERT: A 1165 ASP cc_start: 0.9340 (p0) cc_final: 0.9120 (p0) REVERT: A 1168 LYS cc_start: 0.9426 (mmmt) cc_final: 0.8989 (mtmm) REVERT: A 1194 ASP cc_start: 0.8293 (p0) cc_final: 0.8077 (p0) REVERT: C 681 GLN cc_start: 0.9023 (tp40) cc_final: 0.8686 (tp40) REVERT: C 685 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 741 MET cc_start: 0.9158 (mmt) cc_final: 0.8904 (mmp) REVERT: C 856 THR cc_start: 0.9026 (m) cc_final: 0.8792 (p) REVERT: C 869 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8583 (mm) REVERT: C 902 MET cc_start: 0.8915 (mmm) cc_final: 0.8683 (mmt) REVERT: C 962 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.7902 (mmm-85) REVERT: C 1030 MET cc_start: 0.9533 (mtp) cc_final: 0.9293 (mtp) REVERT: C 1119 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 1135 MET cc_start: 0.7921 (ppp) cc_final: 0.7690 (ppp) REVERT: C 1180 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8304 (tm-30) REVERT: B 146 LEU cc_start: 0.8319 (tp) cc_final: 0.7797 (tp) REVERT: B 179 MET cc_start: 0.9042 (mmm) cc_final: 0.8586 (mmp) REVERT: B 255 MET cc_start: 0.8344 (pmm) cc_final: 0.7483 (ptp) REVERT: B 368 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.5919 (m-10) REVERT: B 474 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9168 (mm-30) REVERT: B 682 LEU cc_start: 0.9550 (mt) cc_final: 0.9211 (mm) REVERT: B 685 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8419 (mt-10) REVERT: B 932 SER cc_start: 0.9105 (m) cc_final: 0.8766 (p) REVERT: B 967 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5644 (t80) REVERT: B 979 MET cc_start: 0.8728 (mmm) cc_final: 0.8484 (mpp) REVERT: B 1080 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8630 (m110) REVERT: B 1168 LYS cc_start: 0.9125 (tptp) cc_final: 0.8789 (tppt) REVERT: D 652 CYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8486 (t) REVERT: D 978 MET cc_start: 0.9191 (mmm) cc_final: 0.8943 (mmm) REVERT: D 999 MET cc_start: 0.8936 (mtp) cc_final: 0.8367 (ttm) outliers start: 123 outliers final: 90 residues processed: 525 average time/residue: 0.1640 time to fit residues: 146.2272 Evaluate side-chains 506 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 411 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1017 TRP Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1080 ASN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 707 LYS Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 874 MET Chi-restraints excluded: chain D residue 894 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1080 ASN Chi-restraints excluded: chain D residue 1113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 5 optimal weight: 30.0000 chunk 112 optimal weight: 0.5980 chunk 385 optimal weight: 1.9990 chunk 219 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 361 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS B 675 ASN D 867 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.074122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056310 restraints weight = 145900.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058143 restraints weight = 75742.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059345 restraints weight = 48796.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060131 restraints weight = 36214.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060658 restraints weight = 29716.230| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32629 Z= 0.150 Angle : 0.676 15.163 44420 Z= 0.335 Chirality : 0.041 0.272 5155 Planarity : 0.004 0.099 5523 Dihedral : 6.695 59.918 5244 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 3.06 % Allowed : 16.81 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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 (0.13), residues: 4045 helix: 0.94 (0.10), residues: 2614 sheet: -0.68 (0.33), residues: 235 loop : -1.88 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1188 TYR 0.020 0.001 TYR D 958 PHE 0.042 0.002 PHE D 854 TRP 0.023 0.001 TRP C 621 HIS 0.008 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00327 (32625) covalent geometry : angle 0.67592 (44412) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.54819 ( 8) hydrogen bonds : bond 0.04463 ( 1950) hydrogen bonds : angle 4.63075 ( 5763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 461 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8684 (mm) cc_final: 0.8168 (mm) REVERT: A 179 MET cc_start: 0.8948 (mmm) cc_final: 0.8488 (mmm) REVERT: A 242 MET cc_start: 0.6145 (tpp) cc_final: 0.5891 (tpp) REVERT: A 255 MET cc_start: 0.7491 (pmm) cc_final: 0.7228 (ptm) REVERT: A 483 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8507 (mm) REVERT: A 681 GLN cc_start: 0.9055 (tp40) cc_final: 0.8642 (tp40) REVERT: A 915 TRP cc_start: 0.8692 (t60) cc_final: 0.8434 (t60) REVERT: A 967 PHE cc_start: 0.8530 (m-10) cc_final: 0.8199 (m-80) REVERT: A 978 MET cc_start: 0.8814 (mmm) cc_final: 0.8605 (mmm) REVERT: A 979 MET cc_start: 0.8988 (mmm) cc_final: 0.8717 (mpp) REVERT: A 987 MET cc_start: 0.8786 (tpp) cc_final: 0.8512 (tmm) REVERT: A 1115 MET cc_start: 0.8702 (mmp) cc_final: 0.8358 (tpp) REVERT: A 1165 ASP cc_start: 0.9323 (p0) cc_final: 0.9042 (p0) REVERT: A 1168 LYS cc_start: 0.9363 (mmmt) cc_final: 0.9053 (mtmm) REVERT: A 1194 ASP cc_start: 0.8245 (p0) cc_final: 0.7943 (p0) REVERT: C 681 GLN cc_start: 0.8999 (tp40) cc_final: 0.8680 (tp40) REVERT: C 685 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8371 (mt-10) REVERT: C 854 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8914 (t80) REVERT: C 856 THR cc_start: 0.8970 (m) cc_final: 0.8717 (p) REVERT: C 902 MET cc_start: 0.8838 (mmm) cc_final: 0.8581 (mmt) REVERT: C 962 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: C 1030 MET cc_start: 0.9525 (mtp) cc_final: 0.9260 (mtp) REVERT: C 1072 MET cc_start: 0.8569 (ttm) cc_final: 0.8117 (ttm) REVERT: C 1119 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 1135 MET cc_start: 0.7878 (ppp) cc_final: 0.7654 (ppp) REVERT: C 1180 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 1221 MET cc_start: 0.8246 (mmt) cc_final: 0.7996 (tpp) REVERT: B 179 MET cc_start: 0.9042 (mmm) cc_final: 0.8579 (mmp) REVERT: B 255 MET cc_start: 0.8315 (pmm) cc_final: 0.7273 (ptp) REVERT: B 474 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9149 (mm-30) REVERT: B 492 TYR cc_start: 0.8707 (m-80) cc_final: 0.8241 (m-80) REVERT: B 553 TYR cc_start: 0.7282 (m-10) cc_final: 0.7015 (m-10) REVERT: B 682 LEU cc_start: 0.9522 (mt) cc_final: 0.9090 (mm) REVERT: B 685 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8419 (mt-10) REVERT: B 854 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8927 (t80) REVERT: B 932 SER cc_start: 0.9169 (m) cc_final: 0.8843 (p) REVERT: B 967 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5622 (t80) REVERT: B 987 MET cc_start: 0.9069 (ttp) cc_final: 0.8844 (ttp) REVERT: B 1168 LYS cc_start: 0.9087 (tptp) cc_final: 0.8744 (tppt) REVERT: B 1207 MET cc_start: 0.8599 (mmm) cc_final: 0.8381 (mmm) REVERT: D 106 PHE cc_start: 0.5728 (p90) cc_final: 0.5350 (p90) REVERT: D 149 LEU cc_start: 0.9377 (tp) cc_final: 0.9098 (tp) REVERT: D 287 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: D 457 MET cc_start: 0.8857 (tpp) cc_final: 0.8557 (mmm) REVERT: D 652 CYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8396 (t) REVERT: D 978 MET cc_start: 0.9194 (mmm) cc_final: 0.8932 (mmm) REVERT: D 999 MET cc_start: 0.8814 (mtp) cc_final: 0.8332 (ttm) outliers start: 97 outliers final: 64 residues processed: 530 average time/residue: 0.1635 time to fit residues: 149.0161 Evaluate side-chains 506 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 436 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 874 MET Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1080 ASN Chi-restraints excluded: chain D residue 1091 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 276 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 293 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 335 optimal weight: 0.0370 chunk 217 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.074343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056627 restraints weight = 145377.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.058460 restraints weight = 75228.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.059661 restraints weight = 48330.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060457 restraints weight = 35677.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.060987 restraints weight = 29069.789| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32629 Z= 0.147 Angle : 0.683 15.469 44420 Z= 0.335 Chirality : 0.042 0.267 5155 Planarity : 0.004 0.097 5523 Dihedral : 6.486 59.819 5242 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.61 % Favored : 94.36 % Rotamer: Outliers : 2.90 % Allowed : 17.66 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.13 (0.13), residues: 4045 helix: 1.02 (0.10), residues: 2617 sheet: -0.57 (0.34), residues: 230 loop : -1.85 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1210 TYR 0.018 0.001 TYR C 958 PHE 0.038 0.001 PHE D 854 TRP 0.022 0.001 TRP C 621 HIS 0.007 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00323 (32625) covalent geometry : angle 0.68326 (44412) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.50535 ( 8) hydrogen bonds : bond 0.04342 ( 1950) hydrogen bonds : angle 4.57749 ( 5763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 452 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8685 (mm) cc_final: 0.8192 (mm) REVERT: A 179 MET cc_start: 0.8941 (mmm) cc_final: 0.8491 (mmm) REVERT: A 242 MET cc_start: 0.6086 (tpp) cc_final: 0.5835 (tpp) REVERT: A 255 MET cc_start: 0.7520 (pmm) cc_final: 0.7055 (ptm) REVERT: A 681 GLN cc_start: 0.9044 (tp40) cc_final: 0.8650 (tp40) REVERT: A 915 TRP cc_start: 0.8702 (t60) cc_final: 0.8498 (t60) REVERT: A 967 PHE cc_start: 0.8517 (m-10) cc_final: 0.8197 (m-80) REVERT: A 983 MET cc_start: 0.9241 (mmm) cc_final: 0.8922 (mmm) REVERT: A 987 MET cc_start: 0.8791 (tpp) cc_final: 0.8506 (tmm) REVERT: A 1115 MET cc_start: 0.8678 (mmp) cc_final: 0.8329 (tpp) REVERT: A 1194 ASP cc_start: 0.8236 (p0) cc_final: 0.7926 (p0) REVERT: C 175 ILE cc_start: 0.8208 (pt) cc_final: 0.7749 (pt) REVERT: C 681 GLN cc_start: 0.9003 (tp40) cc_final: 0.8687 (tp40) REVERT: C 685 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8368 (mt-10) REVERT: C 902 MET cc_start: 0.8848 (mmm) cc_final: 0.8589 (mmt) REVERT: C 962 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.7911 (mmm-85) REVERT: C 1030 MET cc_start: 0.9538 (mtp) cc_final: 0.9261 (mtp) REVERT: C 1072 MET cc_start: 0.8554 (ttm) cc_final: 0.8080 (ttm) REVERT: C 1119 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 1135 MET cc_start: 0.7929 (ppp) cc_final: 0.7683 (ppp) REVERT: C 1180 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8245 (tm-30) REVERT: C 1212 GLU cc_start: 0.8994 (tp30) cc_final: 0.8752 (mm-30) REVERT: B 179 MET cc_start: 0.9057 (mmm) cc_final: 0.8596 (mmp) REVERT: B 474 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9140 (mm-30) REVERT: B 553 TYR cc_start: 0.7258 (m-10) cc_final: 0.6964 (m-80) REVERT: B 682 LEU cc_start: 0.9509 (mt) cc_final: 0.9057 (mm) REVERT: B 734 MET cc_start: 0.8779 (ptm) cc_final: 0.8544 (ppp) REVERT: B 854 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8902 (t80) REVERT: B 932 SER cc_start: 0.9164 (m) cc_final: 0.8829 (p) REVERT: B 967 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5553 (t80) REVERT: B 979 MET cc_start: 0.8732 (mmm) cc_final: 0.8488 (mpp) REVERT: B 1030 MET cc_start: 0.9284 (mtt) cc_final: 0.9051 (mtp) REVERT: B 1080 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8587 (m110) REVERT: B 1168 LYS cc_start: 0.9068 (tptp) cc_final: 0.8717 (tppt) REVERT: D 106 PHE cc_start: 0.5564 (p90) cc_final: 0.5229 (p90) REVERT: D 149 LEU cc_start: 0.9383 (tp) cc_final: 0.9102 (tp) REVERT: D 652 CYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8372 (t) REVERT: D 739 MET cc_start: 0.8794 (tpt) cc_final: 0.8556 (tpp) REVERT: D 978 MET cc_start: 0.9146 (mmm) cc_final: 0.8943 (mmm) REVERT: D 999 MET cc_start: 0.8806 (mtp) cc_final: 0.8399 (ttm) outliers start: 92 outliers final: 65 residues processed: 518 average time/residue: 0.1588 time to fit residues: 140.9722 Evaluate side-chains 499 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 430 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 970 ASN Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1080 ASN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 874 MET Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1000 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 388 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 345 optimal weight: 4.9990 chunk 148 optimal weight: 0.0270 chunk 175 optimal weight: 9.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.073557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055793 restraints weight = 147224.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057596 restraints weight = 77113.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058782 restraints weight = 49868.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.059550 restraints weight = 37110.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060091 restraints weight = 30435.929| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32629 Z= 0.186 Angle : 0.717 15.851 44420 Z= 0.353 Chirality : 0.042 0.261 5155 Planarity : 0.004 0.096 5523 Dihedral : 6.446 59.442 5242 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 3.25 % Allowed : 17.75 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.14 (0.13), residues: 4045 helix: 1.03 (0.10), residues: 2610 sheet: -0.46 (0.34), residues: 226 loop : -1.84 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1188 TYR 0.018 0.002 TYR A 543 PHE 0.036 0.002 PHE D 854 TRP 0.018 0.002 TRP D 709 HIS 0.015 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00410 (32625) covalent geometry : angle 0.71733 (44412) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.58463 ( 8) hydrogen bonds : bond 0.04402 ( 1950) hydrogen bonds : angle 4.66222 ( 5763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 435 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8615 (mm) cc_final: 0.8106 (mm) REVERT: A 179 MET cc_start: 0.8964 (mmm) cc_final: 0.8510 (mmm) REVERT: A 255 MET cc_start: 0.7506 (pmm) cc_final: 0.7134 (ptm) REVERT: A 915 TRP cc_start: 0.8702 (t60) cc_final: 0.8475 (t60) REVERT: A 967 PHE cc_start: 0.8606 (m-10) cc_final: 0.8242 (m-80) REVERT: A 978 MET cc_start: 0.8720 (mmm) cc_final: 0.8428 (mmm) REVERT: A 987 MET cc_start: 0.8841 (tpp) cc_final: 0.8548 (tmm) REVERT: A 1115 MET cc_start: 0.8657 (mmp) cc_final: 0.8319 (tpp) REVERT: A 1168 LYS cc_start: 0.9241 (mmmt) cc_final: 0.8959 (mtmm) REVERT: A 1194 ASP cc_start: 0.8263 (p0) cc_final: 0.7951 (p0) REVERT: A 1207 MET cc_start: 0.8612 (mmm) cc_final: 0.8261 (mtt) REVERT: A 1209 MET cc_start: 0.8555 (mpp) cc_final: 0.8339 (mpp) REVERT: C 242 MET cc_start: 0.8407 (ppp) cc_final: 0.7194 (ppp) REVERT: C 681 GLN cc_start: 0.9032 (tp40) cc_final: 0.8716 (tp40) REVERT: C 685 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8379 (mt-10) REVERT: C 902 MET cc_start: 0.8847 (mmm) cc_final: 0.8581 (mmt) REVERT: C 962 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7927 (mmm-85) REVERT: C 1030 MET cc_start: 0.9551 (mtp) cc_final: 0.9129 (mtp) REVERT: C 1072 MET cc_start: 0.8537 (ttm) cc_final: 0.8094 (ttm) REVERT: C 1119 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8091 (tm-30) REVERT: C 1180 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 1212 GLU cc_start: 0.8995 (tp30) cc_final: 0.8760 (mm-30) REVERT: B 179 MET cc_start: 0.9078 (mmm) cc_final: 0.8610 (mmp) REVERT: B 474 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9190 (mm-30) REVERT: B 734 MET cc_start: 0.8803 (ptm) cc_final: 0.8551 (ppp) REVERT: B 834 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5418 (tt) REVERT: B 854 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8879 (t80) REVERT: B 932 SER cc_start: 0.9132 (m) cc_final: 0.8806 (p) REVERT: B 967 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.5576 (t80) REVERT: B 978 MET cc_start: 0.8892 (mmm) cc_final: 0.8668 (mmm) REVERT: B 979 MET cc_start: 0.8734 (mmm) cc_final: 0.8488 (mpp) REVERT: B 1119 GLU cc_start: 0.8931 (tp30) cc_final: 0.8691 (tm-30) REVERT: B 1168 LYS cc_start: 0.9072 (tptp) cc_final: 0.8743 (tppt) REVERT: B 1207 MET cc_start: 0.8568 (mmm) cc_final: 0.8337 (mmm) REVERT: D 149 LEU cc_start: 0.9364 (tp) cc_final: 0.9074 (tp) REVERT: D 457 MET cc_start: 0.8976 (mmm) cc_final: 0.8310 (mmm) REVERT: D 652 CYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8408 (t) REVERT: D 739 MET cc_start: 0.8840 (tpt) cc_final: 0.8557 (tpp) REVERT: D 978 MET cc_start: 0.9194 (mmm) cc_final: 0.8974 (mmm) REVERT: D 999 MET cc_start: 0.8806 (mtp) cc_final: 0.8417 (ttm) outliers start: 103 outliers final: 80 residues processed: 508 average time/residue: 0.1617 time to fit residues: 141.4470 Evaluate side-chains 504 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 420 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1017 TRP Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 970 ASN Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 707 LYS Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 874 MET Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1000 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 410 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 274 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 ASN ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS ** B1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.073675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055903 restraints weight = 147218.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057692 restraints weight = 77110.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.058886 restraints weight = 49958.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059663 restraints weight = 37173.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.060198 restraints weight = 30490.740| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32629 Z= 0.177 Angle : 0.723 15.282 44420 Z= 0.355 Chirality : 0.042 0.282 5155 Planarity : 0.004 0.096 5523 Dihedral : 6.374 59.505 5242 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.61 % Favored : 94.36 % Rotamer: Outliers : 2.93 % Allowed : 18.10 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4045 helix: 1.07 (0.10), residues: 2616 sheet: -0.49 (0.34), residues: 234 loop : -1.84 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1188 TYR 0.018 0.002 TYR A 492 PHE 0.035 0.002 PHE D 854 TRP 0.023 0.002 TRP C 621 HIS 0.014 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00393 (32625) covalent geometry : angle 0.72337 (44412) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.55869 ( 8) hydrogen bonds : bond 0.04390 ( 1950) hydrogen bonds : angle 4.64492 ( 5763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 435 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8642 (mm) cc_final: 0.8129 (mm) REVERT: A 179 MET cc_start: 0.8987 (mmm) cc_final: 0.8530 (mmm) REVERT: A 255 MET cc_start: 0.7415 (pmm) cc_final: 0.7079 (ptm) REVERT: A 681 GLN cc_start: 0.8814 (tp40) cc_final: 0.8380 (tp40) REVERT: A 685 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8020 (mt-10) REVERT: A 915 TRP cc_start: 0.8666 (t60) cc_final: 0.8455 (t60) REVERT: A 967 PHE cc_start: 0.8593 (m-10) cc_final: 0.8232 (m-80) REVERT: A 978 MET cc_start: 0.8760 (mmm) cc_final: 0.8504 (mmm) REVERT: A 987 MET cc_start: 0.8825 (tpp) cc_final: 0.8534 (tmm) REVERT: A 1115 MET cc_start: 0.8674 (mmp) cc_final: 0.8317 (tpp) REVERT: A 1168 LYS cc_start: 0.9270 (mmmt) cc_final: 0.8968 (mtmm) REVERT: A 1194 ASP cc_start: 0.8249 (p0) cc_final: 0.8041 (p0) REVERT: A 1207 MET cc_start: 0.8612 (mmm) cc_final: 0.8285 (mtt) REVERT: C 242 MET cc_start: 0.8449 (ppp) cc_final: 0.7329 (ppp) REVERT: C 681 GLN cc_start: 0.9031 (tp40) cc_final: 0.8713 (tp40) REVERT: C 685 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8377 (mt-10) REVERT: C 902 MET cc_start: 0.8853 (mmm) cc_final: 0.8566 (mmt) REVERT: C 962 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.7930 (mmm-85) REVERT: C 1030 MET cc_start: 0.9554 (mtp) cc_final: 0.9116 (mtp) REVERT: C 1072 MET cc_start: 0.8498 (ttm) cc_final: 0.8020 (ttm) REVERT: C 1119 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 1180 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 1212 GLU cc_start: 0.8988 (tp30) cc_final: 0.8736 (mm-30) REVERT: B 179 MET cc_start: 0.9089 (mmm) cc_final: 0.8618 (mmp) REVERT: B 457 MET cc_start: 0.9034 (tpp) cc_final: 0.8770 (tpp) REVERT: B 734 MET cc_start: 0.8810 (ptm) cc_final: 0.8606 (ppp) REVERT: B 834 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5393 (tt) REVERT: B 854 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8845 (t80) REVERT: B 932 SER cc_start: 0.9142 (m) cc_final: 0.8811 (p) REVERT: B 967 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.5569 (t80) REVERT: B 978 MET cc_start: 0.8902 (mmm) cc_final: 0.8670 (mmm) REVERT: B 979 MET cc_start: 0.8717 (mmm) cc_final: 0.8504 (mpp) REVERT: B 988 MET cc_start: 0.8752 (mmp) cc_final: 0.8551 (ttt) REVERT: B 1080 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8547 (m110) REVERT: B 1119 GLU cc_start: 0.8947 (tp30) cc_final: 0.8721 (tm-30) REVERT: B 1168 LYS cc_start: 0.9079 (tptp) cc_final: 0.8743 (tppt) REVERT: B 1207 MET cc_start: 0.8566 (mmm) cc_final: 0.8322 (mmm) REVERT: D 149 LEU cc_start: 0.9348 (tp) cc_final: 0.9070 (tp) REVERT: D 457 MET cc_start: 0.9020 (mmm) cc_final: 0.8303 (mmm) REVERT: D 545 MET cc_start: 0.8579 (ptm) cc_final: 0.8097 (ppp) REVERT: D 652 CYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8418 (t) REVERT: D 739 MET cc_start: 0.8859 (tpt) cc_final: 0.8559 (tpp) REVERT: D 978 MET cc_start: 0.9216 (mmm) cc_final: 0.8993 (mmm) REVERT: D 999 MET cc_start: 0.8802 (mtp) cc_final: 0.8399 (ttm) outliers start: 93 outliers final: 76 residues processed: 501 average time/residue: 0.1589 time to fit residues: 136.0291 Evaluate side-chains 501 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 420 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1017 TRP Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 970 ASN Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1214 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1080 ASN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 707 LYS Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 874 MET Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1000 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 376 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 309 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 chunk 333 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS ** B1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.073143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055407 restraints weight = 149050.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057211 restraints weight = 78161.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058386 restraints weight = 50535.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059167 restraints weight = 37686.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.059689 restraints weight = 30889.439| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32629 Z= 0.200 Angle : 0.746 16.473 44420 Z= 0.366 Chirality : 0.043 0.346 5155 Planarity : 0.004 0.095 5523 Dihedral : 6.372 59.637 5242 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 2.87 % Allowed : 18.29 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 4045 helix: 1.04 (0.10), residues: 2611 sheet: -0.52 (0.34), residues: 233 loop : -1.82 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 747 TYR 0.017 0.002 TYR C 958 PHE 0.035 0.002 PHE D 854 TRP 0.021 0.002 TRP C 621 HIS 0.044 0.002 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00440 (32625) covalent geometry : angle 0.74603 (44412) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.61483 ( 8) hydrogen bonds : bond 0.04452 ( 1950) hydrogen bonds : angle 4.69376 ( 5763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8090 Ramachandran restraints generated. 4045 Oldfield, 0 Emsley, 4045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 420 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8617 (mm) cc_final: 0.8365 (mm) REVERT: A 179 MET cc_start: 0.8992 (mmm) cc_final: 0.8545 (mmm) REVERT: A 255 MET cc_start: 0.7418 (pmm) cc_final: 0.7096 (ptm) REVERT: A 681 GLN cc_start: 0.8800 (tp40) cc_final: 0.8349 (tp40) REVERT: A 685 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 915 TRP cc_start: 0.8685 (t60) cc_final: 0.8432 (t60) REVERT: A 967 PHE cc_start: 0.8606 (m-10) cc_final: 0.8251 (m-80) REVERT: A 987 MET cc_start: 0.8827 (tpp) cc_final: 0.8533 (tmm) REVERT: A 1115 MET cc_start: 0.8676 (mmp) cc_final: 0.8323 (tpp) REVERT: A 1168 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9006 (mtmm) REVERT: A 1194 ASP cc_start: 0.8293 (p0) cc_final: 0.7995 (p0) REVERT: A 1207 MET cc_start: 0.8598 (mmm) cc_final: 0.8269 (mtt) REVERT: C 681 GLN cc_start: 0.9026 (tp40) cc_final: 0.8654 (tp40) REVERT: C 685 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8458 (mt-10) REVERT: C 902 MET cc_start: 0.8851 (mmm) cc_final: 0.8565 (mmt) REVERT: C 962 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8169 (mmm-85) REVERT: C 1030 MET cc_start: 0.9554 (mtp) cc_final: 0.9106 (mtp) REVERT: C 1072 MET cc_start: 0.8480 (ttm) cc_final: 0.7996 (ttm) REVERT: C 1119 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8333 (tm-30) REVERT: C 1180 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 1212 GLU cc_start: 0.8988 (tp30) cc_final: 0.8738 (mm-30) REVERT: B 179 MET cc_start: 0.9079 (mmm) cc_final: 0.8615 (mmm) REVERT: B 734 MET cc_start: 0.8816 (ptm) cc_final: 0.8603 (ppp) REVERT: B 834 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5512 (tt) REVERT: B 854 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8824 (t80) REVERT: B 932 SER cc_start: 0.9125 (m) cc_final: 0.8792 (p) REVERT: B 967 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5616 (t80) REVERT: B 978 MET cc_start: 0.8906 (mmm) cc_final: 0.8673 (mmm) REVERT: B 979 MET cc_start: 0.8737 (mmm) cc_final: 0.8494 (mpp) REVERT: B 1030 MET cc_start: 0.9260 (mtp) cc_final: 0.9055 (mtp) REVERT: B 1080 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8542 (m110) REVERT: B 1119 GLU cc_start: 0.8951 (tp30) cc_final: 0.8732 (tm-30) REVERT: B 1168 LYS cc_start: 0.9083 (tptp) cc_final: 0.8754 (tppt) REVERT: B 1207 MET cc_start: 0.8588 (mmm) cc_final: 0.8334 (mmm) REVERT: D 457 MET cc_start: 0.9010 (mmm) cc_final: 0.8320 (mmm) REVERT: D 652 CYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8429 (t) REVERT: D 739 MET cc_start: 0.8869 (tpt) cc_final: 0.8567 (tpp) REVERT: D 978 MET cc_start: 0.9244 (mmm) cc_final: 0.9015 (mmm) REVERT: D 999 MET cc_start: 0.8816 (mtp) cc_final: 0.8417 (ttm) outliers start: 91 outliers final: 78 residues processed: 487 average time/residue: 0.1609 time to fit residues: 133.6504 Evaluate side-chains 500 residues out of total 3666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 417 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1017 TRP Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 475 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1214 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 657 HIS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 673 ASN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 714 CYS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1080 ASN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 652 CYS Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 707 LYS Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 874 MET Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 972 TYR Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1000 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 33 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 187 optimal weight: 0.0270 chunk 302 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS B 867 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.073588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055835 restraints weight = 147049.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.057644 restraints weight = 76484.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.058833 restraints weight = 49279.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059627 restraints weight = 36625.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060150 restraints weight = 29874.151| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32629 Z= 0.169 Angle : 0.734 16.234 44420 Z= 0.359 Chirality : 0.043 0.367 5155 Planarity : 0.004 0.096 5523 Dihedral : 6.308 59.835 5242 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.61 % Favored : 94.36 % Rotamer: Outliers : 2.71 % Allowed : 18.57 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.21 (0.13), residues: 4045 helix: 1.08 (0.10), residues: 2616 sheet: -0.51 (0.34), residues: 236 loop : -1.82 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1217 TYR 0.017 0.001 TYR B 958 PHE 0.034 0.001 PHE D 854 TRP 0.022 0.002 TRP C 621 HIS 0.027 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00376 (32625) covalent geometry : angle 0.73411 (44412) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.57301 ( 8) hydrogen bonds : bond 0.04378 ( 1950) hydrogen bonds : angle 4.61645 ( 5763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5678.00 seconds wall clock time: 99 minutes 5.06 seconds (5945.06 seconds total)