Starting phenix.real_space_refine on Mon Jul 28 08:55:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvp_27012/07_2025/8cvp_27012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvp_27012/07_2025/8cvp_27012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cvp_27012/07_2025/8cvp_27012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvp_27012/07_2025/8cvp_27012.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvp_27012/07_2025/8cvp_27012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvp_27012/07_2025/8cvp_27012.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.055 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 6340 2.51 5 N 1780 2.21 5 O 1943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10112 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 7904 Classifications: {'peptide': 1135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 297} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 39, 'TRANS': 1091} Chain breaks: 1 Unresolved non-hydrogen bonds: 1011 Unresolved non-hydrogen angles: 1287 Unresolved non-hydrogen dihedrals: 813 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 18, 'TYR:plan': 7, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 9, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 536 Chain: "B" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2207 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 330} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 648 Unresolved non-hydrogen angles: 824 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 355 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9622 SG CYS B 323 50.818 30.708 18.486 1.00157.30 S ATOM 9638 SG CYS B 326 48.791 27.319 18.587 1.00163.96 S ATOM 9904 SG CYS B 391 52.433 27.620 17.040 1.00184.67 S ATOM 9920 SG CYS B 394 49.311 28.958 15.432 1.00187.88 S Time building chain proxies: 6.56, per 1000 atoms: 0.65 Number of scatterers: 10112 At special positions: 0 Unit cell: (96.6, 106.95, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 1943 8.00 N 1780 7.00 C 6340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " Number of angles added : 6 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 29 sheets defined 11.3% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1059 Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1101 through 1109 Processing helix chain 'A' and resid 1123 through 1126 removed outlier: 4.281A pdb=" N ALA A1126 " --> pdb=" O GLU A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1123 through 1126' Processing helix chain 'A' and resid 1127 through 1138 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.508A pdb=" N PHE B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.509A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.677A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.562A pdb=" N GLU B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 6.999A pdb=" N GLY A1031 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE A1007 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A1029 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.528A pdb=" N ILE A 41 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 53 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 65 removed outlier: 6.501A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.600A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 7.026A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 194 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169 removed outlier: 7.026A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.572A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.529A pdb=" N CYS A 260 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 306 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 302 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.538A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 364 through 365 removed outlier: 3.690A pdb=" N ARG A 391 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A 711 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 396 through 403 removed outlier: 6.820A pdb=" N ILE A 701 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER A 401 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU A 699 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AB4, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.383A pdb=" N VAL A 476 " --> pdb=" O TRP A 490 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 490 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 488 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER A 480 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU A 486 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 498 through 503 removed outlier: 4.157A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 529 " --> pdb=" O TYR A 518 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 556 through 560 removed outlier: 3.601A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 566 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS A 579 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 568 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 588 through 594 removed outlier: 3.531A pdb=" N SER A 590 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 629 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 639 removed outlier: 3.615A pdb=" N SER A 669 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 727 Processing sheet with id=AC1, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.773A pdb=" N ILE A 794 " --> pdb=" O PHE A 733 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 737 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 790 " --> pdb=" O SER A 737 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS A 789 " --> pdb=" O GLN A 806 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN A 806 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU A 791 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 804 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 793 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 811 through 813 Processing sheet with id=AC3, first strand: chain 'A' and resid 811 through 813 removed outlier: 3.638A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY A 846 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU A 865 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.387A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 913 through 917 removed outlier: 3.569A pdb=" N LYS A 917 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 945 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 936 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 957 through 959 removed outlier: 6.499A pdb=" N LEU A 974 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 997 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 976 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC8, first strand: chain 'B' and resid 65 through 66 removed outlier: 14.037A pdb=" N THR B 119 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL B 80 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ALA B 121 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 123 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 180 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 169 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN B 183 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 167 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 155 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 101 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 65 through 66 removed outlier: 7.134A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR B 144 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 156 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU B 146 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 154 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN B 148 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 155 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 101 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 320 through 322 removed outlier: 4.150A pdb=" N THR B 332 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 368 through 371 removed outlier: 3.671A pdb=" N GLY B 399 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS B 391 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS B 397 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP B 400 " --> pdb=" O GLY B 416 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 978 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: 5.19 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3513 1.34 - 1.46: 2190 1.46 - 1.58: 4511 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 10284 Sorted by residual: bond pdb=" CG1 ILE B 257 " pdb=" CD1 ILE B 257 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 bond pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.40e-01 bond pdb=" CB ASP A 243 " pdb=" CG ASP A 243 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.66e-01 bond pdb=" CB ASP A 986 " pdb=" CG ASP A 986 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.88e-01 bond pdb=" CB ARG A 198 " pdb=" CG ARG A 198 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.82e-01 ... (remaining 10279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 14001 3.09 - 6.18: 61 6.18 - 9.27: 3 9.27 - 12.35: 0 12.35 - 15.44: 1 Bond angle restraints: 14066 Sorted by residual: angle pdb=" C LEU B 423 " pdb=" N PRO B 424 " pdb=" CA PRO B 424 " ideal model delta sigma weight residual 127.00 142.44 -15.44 2.40e+00 1.74e-01 4.14e+01 angle pdb=" N ILE B 398 " pdb=" CA ILE B 398 " pdb=" C ILE B 398 " ideal model delta sigma weight residual 113.47 109.30 4.17 1.01e+00 9.80e-01 1.71e+01 angle pdb=" C GLY A1119 " pdb=" N MET A1120 " pdb=" CA MET A1120 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N ASP A1127 " pdb=" CA ASP A1127 " pdb=" C ASP A1127 " ideal model delta sigma weight residual 114.56 110.40 4.16 1.27e+00 6.20e-01 1.07e+01 angle pdb=" N GLU A1107 " pdb=" CA GLU A1107 " pdb=" CB GLU A1107 " ideal model delta sigma weight residual 110.28 114.87 -4.59 1.55e+00 4.16e-01 8.77e+00 ... (remaining 14061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5706 17.89 - 35.78: 354 35.78 - 53.67: 61 53.67 - 71.56: 13 71.56 - 89.45: 10 Dihedral angle restraints: 6144 sinusoidal: 1847 harmonic: 4297 Sorted by residual: dihedral pdb=" CA TYR A 828 " pdb=" C TYR A 828 " pdb=" N PHE A 829 " pdb=" CA PHE A 829 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA LEU A1112 " pdb=" C LEU A1112 " pdb=" N GLN A1113 " pdb=" CA GLN A1113 " ideal model delta harmonic sigma weight residual 180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL A 836 " pdb=" C VAL A 836 " pdb=" N TYR A 837 " pdb=" CA TYR A 837 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1293 0.048 - 0.096: 267 0.096 - 0.144: 108 0.144 - 0.192: 1 0.192 - 0.240: 1 Chirality restraints: 1670 Sorted by residual: chirality pdb=" CB ILE A 220 " pdb=" CA ILE A 220 " pdb=" CG1 ILE A 220 " pdb=" CG2 ILE A 220 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 957 " pdb=" CA VAL A 957 " pdb=" CG1 VAL A 957 " pdb=" CG2 VAL A 957 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE A 848 " pdb=" N ILE A 848 " pdb=" C ILE A 848 " pdb=" CB ILE A 848 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1667 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 416 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A 417 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 522 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 523 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 276 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO B 277 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " 0.024 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1466 2.77 - 3.30: 9372 3.30 - 3.83: 15159 3.83 - 4.37: 16829 4.37 - 4.90: 31226 Nonbonded interactions: 74052 Sorted by model distance: nonbonded pdb=" OH TYR B 227 " pdb=" OD2 ASP B 249 " model vdw 2.231 3.040 nonbonded pdb=" OE2 GLU A 277 " pdb=" NH1 ARG A 279 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASP A 986 " pdb=" N GLU A 987 " model vdw 2.290 3.120 nonbonded pdb=" NH1 ARG A 301 " pdb=" OE2 GLU A 303 " model vdw 2.309 3.120 nonbonded pdb=" NZ LYS A 141 " pdb=" OD1 ASN A 156 " model vdw 2.320 3.120 ... (remaining 74047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.070 Set scattering table: 0.090 Process input model: 32.060 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.003 0.048 10288 Z= 0.118 Angle : 0.587 15.443 14072 Z= 0.311 Chirality : 0.045 0.240 1670 Planarity : 0.004 0.046 1880 Dihedral : 13.055 89.454 3360 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.23), residues: 1476 helix: 1.38 (0.45), residues: 151 sheet: -1.39 (0.23), residues: 539 loop : -1.37 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 207 HIS 0.002 0.001 HIS A 805 PHE 0.016 0.002 PHE B 208 TYR 0.025 0.001 TYR A 837 ARG 0.013 0.001 ARG B 230 Details of bonding type rmsd hydrogen bonds : bond 0.25304 ( 353) hydrogen bonds : angle 10.65942 ( 978) metal coordination : bond 0.01011 ( 4) metal coordination : angle 5.14899 ( 6) covalent geometry : bond 0.00259 (10284) covalent geometry : angle 0.57760 (14066) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.086 Fit side-chains REVERT: A 25 SER cc_start: 0.9107 (t) cc_final: 0.8810 (p) REVERT: A 90 GLU cc_start: 0.7209 (tt0) cc_final: 0.6803 (tt0) REVERT: A 151 GLU cc_start: 0.7488 (tp30) cc_final: 0.6894 (tp30) REVERT: A 158 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.7988 (tpt90) REVERT: A 193 TYR cc_start: 0.8738 (m-80) cc_final: 0.7912 (m-80) REVERT: A 279 ARG cc_start: 0.8084 (ptp90) cc_final: 0.7844 (ptp-170) REVERT: A 900 ARG cc_start: 0.7002 (ttp80) cc_final: 0.6318 (ptm-80) REVERT: B 283 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.7046 (ttt-90) REVERT: B 313 ASP cc_start: 0.7167 (t0) cc_final: 0.6456 (m-30) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2490 time to fit residues: 56.0798 Evaluate side-chains 126 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 61 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 115 optimal weight: 0.0050 chunk 44 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.208027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.166173 restraints weight = 11902.583| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.50 r_work: 0.3750 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10288 Z= 0.163 Angle : 0.607 10.115 14072 Z= 0.314 Chirality : 0.047 0.234 1670 Planarity : 0.005 0.051 1880 Dihedral : 4.122 20.540 1554 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.62 % Favored : 94.31 % Rotamer: Outliers : 1.44 % Allowed : 8.63 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1476 helix: 0.85 (0.42), residues: 158 sheet: -1.35 (0.23), residues: 549 loop : -1.51 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 386 HIS 0.004 0.001 HIS A 805 PHE 0.016 0.002 PHE B 208 TYR 0.014 0.001 TYR A 837 ARG 0.008 0.001 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 353) hydrogen bonds : angle 6.89427 ( 978) metal coordination : bond 0.00815 ( 4) metal coordination : angle 5.25019 ( 6) covalent geometry : bond 0.00381 (10284) covalent geometry : angle 0.59744 (14066) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7649 (tp30) cc_final: 0.7210 (tp30) REVERT: A 193 TYR cc_start: 0.8801 (m-80) cc_final: 0.8403 (m-80) REVERT: A 784 GLU cc_start: 0.7661 (tp30) cc_final: 0.7443 (tp30) REVERT: A 900 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7317 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7333 (pp30) cc_final: 0.7090 (pp30) REVERT: B 255 ASP cc_start: 0.8199 (t0) cc_final: 0.7962 (t70) REVERT: B 283 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7638 (ttt-90) REVERT: B 313 ASP cc_start: 0.8143 (t0) cc_final: 0.7416 (m-30) REVERT: B 386 TRP cc_start: 0.5931 (p-90) cc_final: 0.5701 (p-90) outliers start: 12 outliers final: 10 residues processed: 140 average time/residue: 0.2577 time to fit residues: 49.1076 Evaluate side-chains 132 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 135 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 125 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 112 optimal weight: 0.4980 chunk 107 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.203929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.162181 restraints weight = 12201.070| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.47 r_work: 0.3723 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10288 Z= 0.184 Angle : 0.599 8.429 14072 Z= 0.308 Chirality : 0.047 0.201 1670 Planarity : 0.004 0.051 1880 Dihedral : 4.194 20.806 1554 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 2.28 % Allowed : 11.15 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1476 helix: 0.72 (0.42), residues: 158 sheet: -1.32 (0.22), residues: 547 loop : -1.57 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 207 HIS 0.004 0.001 HIS A 22 PHE 0.017 0.002 PHE B 208 TYR 0.018 0.002 TYR A 346 ARG 0.011 0.001 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 353) hydrogen bonds : angle 6.13435 ( 978) metal coordination : bond 0.00786 ( 4) metal coordination : angle 4.60152 ( 6) covalent geometry : bond 0.00444 (10284) covalent geometry : angle 0.59150 (14066) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.057 Fit side-chains REVERT: A 57 MET cc_start: 0.8153 (ttm) cc_final: 0.7726 (ttt) REVERT: A 151 GLU cc_start: 0.7888 (tp30) cc_final: 0.7393 (tp30) REVERT: A 193 TYR cc_start: 0.8845 (m-80) cc_final: 0.8600 (m-80) REVERT: A 784 GLU cc_start: 0.7709 (tp30) cc_final: 0.7460 (tp30) REVERT: A 900 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7522 (ptm-80) REVERT: A 989 ARG cc_start: 0.8567 (ptp-170) cc_final: 0.8182 (ptp90) REVERT: A 1015 GLN cc_start: 0.7529 (pp30) cc_final: 0.7226 (pp30) REVERT: B 255 ASP cc_start: 0.8469 (t0) cc_final: 0.8239 (t70) REVERT: B 260 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 283 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7768 (ttt-90) REVERT: B 313 ASP cc_start: 0.8293 (t0) cc_final: 0.8072 (t0) REVERT: B 314 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8218 (mt) REVERT: B 386 TRP cc_start: 0.5913 (p-90) cc_final: 0.5541 (p-90) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.2463 time to fit residues: 45.4145 Evaluate side-chains 132 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A1055 GLN B 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.201505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159702 restraints weight = 12020.441| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.46 r_work: 0.3692 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10288 Z= 0.225 Angle : 0.629 8.654 14072 Z= 0.323 Chirality : 0.047 0.183 1670 Planarity : 0.004 0.049 1880 Dihedral : 4.381 21.204 1554 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.98 % Favored : 92.95 % Rotamer: Outliers : 3.00 % Allowed : 12.59 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.22), residues: 1476 helix: 0.59 (0.42), residues: 158 sheet: -1.44 (0.22), residues: 551 loop : -1.64 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 207 HIS 0.003 0.001 HIS A 22 PHE 0.015 0.002 PHE B 208 TYR 0.018 0.002 TYR A 346 ARG 0.006 0.001 ARG B 262 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 353) hydrogen bonds : angle 5.95405 ( 978) metal coordination : bond 0.00668 ( 4) metal coordination : angle 4.72568 ( 6) covalent geometry : bond 0.00548 (10284) covalent geometry : angle 0.62200 (14066) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.137 Fit side-chains REVERT: A 57 MET cc_start: 0.8177 (ttm) cc_final: 0.7782 (ttt) REVERT: A 151 GLU cc_start: 0.7857 (tp30) cc_final: 0.7555 (tp30) REVERT: A 156 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8642 (m-40) REVERT: A 193 TYR cc_start: 0.8889 (m-80) cc_final: 0.8680 (m-80) REVERT: A 784 GLU cc_start: 0.7673 (tp30) cc_final: 0.7471 (tp30) REVERT: A 876 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: A 900 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7413 (ptm-80) REVERT: A 989 ARG cc_start: 0.8558 (ptp-170) cc_final: 0.8156 (ptp90) REVERT: A 1015 GLN cc_start: 0.7529 (pp30) cc_final: 0.7176 (pp30) REVERT: A 1036 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8595 (ttm) REVERT: B 283 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7757 (ttt-90) REVERT: B 314 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8255 (mt) REVERT: B 386 TRP cc_start: 0.5863 (p-90) cc_final: 0.5367 (p-90) outliers start: 25 outliers final: 18 residues processed: 135 average time/residue: 0.2639 time to fit residues: 48.9187 Evaluate side-chains 139 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 91 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.204421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162789 restraints weight = 12010.114| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.50 r_work: 0.3732 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10288 Z= 0.134 Angle : 0.557 8.128 14072 Z= 0.288 Chirality : 0.045 0.159 1670 Planarity : 0.004 0.051 1880 Dihedral : 4.128 21.183 1554 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Rotamer: Outliers : 2.28 % Allowed : 14.15 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.22), residues: 1476 helix: 0.71 (0.42), residues: 158 sheet: -1.30 (0.22), residues: 542 loop : -1.68 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 207 HIS 0.003 0.001 HIS A1009 PHE 0.013 0.001 PHE A 829 TYR 0.013 0.001 TYR B 221 ARG 0.006 0.000 ARG B 262 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 353) hydrogen bonds : angle 5.56445 ( 978) metal coordination : bond 0.00731 ( 4) metal coordination : angle 4.52487 ( 6) covalent geometry : bond 0.00319 (10284) covalent geometry : angle 0.54920 (14066) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8172 (ttm) cc_final: 0.7697 (ttt) REVERT: A 151 GLU cc_start: 0.7806 (tp30) cc_final: 0.7527 (tp30) REVERT: A 178 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8569 (pt) REVERT: A 312 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 784 GLU cc_start: 0.7644 (tp30) cc_final: 0.7436 (tp30) REVERT: A 876 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: A 900 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7422 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7497 (pp30) cc_final: 0.7100 (pp30) REVERT: B 313 ASP cc_start: 0.8243 (t0) cc_final: 0.7489 (m-30) REVERT: B 314 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8220 (mt) REVERT: B 386 TRP cc_start: 0.6131 (p-90) cc_final: 0.5552 (p-90) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.2470 time to fit residues: 47.3668 Evaluate side-chains 139 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 136 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 123 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS A1055 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.197789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155515 restraints weight = 12170.788| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.64 r_work: 0.3651 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 10288 Z= 0.342 Angle : 0.731 9.845 14072 Z= 0.374 Chirality : 0.050 0.196 1670 Planarity : 0.005 0.052 1880 Dihedral : 4.795 21.530 1554 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.32 % Allowed : 14.51 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.21), residues: 1476 helix: 0.35 (0.42), residues: 158 sheet: -1.57 (0.22), residues: 552 loop : -1.81 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 207 HIS 0.004 0.001 HIS A 789 PHE 0.022 0.003 PHE A 169 TYR 0.026 0.003 TYR A 346 ARG 0.005 0.001 ARG B 262 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 353) hydrogen bonds : angle 6.06718 ( 978) metal coordination : bond 0.00625 ( 4) metal coordination : angle 4.52670 ( 6) covalent geometry : bond 0.00832 (10284) covalent geometry : angle 0.72543 (14066) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8445 (ttm) cc_final: 0.7968 (ttt) REVERT: A 151 GLU cc_start: 0.7964 (tp30) cc_final: 0.7665 (tp30) REVERT: A 156 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8625 (m-40) REVERT: A 178 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8725 (pt) REVERT: A 248 ILE cc_start: 0.7687 (mm) cc_final: 0.7476 (mm) REVERT: A 835 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.7056 (mtt) REVERT: A 900 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7511 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7689 (pp30) cc_final: 0.7281 (pp30) REVERT: A 1036 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8663 (ttm) REVERT: B 260 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8166 (tm-30) REVERT: B 265 ASP cc_start: 0.7685 (t70) cc_final: 0.7201 (t70) REVERT: B 386 TRP cc_start: 0.6187 (p-90) cc_final: 0.5545 (p-90) outliers start: 36 outliers final: 25 residues processed: 140 average time/residue: 0.2590 time to fit residues: 50.0590 Evaluate side-chains 143 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 133 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 142 optimal weight: 40.0000 chunk 122 optimal weight: 40.0000 chunk 126 optimal weight: 0.8980 chunk 48 optimal weight: 40.0000 chunk 73 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.189291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147189 restraints weight = 12417.937| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.71 r_work: 0.3571 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10288 Z= 0.131 Angle : 0.564 8.283 14072 Z= 0.292 Chirality : 0.046 0.174 1670 Planarity : 0.004 0.053 1880 Dihedral : 4.242 21.749 1554 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.40 % Allowed : 16.91 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.21), residues: 1476 helix: 0.63 (0.43), residues: 158 sheet: -1.41 (0.22), residues: 538 loop : -1.73 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 207 HIS 0.003 0.001 HIS A1070 PHE 0.012 0.001 PHE A 771 TYR 0.014 0.001 TYR B 221 ARG 0.010 0.001 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 353) hydrogen bonds : angle 5.47400 ( 978) metal coordination : bond 0.00745 ( 4) metal coordination : angle 4.74406 ( 6) covalent geometry : bond 0.00312 (10284) covalent geometry : angle 0.55525 (14066) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8266 (ttm) cc_final: 0.7886 (ttt) REVERT: A 151 GLU cc_start: 0.7727 (tp30) cc_final: 0.7457 (tp30) REVERT: A 312 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 876 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: A 989 ARG cc_start: 0.8543 (ptp-170) cc_final: 0.7694 (ptp90) REVERT: A 1015 GLN cc_start: 0.7716 (pp30) cc_final: 0.7337 (pp30) REVERT: A 1036 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8556 (ttm) REVERT: B 265 ASP cc_start: 0.7483 (t70) cc_final: 0.7083 (t70) REVERT: B 314 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8319 (mt) REVERT: B 386 TRP cc_start: 0.6089 (p-90) cc_final: 0.5469 (p-90) outliers start: 20 outliers final: 16 residues processed: 137 average time/residue: 0.2434 time to fit residues: 46.2684 Evaluate side-chains 139 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 45 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1055 GLN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.186833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144845 restraints weight = 12449.499| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.61 r_work: 0.3521 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10288 Z= 0.215 Angle : 0.620 8.096 14072 Z= 0.317 Chirality : 0.047 0.174 1670 Planarity : 0.004 0.053 1880 Dihedral : 4.378 21.269 1554 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.00 % Allowed : 16.91 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.21), residues: 1476 helix: 0.56 (0.42), residues: 158 sheet: -1.40 (0.22), residues: 541 loop : -1.77 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 207 HIS 0.003 0.001 HIS A1009 PHE 0.016 0.002 PHE A 829 TYR 0.017 0.002 TYR A 346 ARG 0.008 0.001 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 353) hydrogen bonds : angle 5.52821 ( 978) metal coordination : bond 0.00652 ( 4) metal coordination : angle 4.77314 ( 6) covalent geometry : bond 0.00524 (10284) covalent geometry : angle 0.61195 (14066) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8402 (ttm) cc_final: 0.7940 (ttt) REVERT: A 151 GLU cc_start: 0.7775 (tp30) cc_final: 0.7491 (tp30) REVERT: A 174 GLN cc_start: 0.8271 (tp40) cc_final: 0.8030 (pm20) REVERT: A 178 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8617 (pt) REVERT: A 248 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7439 (mm) REVERT: A 312 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8706 (tm-30) REVERT: A 1015 GLN cc_start: 0.7710 (pp30) cc_final: 0.7316 (pp30) REVERT: A 1036 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8533 (ttm) REVERT: B 260 GLN cc_start: 0.8311 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 265 ASP cc_start: 0.7473 (t70) cc_final: 0.6955 (t70) REVERT: B 386 TRP cc_start: 0.6072 (p-90) cc_final: 0.5490 (p-90) outliers start: 25 outliers final: 19 residues processed: 133 average time/residue: 0.2439 time to fit residues: 45.7448 Evaluate side-chains 139 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 124 optimal weight: 50.0000 chunk 46 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.189882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.147366 restraints weight = 12282.820| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.65 r_work: 0.3561 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10288 Z= 0.120 Angle : 0.558 8.276 14072 Z= 0.287 Chirality : 0.045 0.185 1670 Planarity : 0.004 0.053 1880 Dihedral : 4.092 21.407 1554 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.52 % Allowed : 17.75 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.21), residues: 1476 helix: 0.59 (0.42), residues: 158 sheet: -1.30 (0.22), residues: 529 loop : -1.70 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 207 HIS 0.003 0.001 HIS A1009 PHE 0.012 0.001 PHE A 829 TYR 0.013 0.001 TYR B 221 ARG 0.007 0.001 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 353) hydrogen bonds : angle 5.25283 ( 978) metal coordination : bond 0.00703 ( 4) metal coordination : angle 4.71034 ( 6) covalent geometry : bond 0.00288 (10284) covalent geometry : angle 0.54989 (14066) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8117 (ttm) cc_final: 0.7779 (ttt) REVERT: A 151 GLU cc_start: 0.7510 (tp30) cc_final: 0.7310 (tp30) REVERT: A 156 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8528 (m-40) REVERT: A 193 TYR cc_start: 0.8693 (m-80) cc_final: 0.8476 (m-80) REVERT: A 312 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 876 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: A 989 ARG cc_start: 0.8452 (ptp-170) cc_final: 0.7533 (ptp90) REVERT: A 1015 GLN cc_start: 0.7543 (pp30) cc_final: 0.7154 (pp30) REVERT: A 1036 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8402 (ttm) REVERT: B 260 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 386 TRP cc_start: 0.5968 (p-90) cc_final: 0.5423 (p-90) outliers start: 21 outliers final: 18 residues processed: 138 average time/residue: 0.2354 time to fit residues: 45.8490 Evaluate side-chains 143 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 146 optimal weight: 40.0000 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 140 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.191762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.150050 restraints weight = 12344.109| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.59 r_work: 0.3581 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10288 Z= 0.120 Angle : 0.553 8.313 14072 Z= 0.285 Chirality : 0.045 0.184 1670 Planarity : 0.004 0.053 1880 Dihedral : 3.982 21.264 1554 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.52 % Allowed : 17.75 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.21), residues: 1476 helix: 0.60 (0.42), residues: 160 sheet: -1.24 (0.22), residues: 530 loop : -1.71 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 207 HIS 0.003 0.001 HIS A1070 PHE 0.012 0.001 PHE A 829 TYR 0.013 0.001 TYR B 221 ARG 0.006 0.000 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 353) hydrogen bonds : angle 5.08935 ( 978) metal coordination : bond 0.00676 ( 4) metal coordination : angle 4.77219 ( 6) covalent geometry : bond 0.00287 (10284) covalent geometry : angle 0.54420 (14066) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8229 (ttm) cc_final: 0.7839 (ttt) REVERT: A 151 GLU cc_start: 0.7636 (tp30) cc_final: 0.7384 (tp30) REVERT: A 156 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8560 (m-40) REVERT: A 193 TYR cc_start: 0.8784 (m-80) cc_final: 0.8579 (m-80) REVERT: A 312 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 989 ARG cc_start: 0.8486 (ptp-170) cc_final: 0.7572 (ptp90) REVERT: A 1015 GLN cc_start: 0.7682 (pp30) cc_final: 0.7282 (pp30) REVERT: A 1036 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8674 (ttt) REVERT: B 260 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 386 TRP cc_start: 0.5982 (p-90) cc_final: 0.5411 (p-90) outliers start: 21 outliers final: 18 residues processed: 138 average time/residue: 0.2221 time to fit residues: 43.3583 Evaluate side-chains 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 877 ASN Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN B 236 ASN B 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.186529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144697 restraints weight = 12311.130| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.58 r_work: 0.3519 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10288 Z= 0.246 Angle : 0.640 8.284 14072 Z= 0.329 Chirality : 0.047 0.182 1670 Planarity : 0.005 0.052 1880 Dihedral : 4.353 21.324 1554 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.12 % Allowed : 17.27 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1476 helix: 0.48 (0.42), residues: 158 sheet: -1.31 (0.22), residues: 532 loop : -1.76 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 207 HIS 0.004 0.001 HIS A1009 PHE 0.022 0.002 PHE A 876 TYR 0.019 0.002 TYR A 239 ARG 0.006 0.001 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 353) hydrogen bonds : angle 5.40321 ( 978) metal coordination : bond 0.00621 ( 4) metal coordination : angle 4.31009 ( 6) covalent geometry : bond 0.00598 (10284) covalent geometry : angle 0.63428 (14066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5842.06 seconds wall clock time: 100 minutes 30.84 seconds (6030.84 seconds total)