Starting phenix.real_space_refine on Sat Feb 7 14:30:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n1k_48815/02_2026/9n1k_48815.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n1k_48815/02_2026/9n1k_48815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n1k_48815/02_2026/9n1k_48815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n1k_48815/02_2026/9n1k_48815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n1k_48815/02_2026/9n1k_48815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n1k_48815/02_2026/9n1k_48815.map" } resolution = 3.68 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 228 5.16 5 C 21512 2.51 5 N 5472 2.21 5 O 5732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s 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: 32944 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8026 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 1006} Chain breaks: 6 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 17, 'ARG:plan': 11, 'ASP:plan': 8, 'HIS:plan': 5, 'GLN:plan1': 13, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 293 Chain: "C" Number of atoms: 8026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8026 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 1006} Chain breaks: 6 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 17, 'ARG:plan': 11, 'ASP:plan': 8, 'HIS:plan': 5, 'GLN:plan1': 13, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 293 Chain: "B" Number of atoms: 8026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8026 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 1006} Chain breaks: 6 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 17, 'ARG:plan': 11, 'ASP:plan': 8, 'HIS:plan': 5, 'GLN:plan1': 13, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 293 Chain: "D" Number of atoms: 8026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8026 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 1006} Chain breaks: 6 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 17, 'ARG:plan': 11, 'ASP:plan': 8, 'HIS:plan': 5, 'GLN:plan1': 13, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 293 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.31, per 1000 atoms: 0.19 Number of scatterers: 32944 At special positions: 0 Unit cell: (147.854, 147.854, 161.896, 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 228 16.00 O 5732 8.00 N 5472 7.00 C 21512 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7904 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 12 sheets defined 65.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.748A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.510A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 206 removed outlier: 3.670A pdb=" N HIS A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.223A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.781A pdb=" N TYR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 404 through 418 removed outlier: 4.234A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.933A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) 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 removed outlier: 3.686A pdb=" N LEU A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 501 through 514 removed outlier: 3.913A pdb=" N TYR A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 555 through 565 removed outlier: 3.790A pdb=" N LEU A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 625 removed outlier: 4.125A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.562A pdb=" N HIS A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 662 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.901A 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: 3.529A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 763 through 767 removed outlier: 3.563A pdb=" N SER A 766 " --> pdb=" O SER A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 846 removed outlier: 3.801A pdb=" N LYS A 840 " --> pdb=" O PRO A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 872 removed outlier: 3.562A pdb=" N VAL A 872 " --> pdb=" O TYR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 902 Processing helix chain 'A' and resid 907 through 917 removed outlier: 3.733A pdb=" N VAL A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 939 removed outlier: 3.518A pdb=" N VAL A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 967 removed outlier: 3.859A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 972 through 1009 removed outlier: 3.563A pdb=" N TYR A 976 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1026 removed outlier: 3.944A pdb=" N LYS A1021 " --> pdb=" O TRP A1017 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1100 removed outlier: 3.999A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A1100 " --> pdb=" O PHE A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1120 removed outlier: 3.818A pdb=" N TRP A1106 " --> pdb=" O SER A1102 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1126 No H-bonds generated for 'chain 'A' and resid 1124 through 1126' Processing helix chain 'A' and resid 1127 through 1142 removed outlier: 4.124A pdb=" N SER A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1191 Processing helix chain 'A' and resid 1192 through 1231 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 130 through 140 removed outlier: 3.747A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 182 removed outlier: 3.511A pdb=" N LEU C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 206 removed outlier: 3.670A pdb=" N HIS C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 308 through 319 removed outlier: 4.223A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.780A 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 418 removed outlier: 4.234A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.933A 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 475 Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.685A pdb=" N LEU C 483 " --> pdb=" O MET C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 501 through 514 removed outlier: 3.913A pdb=" N TYR C 514 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 546 Processing helix chain 'C' and resid 555 through 565 removed outlier: 3.790A pdb=" N LEU C 561 " --> pdb=" O ARG C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 625 removed outlier: 4.124A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.562A pdb=" N HIS C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 662 Processing helix chain 'C' and resid 665 through 694 removed outlier: 3.901A pdb=" N SER C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 704 Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'C' and resid 723 through 728 removed outlier: 3.529A pdb=" N ILE C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) 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: 3.562A pdb=" N SER C 766 " --> pdb=" O SER C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 846 removed outlier: 3.802A pdb=" N LYS C 840 " --> pdb=" O PRO C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 872 removed outlier: 3.562A 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 removed outlier: 3.733A pdb=" N VAL C 912 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 939 removed outlier: 3.518A pdb=" N VAL C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 967 removed outlier: 3.860A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 970 No H-bonds generated for 'chain 'C' and resid 968 through 970' Processing helix chain 'C' and resid 972 through 1009 removed outlier: 3.562A pdb=" N TYR C 976 " --> pdb=" O TYR C 972 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1026 removed outlier: 3.944A pdb=" N LYS C1021 " --> pdb=" O TRP C1017 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C1026 " --> pdb=" O ASN C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1100 removed outlier: 3.999A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C1100 " --> pdb=" O PHE C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1120 removed outlier: 3.818A pdb=" N TRP C1106 " --> pdb=" O SER C1102 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1126 No H-bonds generated for 'chain 'C' and resid 1124 through 1126' Processing helix chain 'C' and resid 1127 through 1142 removed outlier: 4.124A pdb=" N SER C1131 " --> pdb=" O LEU C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1191 Processing helix chain 'C' and resid 1192 through 1231 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.748A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.510A pdb=" N LEU B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 removed outlier: 3.670A pdb=" N HIS B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.224A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.780A pdb=" N TYR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 404 through 418 removed outlier: 4.234A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.933A 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 removed outlier: 3.685A pdb=" N LEU B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 514 removed outlier: 3.912A pdb=" N TYR B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 546 Processing helix chain 'B' and resid 555 through 565 removed outlier: 3.790A pdb=" N LEU B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 625 removed outlier: 4.125A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.562A pdb=" N HIS B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.901A pdb=" N SER B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 704 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 728 removed outlier: 3.529A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 749 through 759 Processing helix chain 'B' and resid 763 through 767 removed outlier: 3.563A pdb=" N SER B 766 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 846 removed outlier: 3.801A pdb=" N LYS B 840 " --> pdb=" O PRO B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 872 removed outlier: 3.563A pdb=" N VAL B 872 " --> pdb=" O TYR B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 902 Processing helix chain 'B' and resid 907 through 917 removed outlier: 3.733A pdb=" N VAL B 912 " --> pdb=" O LEU B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 939 removed outlier: 3.518A pdb=" N VAL B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 967 removed outlier: 3.860A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 970 No H-bonds generated for 'chain 'B' and resid 968 through 970' Processing helix chain 'B' and resid 972 through 1009 removed outlier: 3.563A pdb=" N TYR B 976 " --> pdb=" O TYR B 972 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1026 removed outlier: 3.944A pdb=" N LYS B1021 " --> pdb=" O TRP B1017 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET B1026 " --> pdb=" O ASN B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1100 removed outlier: 4.000A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1120 removed outlier: 3.818A pdb=" N TRP B1106 " --> pdb=" O SER B1102 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1126 No H-bonds generated for 'chain 'B' and resid 1124 through 1126' Processing helix chain 'B' and resid 1127 through 1142 removed outlier: 4.125A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 Processing helix chain 'B' and resid 1192 through 1231 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 130 through 140 removed outlier: 3.747A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 182 removed outlier: 3.511A pdb=" N LEU D 174 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.670A pdb=" N HIS D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 308 through 319 removed outlier: 4.223A pdb=" N SER D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 313 " --> pdb=" O ASN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 removed outlier: 3.781A pdb=" N TYR D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 404 through 418 removed outlier: 4.234A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.934A pdb=" N ALA D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 465 through 475 Processing helix chain 'D' and resid 478 through 483 removed outlier: 3.686A pdb=" N LEU D 483 " --> pdb=" O MET D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 501 through 514 removed outlier: 3.913A pdb=" N TYR D 514 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 555 through 565 removed outlier: 3.790A pdb=" N LEU D 561 " --> pdb=" O ARG D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 625 removed outlier: 4.124A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.562A 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: 3.901A pdb=" N SER D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 704 Processing helix chain 'D' and resid 713 through 721 Processing helix chain 'D' and resid 723 through 728 removed outlier: 3.529A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 749 through 759 Processing helix chain 'D' and resid 763 through 767 removed outlier: 3.563A pdb=" N SER D 766 " --> pdb=" O SER D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 846 removed outlier: 3.801A pdb=" N LYS D 840 " --> pdb=" O PRO D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 872 removed outlier: 3.562A pdb=" N VAL D 872 " --> pdb=" O TYR D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 902 Processing helix chain 'D' and resid 907 through 917 removed outlier: 3.733A pdb=" N VAL D 912 " --> pdb=" O LEU D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 939 removed outlier: 3.518A pdb=" N VAL D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 967 removed outlier: 3.860A pdb=" N ASP D 947 " --> pdb=" O PRO D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 970 No H-bonds generated for 'chain 'D' and resid 968 through 970' Processing helix chain 'D' and resid 972 through 1009 removed outlier: 3.563A pdb=" N TYR D 976 " --> pdb=" O TYR D 972 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1026 removed outlier: 3.944A pdb=" N LYS D1021 " --> pdb=" O TRP D1017 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET D1026 " --> pdb=" O ASN D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1100 removed outlier: 3.999A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER D1100 " --> pdb=" O PHE D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1120 removed outlier: 3.818A pdb=" N TRP D1106 " --> pdb=" O SER D1102 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1124 through 1126 No H-bonds generated for 'chain 'D' and resid 1124 through 1126' Processing helix chain 'D' and resid 1127 through 1142 removed outlier: 4.125A pdb=" N SER D1131 " --> pdb=" O LEU D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1191 Processing helix chain 'D' and resid 1192 through 1231 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.615A pdb=" N GLN A 99 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 240 removed outlier: 6.808A pdb=" N PHE A 106 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A 108 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR A 239 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU A 110 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA A 105 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 123 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR A 215 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE A 260 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY A 217 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA A 262 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 219 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 216 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE A 185 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 218 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR A 187 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL A 327 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA A 301 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS A 329 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE A 303 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE A 395 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 328 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1047 through 1049 Processing sheet with id=AA4, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.615A pdb=" N GLN C 99 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.808A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ALA C 105 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 123 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 215 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE C 260 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY C 217 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA C 262 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 219 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE C 216 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE C 185 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 218 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR C 187 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL C 327 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA C 301 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS C 329 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE C 303 " --> pdb=" O CYS C 329 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1047 through 1049 Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.616A pdb=" N GLN B 99 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 240 removed outlier: 6.809A pdb=" N PHE B 106 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR B 239 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU B 110 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA B 105 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 123 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR B 215 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE B 260 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY B 217 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA B 262 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 219 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 216 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE B 185 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 218 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR B 187 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL B 327 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA B 301 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS B 329 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE B 303 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE B 395 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 328 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1047 through 1049 Processing sheet with id=AB1, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.616A pdb=" N GLN D 99 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 232 through 240 removed outlier: 6.808A pdb=" N PHE D 106 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG D 237 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR D 108 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR D 239 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU D 110 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA D 105 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 123 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR D 215 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 260 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY D 217 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA D 262 " --> pdb=" O GLY D 217 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA D 219 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE D 216 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE D 185 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE D 218 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR D 187 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N VAL D 327 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA D 301 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS D 329 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE D 303 " --> pdb=" O CYS D 329 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE D 395 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 1047 through 1049 1997 hydrogen bonds defined for protein. 5955 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: 6.34 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5702 1.32 - 1.45: 8423 1.45 - 1.57: 19227 1.57 - 1.70: 0 1.70 - 1.82: 380 Bond restraints: 33732 Sorted by residual: bond pdb=" N ILE C 956 " pdb=" CA ILE C 956 " ideal model delta sigma weight residual 1.461 1.508 -0.047 1.17e-02 7.31e+03 1.60e+01 bond pdb=" N ILE A 956 " pdb=" CA ILE A 956 " ideal model delta sigma weight residual 1.461 1.508 -0.047 1.17e-02 7.31e+03 1.60e+01 bond pdb=" N ILE B 956 " pdb=" CA ILE B 956 " ideal model delta sigma weight residual 1.461 1.508 -0.047 1.17e-02 7.31e+03 1.60e+01 bond pdb=" N ILE D 956 " pdb=" CA ILE D 956 " ideal model delta sigma weight residual 1.461 1.508 -0.047 1.17e-02 7.31e+03 1.60e+01 bond pdb=" N LEU B 565 " pdb=" CA LEU B 565 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.19e+01 ... (remaining 33727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 44666 2.94 - 5.87: 1042 5.87 - 8.81: 212 8.81 - 11.75: 36 11.75 - 14.69: 4 Bond angle restraints: 45960 Sorted by residual: angle pdb=" N ILE C 956 " pdb=" CA ILE C 956 " pdb=" CB ILE C 956 " ideal model delta sigma weight residual 110.55 118.79 -8.24 1.17e+00 7.31e-01 4.96e+01 angle pdb=" N ILE B 956 " pdb=" CA ILE B 956 " pdb=" CB ILE B 956 " ideal model delta sigma weight residual 110.55 118.77 -8.22 1.17e+00 7.31e-01 4.93e+01 angle pdb=" N ILE A 956 " pdb=" CA ILE A 956 " pdb=" CB ILE A 956 " ideal model delta sigma weight residual 110.55 118.77 -8.22 1.17e+00 7.31e-01 4.93e+01 angle pdb=" N ILE D 956 " pdb=" CA ILE D 956 " pdb=" CB ILE D 956 " ideal model delta sigma weight residual 110.55 118.74 -8.19 1.17e+00 7.31e-01 4.90e+01 angle pdb=" N ILE D 956 " pdb=" CA ILE D 956 " pdb=" C ILE D 956 " ideal model delta sigma weight residual 110.42 104.42 6.00 9.60e-01 1.09e+00 3.91e+01 ... (remaining 45955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 19525 24.96 - 49.92: 1443 49.92 - 74.88: 180 74.88 - 99.83: 44 99.83 - 124.79: 12 Dihedral angle restraints: 21204 sinusoidal: 8996 harmonic: 12208 Sorted by residual: dihedral pdb=" CA MET A 121 " pdb=" C MET A 121 " pdb=" N TYR A 122 " pdb=" CA TYR A 122 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA MET B 121 " pdb=" C MET B 121 " pdb=" N TYR B 122 " pdb=" CA TYR B 122 " ideal model delta harmonic sigma weight residual 180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA MET D 121 " pdb=" C MET D 121 " pdb=" N TYR D 122 " pdb=" CA TYR D 122 " ideal model delta harmonic sigma weight residual -180.00 -152.15 -27.85 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 21201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4302 0.068 - 0.137: 849 0.137 - 0.205: 120 0.205 - 0.274: 45 0.274 - 0.342: 12 Chirality restraints: 5328 Sorted by residual: chirality pdb=" CG LEU C1083 " pdb=" CB LEU C1083 " pdb=" CD1 LEU C1083 " pdb=" CD2 LEU C1083 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CG LEU B1083 " pdb=" CB LEU B1083 " pdb=" CD1 LEU B1083 " pdb=" CD2 LEU B1083 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CG LEU A1083 " pdb=" CB LEU A1083 " pdb=" CD1 LEU A1083 " pdb=" CD2 LEU A1083 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 5325 not shown) Planarity restraints: 5676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 966 " -0.021 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ILE B 966 " 0.070 2.00e-02 2.50e+03 pdb=" O ILE B 966 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 967 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 966 " -0.021 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ILE A 966 " 0.070 2.00e-02 2.50e+03 pdb=" O ILE A 966 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 967 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 966 " 0.021 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ILE D 966 " -0.070 2.00e-02 2.50e+03 pdb=" O ILE D 966 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE D 967 " 0.023 2.00e-02 2.50e+03 ... (remaining 5673 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8907 2.81 - 3.34: 32674 3.34 - 3.86: 55344 3.86 - 4.38: 61830 4.38 - 4.90: 103810 Nonbonded interactions: 262565 Sorted by model distance: nonbonded pdb=" OD1 ASP D 688 " pdb=" NE2 HIS D 729 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASP C 688 " pdb=" NE2 HIS C 729 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASP A 688 " pdb=" NE2 HIS A 729 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASP B 688 " pdb=" NE2 HIS B 729 " model vdw 2.294 3.120 nonbonded pdb=" O VAL A 477 " pdb=" CG1 VAL A 477 " model vdw 2.494 3.460 ... (remaining 262560 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 27.570 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.006 0.062 33736 Z= 0.319 Angle : 1.098 14.685 45968 Z= 0.614 Chirality : 0.059 0.342 5328 Planarity : 0.007 0.094 5676 Dihedral : 17.004 124.792 13288 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.28 % Allowed : 26.45 % Favored : 73.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.11), residues: 4136 helix: -1.21 (0.08), residues: 2612 sheet: -0.70 (0.31), residues: 280 loop : -1.72 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D1203 TYR 0.039 0.002 TYR B 543 PHE 0.029 0.002 PHE D 990 TRP 0.028 0.002 TRP A 915 HIS 0.007 0.001 HIS D1118 Details of bonding type rmsd covalent geometry : bond 0.00601 (33732) covalent geometry : angle 1.09839 (45960) SS BOND : bond 0.00191 ( 4) SS BOND : angle 0.94045 ( 8) hydrogen bonds : bond 0.15412 ( 1997) hydrogen bonds : angle 6.80288 ( 5955) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 584 time to evaluate : 1.275 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: A 133 LEU cc_start: 0.9130 (mp) cc_final: 0.8905 (tp) REVERT: A 492 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: A 621 TRP cc_start: 0.8973 (t60) cc_final: 0.8488 (t60) REVERT: A 685 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 915 TRP cc_start: 0.9104 (t60) cc_final: 0.8742 (t60) REVERT: A 1026 MET cc_start: 0.8996 (mmt) cc_final: 0.8483 (mmt) REVERT: A 1168 LYS cc_start: 0.9401 (tppt) cc_final: 0.8612 (tppt) REVERT: A 1172 ASP cc_start: 0.8415 (m-30) cc_final: 0.8119 (m-30) REVERT: C 133 LEU cc_start: 0.9098 (mp) cc_final: 0.8888 (tp) REVERT: C 492 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: C 621 TRP cc_start: 0.8968 (t60) cc_final: 0.8472 (t60) REVERT: C 685 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7946 (mt-10) REVERT: C 915 TRP cc_start: 0.9113 (t60) cc_final: 0.8745 (t60) REVERT: C 1026 MET cc_start: 0.8980 (mmt) cc_final: 0.8463 (mmt) REVERT: C 1168 LYS cc_start: 0.9399 (tppt) cc_final: 0.8609 (tppt) REVERT: C 1172 ASP cc_start: 0.8409 (m-30) cc_final: 0.8105 (m-30) REVERT: B 133 LEU cc_start: 0.9128 (mp) cc_final: 0.8906 (tp) REVERT: B 492 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: B 621 TRP cc_start: 0.8979 (t60) cc_final: 0.8522 (t60) REVERT: B 685 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 915 TRP cc_start: 0.9124 (t60) cc_final: 0.8748 (t60) REVERT: B 1026 MET cc_start: 0.8979 (mmt) cc_final: 0.8468 (mmt) REVERT: B 1168 LYS cc_start: 0.9404 (tppt) cc_final: 0.8610 (tppt) REVERT: B 1172 ASP cc_start: 0.8423 (m-30) cc_final: 0.8113 (m-30) REVERT: D 133 LEU cc_start: 0.9113 (mp) cc_final: 0.8894 (tp) REVERT: D 492 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: D 621 TRP cc_start: 0.8975 (t60) cc_final: 0.8483 (t60) REVERT: D 685 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7962 (mt-10) REVERT: D 915 TRP cc_start: 0.9102 (t60) cc_final: 0.8742 (t60) REVERT: D 1026 MET cc_start: 0.9005 (mmt) cc_final: 0.8482 (mmt) REVERT: D 1168 LYS cc_start: 0.9397 (tppt) cc_final: 0.8605 (tppt) REVERT: D 1172 ASP cc_start: 0.8398 (m-30) cc_final: 0.8100 (m-30) outliers start: 9 outliers final: 0 residues processed: 589 average time/residue: 0.1962 time to fit residues: 188.8492 Evaluate side-chains 495 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 491 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 205 HIS A 283 HIS A 447 GLN A 636 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN C 205 HIS C 283 HIS C 447 GLN C 636 GLN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 ASN B 205 HIS B 283 HIS ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1085 ASN D 205 HIS D 283 HIS D 447 GLN D 636 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN ** D1132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.089636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065821 restraints weight = 115431.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.068093 restraints weight = 57928.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069583 restraints weight = 37804.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.070507 restraints weight = 28814.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071130 restraints weight = 24333.628| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33736 Z= 0.133 Angle : 0.622 14.597 45968 Z= 0.311 Chirality : 0.038 0.164 5328 Planarity : 0.004 0.044 5676 Dihedral : 8.940 95.938 6200 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.14 % Allowed : 25.74 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4136 helix: 0.55 (0.10), residues: 2620 sheet: -0.22 (0.30), residues: 304 loop : -1.49 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1217 TYR 0.015 0.001 TYR A 958 PHE 0.015 0.001 PHE C1182 TRP 0.014 0.001 TRP D 740 HIS 0.003 0.001 HIS D 729 Details of bonding type rmsd covalent geometry : bond 0.00285 (33732) covalent geometry : angle 0.62224 (45960) SS BOND : bond 0.00022 ( 4) SS BOND : angle 0.19667 ( 8) hydrogen bonds : bond 0.04622 ( 1997) hydrogen bonds : angle 4.58740 ( 5955) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 486 time to evaluate : 1.332 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 242 MET cc_start: 0.3074 (tpt) cc_final: 0.2571 (tpt) REVERT: A 492 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: A 621 TRP cc_start: 0.9044 (t60) cc_final: 0.8710 (t60) REVERT: A 681 GLN cc_start: 0.8676 (tp40) cc_final: 0.8130 (tp40) REVERT: A 685 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7755 (mp0) REVERT: A 752 LEU cc_start: 0.8666 (mt) cc_final: 0.8427 (mp) REVERT: A 978 MET cc_start: 0.8512 (mmm) cc_final: 0.8240 (mmm) REVERT: A 1026 MET cc_start: 0.8944 (mmt) cc_final: 0.8545 (mmt) REVERT: A 1168 LYS cc_start: 0.9417 (tppt) cc_final: 0.8715 (tppt) REVERT: A 1172 ASP cc_start: 0.8596 (m-30) cc_final: 0.8272 (m-30) REVERT: C 242 MET cc_start: 0.2971 (tpt) cc_final: 0.2474 (tpt) REVERT: C 492 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: C 621 TRP cc_start: 0.9046 (t60) cc_final: 0.8708 (t60) REVERT: C 681 GLN cc_start: 0.8676 (tp40) cc_final: 0.8134 (tp40) REVERT: C 685 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7754 (mp0) REVERT: C 1026 MET cc_start: 0.8896 (mmt) cc_final: 0.8516 (mmt) REVERT: C 1168 LYS cc_start: 0.9418 (tppt) cc_final: 0.8676 (tppt) REVERT: C 1172 ASP cc_start: 0.8602 (m-30) cc_final: 0.8255 (m-30) REVERT: B 492 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: B 621 TRP cc_start: 0.9046 (t60) cc_final: 0.8625 (t60) REVERT: B 681 GLN cc_start: 0.8654 (tp40) cc_final: 0.8120 (tp40) REVERT: B 685 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7770 (mp0) REVERT: B 752 LEU cc_start: 0.8651 (mt) cc_final: 0.8412 (mp) REVERT: B 978 MET cc_start: 0.8518 (mmm) cc_final: 0.8251 (mmm) REVERT: B 1026 MET cc_start: 0.8913 (mmt) cc_final: 0.8514 (mmt) REVERT: B 1168 LYS cc_start: 0.9426 (tppt) cc_final: 0.8721 (tppt) REVERT: B 1172 ASP cc_start: 0.8603 (m-30) cc_final: 0.8264 (m-30) REVERT: D 492 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: D 621 TRP cc_start: 0.9044 (t60) cc_final: 0.8708 (t60) REVERT: D 681 GLN cc_start: 0.8672 (tp40) cc_final: 0.8122 (tp40) REVERT: D 685 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7744 (mp0) REVERT: D 978 MET cc_start: 0.8509 (mmm) cc_final: 0.8234 (mmm) REVERT: D 1026 MET cc_start: 0.8940 (mmt) cc_final: 0.8551 (mmt) REVERT: D 1168 LYS cc_start: 0.9414 (tppt) cc_final: 0.8633 (tppt) REVERT: D 1172 ASP cc_start: 0.8596 (m-30) cc_final: 0.8096 (m-30) outliers start: 134 outliers final: 66 residues processed: 570 average time/residue: 0.1825 time to fit residues: 175.5451 Evaluate side-chains 507 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 437 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1219 HIS 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 393 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1219 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 255 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 415 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 40.0000 chunk 87 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 636 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 HIS C 43 HIS C 205 HIS C 636 GLN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 HIS B 43 HIS B 205 HIS B 447 GLN B 636 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 HIS D 43 HIS D 205 HIS D 636 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.087348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063472 restraints weight = 115745.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065685 restraints weight = 58177.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.067132 restraints weight = 37843.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068048 restraints weight = 28812.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068673 restraints weight = 24249.235| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33736 Z= 0.174 Angle : 0.636 15.768 45968 Z= 0.314 Chirality : 0.040 0.248 5328 Planarity : 0.004 0.042 5676 Dihedral : 7.993 71.496 6200 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.28 % Allowed : 24.54 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.13), residues: 4136 helix: 1.31 (0.10), residues: 2628 sheet: -0.02 (0.31), residues: 300 loop : -1.25 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1210 TYR 0.014 0.001 TYR A 958 PHE 0.017 0.001 PHE C1182 TRP 0.028 0.002 TRP D 915 HIS 0.012 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00382 (33732) covalent geometry : angle 0.63643 (45960) SS BOND : bond 0.00006 ( 4) SS BOND : angle 0.19244 ( 8) hydrogen bonds : bond 0.04387 ( 1997) hydrogen bonds : angle 4.31566 ( 5955) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 449 time to evaluate : 1.345 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 242 MET cc_start: 0.3647 (tpt) cc_final: 0.2765 (tpt) REVERT: A 295 GLN cc_start: 0.4825 (OUTLIER) cc_final: 0.4624 (pm20) REVERT: A 619 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8866 (ttm) REVERT: A 625 MET cc_start: 0.8885 (mtt) cc_final: 0.8546 (mtt) REVERT: A 681 GLN cc_start: 0.8836 (tp40) cc_final: 0.8385 (tp40) REVERT: A 685 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 999 MET cc_start: 0.8912 (ppp) cc_final: 0.8632 (ppp) REVERT: A 1168 LYS cc_start: 0.9403 (tppt) cc_final: 0.8587 (tppt) REVERT: A 1172 ASP cc_start: 0.8660 (m-30) cc_final: 0.8077 (m-30) REVERT: C 242 MET cc_start: 0.3561 (tpt) cc_final: 0.2723 (tpt) REVERT: C 619 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8845 (ttm) REVERT: C 625 MET cc_start: 0.8882 (mtt) cc_final: 0.8569 (mtt) REVERT: C 681 GLN cc_start: 0.8815 (tp40) cc_final: 0.8363 (tp40) REVERT: C 685 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8086 (mt-10) REVERT: C 999 MET cc_start: 0.8908 (ppp) cc_final: 0.8626 (ppp) REVERT: C 1168 LYS cc_start: 0.9398 (tppt) cc_final: 0.8586 (tppt) REVERT: C 1172 ASP cc_start: 0.8669 (m-30) cc_final: 0.8084 (m-30) REVERT: B 295 GLN cc_start: 0.4791 (OUTLIER) cc_final: 0.4582 (pm20) REVERT: B 492 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: B 619 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8874 (ttm) REVERT: B 621 TRP cc_start: 0.9087 (t60) cc_final: 0.8813 (t60) REVERT: B 625 MET cc_start: 0.8631 (mtt) cc_final: 0.8379 (mtt) REVERT: B 681 GLN cc_start: 0.8816 (tp40) cc_final: 0.8359 (tp40) REVERT: B 685 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8062 (mt-10) REVERT: B 999 MET cc_start: 0.8918 (ppp) cc_final: 0.8637 (ppp) REVERT: B 1168 LYS cc_start: 0.9403 (tppt) cc_final: 0.8590 (tppt) REVERT: B 1172 ASP cc_start: 0.8652 (m-30) cc_final: 0.8092 (m-30) REVERT: D 619 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8847 (ttm) REVERT: D 625 MET cc_start: 0.8864 (mtt) cc_final: 0.8537 (mtt) REVERT: D 681 GLN cc_start: 0.8824 (tp40) cc_final: 0.8377 (tp40) REVERT: D 685 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8064 (mt-10) REVERT: D 978 MET cc_start: 0.8674 (mmm) cc_final: 0.8281 (mmm) REVERT: D 999 MET cc_start: 0.8912 (ppp) cc_final: 0.8630 (ppp) REVERT: D 1168 LYS cc_start: 0.9404 (tppt) cc_final: 0.8607 (tppt) REVERT: D 1172 ASP cc_start: 0.8669 (m-30) cc_final: 0.8086 (m-30) outliers start: 171 outliers final: 108 residues processed: 565 average time/residue: 0.1805 time to fit residues: 176.3689 Evaluate side-chains 536 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 421 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 563 HIS Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 926 ILE Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1214 VAL Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 967 PHE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 349 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 329 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 406 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 253 ASN A 636 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 253 ASN C 636 GLN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 253 ASN B 636 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS D 253 ASN D 636 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064843 restraints weight = 113968.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.067079 restraints weight = 56835.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068545 restraints weight = 36849.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069478 restraints weight = 27990.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070079 restraints weight = 23545.955| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33736 Z= 0.120 Angle : 0.595 16.118 45968 Z= 0.288 Chirality : 0.038 0.205 5328 Planarity : 0.004 0.045 5676 Dihedral : 7.093 56.888 6200 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.83 % Allowed : 27.81 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.13), residues: 4136 helix: 1.58 (0.10), residues: 2628 sheet: 0.31 (0.31), residues: 300 loop : -1.31 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1210 TYR 0.015 0.001 TYR D 958 PHE 0.015 0.001 PHE A1182 TRP 0.019 0.001 TRP C 621 HIS 0.003 0.001 HIS B1118 Details of bonding type rmsd covalent geometry : bond 0.00262 (33732) covalent geometry : angle 0.59467 (45960) SS BOND : bond 0.00006 ( 4) SS BOND : angle 0.13982 ( 8) hydrogen bonds : bond 0.04036 ( 1997) hydrogen bonds : angle 4.16546 ( 5955) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 470 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: A 242 MET cc_start: 0.3767 (OUTLIER) cc_final: 0.2812 (tpt) REVERT: A 472 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9425 (mp) REVERT: A 625 MET cc_start: 0.8761 (mtt) cc_final: 0.8508 (mtt) REVERT: A 681 GLN cc_start: 0.8872 (tp40) cc_final: 0.8330 (tp40) REVERT: A 685 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 697 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8932 (mm) REVERT: A 917 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8496 (mm-40) REVERT: A 979 MET cc_start: 0.8739 (mtp) cc_final: 0.8455 (mtp) REVERT: A 999 MET cc_start: 0.8893 (ppp) cc_final: 0.8508 (ppp) REVERT: A 1168 LYS cc_start: 0.9394 (tppt) cc_final: 0.8582 (tppt) REVERT: A 1172 ASP cc_start: 0.8647 (m-30) cc_final: 0.8040 (m-30) REVERT: A 1205 GLU cc_start: 0.8549 (tp30) cc_final: 0.8294 (mm-30) REVERT: C 242 MET cc_start: 0.3637 (OUTLIER) cc_final: 0.2701 (tpt) REVERT: C 472 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9423 (mp) REVERT: C 625 MET cc_start: 0.8744 (mtt) cc_final: 0.8498 (mtt) REVERT: C 681 GLN cc_start: 0.8874 (tp40) cc_final: 0.8330 (tp40) REVERT: C 685 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8027 (mt-10) REVERT: C 697 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8933 (mm) REVERT: C 917 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8510 (mm-40) REVERT: C 979 MET cc_start: 0.8730 (mtp) cc_final: 0.8424 (mtp) REVERT: C 999 MET cc_start: 0.8897 (ppp) cc_final: 0.8509 (ppp) REVERT: C 1168 LYS cc_start: 0.9392 (tppt) cc_final: 0.8576 (tppt) REVERT: C 1172 ASP cc_start: 0.8660 (m-30) cc_final: 0.8043 (m-30) REVERT: C 1205 GLU cc_start: 0.8579 (tp30) cc_final: 0.8329 (mm-30) REVERT: B 472 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9427 (mp) REVERT: B 492 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 621 TRP cc_start: 0.9079 (t60) cc_final: 0.8650 (t60) REVERT: B 625 MET cc_start: 0.8635 (mtt) cc_final: 0.8385 (mtt) REVERT: B 681 GLN cc_start: 0.8861 (tp40) cc_final: 0.8290 (tp40) REVERT: B 685 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8028 (mt-10) REVERT: B 697 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8931 (mm) REVERT: B 917 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8518 (mm-40) REVERT: B 999 MET cc_start: 0.8899 (ppp) cc_final: 0.8509 (ppp) REVERT: B 1168 LYS cc_start: 0.9399 (tppt) cc_final: 0.8578 (tppt) REVERT: B 1172 ASP cc_start: 0.8650 (m-30) cc_final: 0.8047 (m-30) REVERT: B 1205 GLU cc_start: 0.8563 (tp30) cc_final: 0.8312 (mm-30) REVERT: D 472 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9432 (mp) REVERT: D 625 MET cc_start: 0.8707 (mtt) cc_final: 0.8469 (mtt) REVERT: D 681 GLN cc_start: 0.8871 (tp40) cc_final: 0.8309 (tp40) REVERT: D 685 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8018 (mt-10) REVERT: D 697 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8931 (mm) REVERT: D 999 MET cc_start: 0.8892 (ppp) cc_final: 0.8503 (ppp) REVERT: D 1168 LYS cc_start: 0.9392 (tppt) cc_final: 0.8581 (tppt) REVERT: D 1172 ASP cc_start: 0.8657 (m-30) cc_final: 0.8038 (m-30) REVERT: D 1205 GLU cc_start: 0.8560 (tp30) cc_final: 0.8308 (mm-30) outliers start: 124 outliers final: 91 residues processed: 551 average time/residue: 0.1832 time to fit residues: 172.8945 Evaluate side-chains 542 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 440 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 563 HIS Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 967 PHE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1158 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 160 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 318 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 315 optimal weight: 50.0000 chunk 72 optimal weight: 6.9990 chunk 410 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 636 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN C 118 ASN C 636 GLN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 ASN B 205 HIS B 636 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN D 118 ASN D 205 HIS D 636 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.086873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062882 restraints weight = 116067.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.065093 restraints weight = 58315.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.066565 restraints weight = 37877.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067454 restraints weight = 28780.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068051 restraints weight = 24296.882| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33736 Z= 0.180 Angle : 0.630 16.550 45968 Z= 0.307 Chirality : 0.040 0.209 5328 Planarity : 0.004 0.048 5676 Dihedral : 6.934 55.768 6200 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.09 % Allowed : 27.25 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.13), residues: 4136 helix: 1.82 (0.10), residues: 2596 sheet: 0.50 (0.32), residues: 284 loop : -1.23 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1203 TYR 0.013 0.001 TYR A 549 PHE 0.016 0.001 PHE C1182 TRP 0.015 0.001 TRP C 621 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00394 (33732) covalent geometry : angle 0.62994 (45960) SS BOND : bond 0.00026 ( 4) SS BOND : angle 0.19145 ( 8) hydrogen bonds : bond 0.04201 ( 1997) hydrogen bonds : angle 4.18108 ( 5955) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 447 time to evaluate : 1.344 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: A 242 MET cc_start: 0.3839 (OUTLIER) cc_final: 0.2890 (tpt) REVERT: A 619 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8838 (ttm) REVERT: A 625 MET cc_start: 0.8756 (mtt) cc_final: 0.8461 (mtt) REVERT: A 681 GLN cc_start: 0.8870 (tp40) cc_final: 0.8395 (tp40) REVERT: A 685 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8136 (mt-10) REVERT: A 978 MET cc_start: 0.8698 (mmm) cc_final: 0.8301 (mmm) REVERT: A 999 MET cc_start: 0.8932 (ppp) cc_final: 0.8682 (ppp) REVERT: A 1168 LYS cc_start: 0.9390 (tppt) cc_final: 0.8579 (tppt) REVERT: A 1172 ASP cc_start: 0.8656 (m-30) cc_final: 0.8041 (m-30) REVERT: A 1205 GLU cc_start: 0.8562 (tp30) cc_final: 0.8285 (mm-30) REVERT: A 1221 MET cc_start: 0.8886 (mmp) cc_final: 0.8455 (mmm) REVERT: C 242 MET cc_start: 0.3847 (OUTLIER) cc_final: 0.2886 (tpt) REVERT: C 619 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8859 (ttm) REVERT: C 625 MET cc_start: 0.8757 (mtt) cc_final: 0.8465 (mtt) REVERT: C 681 GLN cc_start: 0.8885 (tp40) cc_final: 0.8423 (tp40) REVERT: C 685 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8144 (mt-10) REVERT: C 895 GLU cc_start: 0.8313 (tp30) cc_final: 0.7904 (tp30) REVERT: C 978 MET cc_start: 0.8630 (mmm) cc_final: 0.8277 (mmm) REVERT: C 999 MET cc_start: 0.8927 (ppp) cc_final: 0.8676 (ppp) REVERT: C 1168 LYS cc_start: 0.9382 (tppt) cc_final: 0.8565 (tppt) REVERT: C 1172 ASP cc_start: 0.8662 (m-30) cc_final: 0.8033 (m-30) REVERT: C 1205 GLU cc_start: 0.8575 (tp30) cc_final: 0.8301 (mm-30) REVERT: C 1221 MET cc_start: 0.8905 (mmp) cc_final: 0.8510 (mmm) REVERT: B 619 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8861 (ttm) REVERT: B 621 TRP cc_start: 0.9072 (t60) cc_final: 0.8490 (t60) REVERT: B 625 MET cc_start: 0.8710 (mtt) cc_final: 0.8398 (mtt) REVERT: B 681 GLN cc_start: 0.8863 (tp40) cc_final: 0.8389 (tp40) REVERT: B 685 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 697 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8972 (mm) REVERT: B 999 MET cc_start: 0.8939 (ppp) cc_final: 0.8690 (ppp) REVERT: B 1168 LYS cc_start: 0.9390 (tppt) cc_final: 0.8569 (tppt) REVERT: B 1172 ASP cc_start: 0.8659 (m-30) cc_final: 0.8044 (m-30) REVERT: B 1205 GLU cc_start: 0.8573 (tp30) cc_final: 0.8300 (mm-30) REVERT: B 1221 MET cc_start: 0.8899 (mmp) cc_final: 0.8525 (mmm) REVERT: D 619 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8832 (ttm) REVERT: D 625 MET cc_start: 0.8727 (mtt) cc_final: 0.8421 (mtt) REVERT: D 681 GLN cc_start: 0.8867 (tp40) cc_final: 0.8573 (tp40) REVERT: D 999 MET cc_start: 0.8928 (ppp) cc_final: 0.8680 (ppp) REVERT: D 1168 LYS cc_start: 0.9382 (tppt) cc_final: 0.8574 (tppt) REVERT: D 1172 ASP cc_start: 0.8660 (m-30) cc_final: 0.8031 (m-30) REVERT: D 1205 GLU cc_start: 0.8570 (tp30) cc_final: 0.8294 (mm-30) REVERT: D 1221 MET cc_start: 0.8891 (mmp) cc_final: 0.8454 (mmm) outliers start: 165 outliers final: 116 residues processed: 568 average time/residue: 0.1740 time to fit residues: 168.2366 Evaluate side-chains 551 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 428 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 563 HIS Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 LEU Chi-restraints excluded: chain C residue 1214 VAL Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 967 PHE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1160 LEU Chi-restraints excluded: chain D residue 1214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 107 optimal weight: 50.0000 chunk 397 optimal weight: 0.5980 chunk 361 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 335 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 190 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.087648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063847 restraints weight = 114245.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066064 restraints weight = 57396.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.067512 restraints weight = 37248.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.068480 restraints weight = 28360.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069112 restraints weight = 23780.929| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33736 Z= 0.144 Angle : 0.633 15.548 45968 Z= 0.303 Chirality : 0.039 0.206 5328 Planarity : 0.004 0.048 5676 Dihedral : 6.766 55.241 6200 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.28 % Allowed : 27.81 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.13), residues: 4136 helix: 1.86 (0.10), residues: 2596 sheet: 0.52 (0.31), residues: 292 loop : -1.26 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 396 TYR 0.014 0.001 TYR D 958 PHE 0.016 0.001 PHE C1182 TRP 0.015 0.001 TRP A 621 HIS 0.005 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00322 (33732) covalent geometry : angle 0.63300 (45960) SS BOND : bond 0.00007 ( 4) SS BOND : angle 0.11291 ( 8) hydrogen bonds : bond 0.04052 ( 1997) hydrogen bonds : angle 4.14568 ( 5955) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 442 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: 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 242 MET cc_start: 0.3760 (OUTLIER) cc_final: 0.2769 (tpt) REVERT: A 625 MET cc_start: 0.8715 (mtt) cc_final: 0.8456 (mtt) REVERT: A 646 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9388 (mm) REVERT: A 685 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 697 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8974 (mm) REVERT: A 1030 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8718 (mmm) REVERT: A 1168 LYS cc_start: 0.9373 (tppt) cc_final: 0.8562 (tppt) REVERT: A 1172 ASP cc_start: 0.8618 (m-30) cc_final: 0.8003 (m-30) REVERT: A 1205 GLU cc_start: 0.8468 (tp30) cc_final: 0.8234 (mm-30) REVERT: C 242 MET cc_start: 0.3858 (OUTLIER) cc_final: 0.2909 (tpt) REVERT: C 625 MET cc_start: 0.8726 (mtt) cc_final: 0.8470 (mtt) REVERT: C 646 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9386 (mm) REVERT: C 685 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 697 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8974 (mm) REVERT: C 978 MET cc_start: 0.8564 (mmm) cc_final: 0.8251 (mmm) REVERT: C 1168 LYS cc_start: 0.9366 (tppt) cc_final: 0.8551 (tppt) REVERT: C 1172 ASP cc_start: 0.8624 (m-30) cc_final: 0.7997 (m-30) REVERT: C 1205 GLU cc_start: 0.8477 (tp30) cc_final: 0.8237 (mm-30) REVERT: B 492 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: B 646 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9376 (mm) REVERT: B 685 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 697 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8963 (mm) REVERT: B 1168 LYS cc_start: 0.9375 (tppt) cc_final: 0.8551 (tppt) REVERT: B 1172 ASP cc_start: 0.8613 (m-30) cc_final: 0.7999 (m-30) REVERT: B 1205 GLU cc_start: 0.8474 (tp30) cc_final: 0.8243 (mm-30) REVERT: B 1221 MET cc_start: 0.8830 (mmp) cc_final: 0.8560 (mmm) REVERT: D 625 MET cc_start: 0.8681 (mtt) cc_final: 0.8441 (mtt) REVERT: D 697 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8969 (mm) REVERT: D 1168 LYS cc_start: 0.9369 (tppt) cc_final: 0.8557 (tppt) REVERT: D 1172 ASP cc_start: 0.8632 (m-30) cc_final: 0.8010 (m-30) REVERT: D 1205 GLU cc_start: 0.8473 (tp30) cc_final: 0.8219 (mm-30) outliers start: 171 outliers final: 118 residues processed: 559 average time/residue: 0.1736 time to fit residues: 168.6636 Evaluate side-chains 553 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 424 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1219 HIS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 563 HIS Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 967 PHE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1160 LEU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1219 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 411 optimal weight: 0.6980 chunk 353 optimal weight: 8.9990 chunk 354 optimal weight: 0.0570 chunk 55 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 347 optimal weight: 0.9980 overall best weight: 2.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 ASN B 205 HIS B 253 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064159 restraints weight = 116198.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066461 restraints weight = 56553.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067998 restraints weight = 36269.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068917 restraints weight = 27372.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069566 restraints weight = 23031.847| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33736 Z= 0.152 Angle : 0.638 14.996 45968 Z= 0.306 Chirality : 0.040 0.204 5328 Planarity : 0.004 0.048 5676 Dihedral : 6.680 54.844 6200 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.81 % Allowed : 27.90 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.13), residues: 4136 helix: 1.92 (0.10), residues: 2596 sheet: 0.44 (0.30), residues: 292 loop : -1.27 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 396 TYR 0.015 0.001 TYR D 549 PHE 0.015 0.001 PHE D 854 TRP 0.022 0.001 TRP B 621 HIS 0.005 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00341 (33732) covalent geometry : angle 0.63818 (45960) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.13624 ( 8) hydrogen bonds : bond 0.04060 ( 1997) hydrogen bonds : angle 4.12451 ( 5955) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 431 time to evaluate : 1.325 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: A 242 MET cc_start: 0.3851 (OUTLIER) cc_final: 0.2894 (tpt) REVERT: A 681 GLN cc_start: 0.8778 (tp40) cc_final: 0.8158 (tp40) REVERT: A 685 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8164 (mt-10) REVERT: A 697 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8969 (mm) REVERT: A 999 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8544 (ppp) REVERT: A 1168 LYS cc_start: 0.9370 (tppt) cc_final: 0.8559 (tppt) REVERT: A 1172 ASP cc_start: 0.8614 (m-30) cc_final: 0.7996 (m-30) REVERT: A 1205 GLU cc_start: 0.8450 (tp30) cc_final: 0.8234 (mm-30) REVERT: C 122 TYR cc_start: 0.7646 (p90) cc_final: 0.6648 (p90) REVERT: C 242 MET cc_start: 0.3910 (OUTLIER) cc_final: 0.2931 (tpt) REVERT: C 681 GLN cc_start: 0.8790 (tp40) cc_final: 0.8187 (tp40) REVERT: C 697 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8971 (mm) REVERT: C 978 MET cc_start: 0.8553 (mmm) cc_final: 0.8260 (mmm) REVERT: C 999 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8538 (ppp) REVERT: C 1030 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8739 (mmm) REVERT: C 1168 LYS cc_start: 0.9367 (tppt) cc_final: 0.8544 (tppt) REVERT: C 1172 ASP cc_start: 0.8624 (m-30) cc_final: 0.7982 (m-30) REVERT: C 1205 GLU cc_start: 0.8488 (tp30) cc_final: 0.8272 (mm-30) REVERT: B 492 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: B 681 GLN cc_start: 0.8800 (tp40) cc_final: 0.8451 (tp40) REVERT: B 697 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8980 (mm) REVERT: B 999 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8373 (tmm) REVERT: B 1168 LYS cc_start: 0.9372 (tppt) cc_final: 0.8557 (tppt) REVERT: B 1172 ASP cc_start: 0.8616 (m-30) cc_final: 0.8001 (m-30) REVERT: B 1205 GLU cc_start: 0.8488 (tp30) cc_final: 0.8268 (mm-30) REVERT: B 1221 MET cc_start: 0.8794 (mmp) cc_final: 0.8565 (mmm) REVERT: D 625 MET cc_start: 0.8662 (mtt) cc_final: 0.8460 (mtp) REVERT: D 681 GLN cc_start: 0.8963 (tp40) cc_final: 0.8656 (tp40) REVERT: D 685 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8237 (mt-10) REVERT: D 697 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8962 (mm) REVERT: D 999 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8541 (ppp) REVERT: D 1030 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8875 (mmm) REVERT: D 1168 LYS cc_start: 0.9364 (tppt) cc_final: 0.8553 (tppt) REVERT: D 1172 ASP cc_start: 0.8630 (m-30) cc_final: 0.8003 (m-30) REVERT: D 1180 GLU cc_start: 0.8906 (tp30) cc_final: 0.8576 (tm-30) REVERT: D 1205 GLU cc_start: 0.8460 (tp30) cc_final: 0.8241 (mm-30) outliers start: 156 outliers final: 124 residues processed: 537 average time/residue: 0.1815 time to fit residues: 168.4123 Evaluate side-chains 558 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 421 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 563 HIS Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 MET Chi-restraints excluded: chain C residue 1030 MET Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1030 MET Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 967 PHE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 999 MET Chi-restraints excluded: chain D residue 1030 MET Chi-restraints excluded: chain D residue 1068 VAL Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1160 LEU Chi-restraints excluded: chain D residue 1163 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 250 optimal weight: 4.9990 chunk 322 optimal weight: 9.9990 chunk 316 optimal weight: 7.9990 chunk 348 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 271 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 315 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN A1118 HIS ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1118 HIS ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B1118 HIS ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN D1118 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.085432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061926 restraints weight = 116952.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064179 restraints weight = 57343.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065659 restraints weight = 36916.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066564 restraints weight = 27912.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067178 restraints weight = 23504.471| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33736 Z= 0.244 Angle : 0.700 14.584 45968 Z= 0.343 Chirality : 0.042 0.215 5328 Planarity : 0.004 0.049 5676 Dihedral : 6.861 55.246 6200 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.85 % Allowed : 27.78 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.13), residues: 4136 helix: 1.81 (0.10), residues: 2592 sheet: 0.09 (0.31), residues: 288 loop : -1.26 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1203 TYR 0.015 0.001 TYR D 549 PHE 0.020 0.002 PHE A1182 TRP 0.019 0.002 TRP B 621 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00541 (33732) covalent geometry : angle 0.69997 (45960) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.22100 ( 8) hydrogen bonds : bond 0.04517 ( 1997) hydrogen bonds : angle 4.35048 ( 5955) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 408 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7641 (p90) cc_final: 0.6708 (p90) REVERT: A 242 MET cc_start: 0.3856 (OUTLIER) cc_final: 0.2948 (tpt) REVERT: A 492 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8253 (t80) REVERT: A 619 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8822 (ttm) REVERT: A 685 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8102 (mt-10) REVERT: A 697 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9036 (mm) REVERT: A 875 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: A 999 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8517 (ppp) REVERT: A 1168 LYS cc_start: 0.9368 (tppt) cc_final: 0.8555 (tppt) REVERT: A 1172 ASP cc_start: 0.8635 (m-30) cc_final: 0.7993 (m-30) REVERT: A 1209 MET cc_start: 0.8517 (mmm) cc_final: 0.8291 (mpp) REVERT: C 122 TYR cc_start: 0.7598 (p90) cc_final: 0.6702 (p90) REVERT: C 242 MET cc_start: 0.3863 (OUTLIER) cc_final: 0.2938 (tpt) REVERT: C 492 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8242 (t80) REVERT: C 619 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8825 (ttm) REVERT: C 697 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9033 (mm) REVERT: C 875 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: C 978 MET cc_start: 0.8609 (mmm) cc_final: 0.8324 (mmm) REVERT: C 999 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8251 (tmm) REVERT: C 1168 LYS cc_start: 0.9366 (tppt) cc_final: 0.8541 (tppt) REVERT: C 1172 ASP cc_start: 0.8654 (m-30) cc_final: 0.7989 (m-30) REVERT: C 1180 GLU cc_start: 0.8951 (tp30) cc_final: 0.8663 (tm-30) REVERT: B 122 TYR cc_start: 0.7580 (p90) cc_final: 0.6692 (p90) REVERT: B 619 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8857 (ttm) REVERT: B 697 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9039 (mm) REVERT: B 875 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: B 999 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8556 (ppp) REVERT: B 1168 LYS cc_start: 0.9369 (tppt) cc_final: 0.8545 (tppt) REVERT: B 1172 ASP cc_start: 0.8642 (m-30) cc_final: 0.8000 (m-30) REVERT: B 1209 MET cc_start: 0.8491 (mmm) cc_final: 0.8275 (mpp) REVERT: D 122 TYR cc_start: 0.7598 (p90) cc_final: 0.6682 (p90) REVERT: D 619 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8844 (ttm) REVERT: D 681 GLN cc_start: 0.9028 (tp40) cc_final: 0.8619 (tp40) REVERT: D 697 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9033 (mm) REVERT: D 875 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: D 999 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8513 (ppp) REVERT: D 1168 LYS cc_start: 0.9364 (tppt) cc_final: 0.8548 (tppt) REVERT: D 1172 ASP cc_start: 0.8640 (m-30) cc_final: 0.7988 (m-30) REVERT: D 1180 GLU cc_start: 0.8935 (tp30) cc_final: 0.8645 (tm-30) outliers start: 157 outliers final: 121 residues processed: 516 average time/residue: 0.1692 time to fit residues: 152.3280 Evaluate side-chains 541 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 400 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1219 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 563 HIS Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 875 GLU Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 MET Chi-restraints excluded: chain C residue 1030 MET Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1214 VAL Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1030 MET Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 967 PHE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 999 MET Chi-restraints excluded: chain D residue 1030 MET Chi-restraints excluded: chain D residue 1068 VAL Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1160 LEU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1219 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 13 optimal weight: 2.9990 chunk 399 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 121 optimal weight: 30.0000 chunk 375 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.085835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062468 restraints weight = 117308.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064740 restraints weight = 57252.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.066224 restraints weight = 36775.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.067114 restraints weight = 27820.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.067741 restraints weight = 23475.684| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33736 Z= 0.205 Angle : 0.691 14.409 45968 Z= 0.333 Chirality : 0.042 0.214 5328 Planarity : 0.004 0.049 5676 Dihedral : 6.809 55.809 6200 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.72 % Allowed : 28.15 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.13), residues: 4136 helix: 1.78 (0.10), residues: 2600 sheet: 0.07 (0.31), residues: 288 loop : -1.26 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 396 TYR 0.014 0.001 TYR D 549 PHE 0.018 0.001 PHE B1182 TRP 0.021 0.001 TRP B 621 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00457 (33732) covalent geometry : angle 0.69122 (45960) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.21293 ( 8) hydrogen bonds : bond 0.04425 ( 1997) hydrogen bonds : angle 4.29350 ( 5955) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 417 time to evaluate : 1.231 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 122 TYR cc_start: 0.7674 (p90) cc_final: 0.6767 (p90) REVERT: A 242 MET cc_start: 0.3931 (OUTLIER) cc_final: 0.3167 (tpt) REVERT: A 492 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8248 (t80) REVERT: A 619 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8822 (ttm) REVERT: A 681 GLN cc_start: 0.8805 (tp40) cc_final: 0.8275 (tp40) REVERT: A 685 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 697 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9031 (mm) REVERT: A 875 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: A 978 MET cc_start: 0.8673 (mmm) cc_final: 0.8326 (mmm) REVERT: A 999 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8575 (ppp) REVERT: A 1168 LYS cc_start: 0.9370 (tppt) cc_final: 0.8557 (tppt) REVERT: A 1172 ASP cc_start: 0.8638 (m-30) cc_final: 0.7993 (m-30) REVERT: A 1221 MET cc_start: 0.8900 (mmp) cc_final: 0.8470 (mmm) REVERT: C 122 TYR cc_start: 0.7601 (p90) cc_final: 0.6694 (p90) REVERT: C 242 MET cc_start: 0.3882 (OUTLIER) cc_final: 0.3102 (tpt) REVERT: C 492 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8246 (t80) REVERT: C 619 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8800 (ttm) REVERT: C 697 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9030 (mm) REVERT: C 875 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: C 978 MET cc_start: 0.8652 (mmm) cc_final: 0.8352 (mmm) REVERT: C 999 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8549 (ppp) REVERT: C 1168 LYS cc_start: 0.9368 (tppt) cc_final: 0.8556 (tppt) REVERT: C 1172 ASP cc_start: 0.8654 (m-30) cc_final: 0.8000 (m-30) REVERT: C 1180 GLU cc_start: 0.8936 (tp30) cc_final: 0.8657 (tm-30) REVERT: C 1221 MET cc_start: 0.8910 (mmp) cc_final: 0.8495 (mmm) REVERT: B 122 TYR cc_start: 0.7622 (p90) cc_final: 0.6726 (p90) REVERT: B 630 MET cc_start: 0.8134 (tpp) cc_final: 0.7919 (tpp) REVERT: B 697 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9041 (mm) REVERT: B 875 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8221 (pm20) REVERT: B 978 MET cc_start: 0.8663 (mmm) cc_final: 0.8313 (mmm) REVERT: B 999 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8571 (ppp) REVERT: B 1168 LYS cc_start: 0.9376 (tppt) cc_final: 0.8560 (tppt) REVERT: B 1172 ASP cc_start: 0.8640 (m-30) cc_final: 0.7995 (m-30) REVERT: D 122 TYR cc_start: 0.7641 (p90) cc_final: 0.6705 (p90) REVERT: D 492 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8155 (t80) REVERT: D 619 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8821 (ttm) REVERT: D 681 GLN cc_start: 0.9066 (tp40) cc_final: 0.8576 (tm-30) REVERT: D 697 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9027 (mm) REVERT: D 999 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8575 (ppp) REVERT: D 1168 LYS cc_start: 0.9358 (tppt) cc_final: 0.8553 (tppt) REVERT: D 1172 ASP cc_start: 0.8647 (m-30) cc_final: 0.8000 (m-30) REVERT: D 1180 GLU cc_start: 0.8941 (tp30) cc_final: 0.8637 (tm-30) REVERT: D 1221 MET cc_start: 0.8872 (mmp) cc_final: 0.8468 (mmm) outliers start: 153 outliers final: 124 residues processed: 518 average time/residue: 0.1705 time to fit residues: 154.0620 Evaluate side-chains 549 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 406 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1219 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 563 HIS Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 875 GLU Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 MET Chi-restraints excluded: chain C residue 1030 MET Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1214 VAL Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1030 MET Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 967 PHE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 999 MET Chi-restraints excluded: chain D residue 1030 MET Chi-restraints excluded: chain D residue 1068 VAL Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1160 LEU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 335 optimal weight: 30.0000 chunk 348 optimal weight: 0.0670 chunk 311 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 390 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** 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 = 0.3624 r_free = 0.3624 target = 0.087202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063678 restraints weight = 116529.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066071 restraints weight = 55419.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067595 restraints weight = 35001.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068596 restraints weight = 26255.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.069171 restraints weight = 21848.011| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33736 Z= 0.143 Angle : 0.671 14.429 45968 Z= 0.319 Chirality : 0.041 0.205 5328 Planarity : 0.004 0.049 5676 Dihedral : 6.670 59.341 6200 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.23 % Allowed : 28.77 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.13), residues: 4136 helix: 1.89 (0.10), residues: 2600 sheet: 0.04 (0.31), residues: 296 loop : -1.23 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1210 TYR 0.014 0.001 TYR B 958 PHE 0.014 0.001 PHE A1182 TRP 0.021 0.001 TRP B 621 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00321 (33732) covalent geometry : angle 0.67066 (45960) SS BOND : bond 0.00005 ( 4) SS BOND : angle 0.23737 ( 8) hydrogen bonds : bond 0.04149 ( 1997) hydrogen bonds : angle 4.16199 ( 5955) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 437 time to evaluate : 1.305 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 122 TYR cc_start: 0.7698 (p90) cc_final: 0.6775 (p90) REVERT: A 190 VAL cc_start: 0.8638 (m) cc_final: 0.8424 (t) REVERT: A 242 MET cc_start: 0.3812 (OUTLIER) cc_final: 0.2952 (tpt) REVERT: A 646 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9391 (mm) REVERT: A 681 GLN cc_start: 0.8791 (tp40) cc_final: 0.8504 (tp40) REVERT: A 685 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 697 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8989 (mm) REVERT: A 875 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: A 978 MET cc_start: 0.8718 (mmm) cc_final: 0.8385 (mmm) REVERT: A 999 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8515 (ppp) REVERT: A 1168 LYS cc_start: 0.9353 (tppt) cc_final: 0.8530 (tppt) REVERT: A 1172 ASP cc_start: 0.8648 (m-30) cc_final: 0.8007 (m-30) REVERT: A 1221 MET cc_start: 0.8889 (mmp) cc_final: 0.8434 (mmm) REVERT: C 122 TYR cc_start: 0.7575 (p90) cc_final: 0.6666 (p90) REVERT: C 242 MET cc_start: 0.3772 (OUTLIER) cc_final: 0.3065 (tpt) REVERT: C 646 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9392 (mm) REVERT: C 697 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8991 (mm) REVERT: C 978 MET cc_start: 0.8678 (mmm) cc_final: 0.8324 (mmm) REVERT: C 999 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8412 (tmm) REVERT: C 1168 LYS cc_start: 0.9355 (tppt) cc_final: 0.8528 (tppt) REVERT: C 1172 ASP cc_start: 0.8667 (m-30) cc_final: 0.8019 (m-30) REVERT: C 1180 GLU cc_start: 0.8943 (tp30) cc_final: 0.8531 (tp30) REVERT: C 1205 GLU cc_start: 0.8375 (tp30) cc_final: 0.8125 (mm-30) REVERT: C 1221 MET cc_start: 0.8923 (mmp) cc_final: 0.8525 (mmm) REVERT: B 122 TYR cc_start: 0.7594 (p90) cc_final: 0.6679 (p90) REVERT: B 492 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: B 646 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9390 (mm) REVERT: B 697 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 875 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: B 978 MET cc_start: 0.8693 (mmm) cc_final: 0.8352 (mmm) REVERT: B 999 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8407 (tmm) REVERT: B 1168 LYS cc_start: 0.9358 (tppt) cc_final: 0.8537 (tppt) REVERT: B 1172 ASP cc_start: 0.8665 (m-30) cc_final: 0.8048 (m-30) REVERT: D 122 TYR cc_start: 0.7616 (p90) cc_final: 0.6674 (p90) REVERT: D 492 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8166 (t80) REVERT: D 681 GLN cc_start: 0.9032 (tp40) cc_final: 0.8616 (tm-30) REVERT: D 697 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8986 (mm) REVERT: D 875 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: D 978 MET cc_start: 0.8671 (mmm) cc_final: 0.8414 (mmm) REVERT: D 999 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8517 (ppp) REVERT: D 1168 LYS cc_start: 0.9355 (tppt) cc_final: 0.8533 (tppt) REVERT: D 1172 ASP cc_start: 0.8666 (m-30) cc_final: 0.8022 (m-30) REVERT: D 1180 GLU cc_start: 0.8967 (tp30) cc_final: 0.8601 (tm-30) REVERT: D 1205 GLU cc_start: 0.8525 (tp30) cc_final: 0.8254 (mm-30) REVERT: D 1221 MET cc_start: 0.8885 (mmp) cc_final: 0.8459 (mmm) outliers start: 137 outliers final: 110 residues processed: 526 average time/residue: 0.1696 time to fit residues: 155.1488 Evaluate side-chains 553 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 425 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 563 HIS Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 SER Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 967 PHE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 MET Chi-restraints excluded: chain C residue 1030 MET Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 966 ILE Chi-restraints excluded: chain B residue 967 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1030 MET Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 713 THR Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 966 ILE Chi-restraints excluded: chain D residue 967 PHE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 999 MET Chi-restraints excluded: chain D residue 1030 MET Chi-restraints excluded: chain D residue 1068 VAL Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1160 LEU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 125 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 297 optimal weight: 4.9990 chunk 344 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 374 optimal weight: 0.9980 chunk 405 optimal weight: 0.8980 chunk 340 optimal weight: 8.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1215 ASN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** 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 = 0.3616 r_free = 0.3616 target = 0.086792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063415 restraints weight = 116609.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065726 restraints weight = 56451.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067196 restraints weight = 35976.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068176 restraints weight = 27138.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068798 restraints weight = 22639.918| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33736 Z= 0.162 Angle : 0.680 14.360 45968 Z= 0.325 Chirality : 0.041 0.203 5328 Planarity : 0.004 0.049 5676 Dihedral : 6.568 58.671 6196 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.17 % Allowed : 29.04 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.13), residues: 4136 helix: 1.91 (0.10), residues: 2592 sheet: -0.02 (0.31), residues: 296 loop : -1.25 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 396 TYR 0.014 0.001 TYR D 549 PHE 0.015 0.001 PHE A1182 TRP 0.027 0.001 TRP D 621 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00365 (33732) covalent geometry : angle 0.67994 (45960) SS BOND : bond 0.00008 ( 4) SS BOND : angle 0.24954 ( 8) hydrogen bonds : bond 0.04176 ( 1997) hydrogen bonds : angle 4.17135 ( 5955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6209.08 seconds wall clock time: 108 minutes 0.31 seconds (6480.31 seconds total)