Starting phenix.real_space_refine on Fri Feb 14 12:27:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvp_27012/02_2025/8cvp_27012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvp_27012/02_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_27012/02_2025/8cvp_27012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvp_27012/02_2025/8cvp_27012.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvp_27012/02_2025/8cvp_27012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvp_27012/02_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-5592/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: 6.19, per 1000 atoms: 0.61 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: 2.67 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: 1.73 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: 4.90 Time building geometry restraints manager: 3.02 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: 0.480 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.190 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- 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 10284 Z= 0.179 Angle : 0.578 15.443 14066 Z= 0.310 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 *********************** 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 : 1.110 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: 0.2678 time to fit residues: 59.9186 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 : 1.083 ------------------------------------------------------------------------------- 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 = 0.208026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.166172 restraints weight = 11902.594| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.50 r_work: 0.3753 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 10284 Z= 0.258 Angle : 0.597 7.492 14066 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 *********************** 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 : 1.089 Fit side-chains revert: symmetry clash REVERT: A 25 SER cc_start: 0.9108 (t) cc_final: 0.8899 (p) REVERT: A 151 GLU cc_start: 0.7904 (tp30) cc_final: 0.7386 (tp30) REVERT: A 193 TYR cc_start: 0.8894 (m-80) cc_final: 0.8510 (m-80) REVERT: A 784 GLU cc_start: 0.7826 (tp30) cc_final: 0.7589 (tp30) REVERT: A 900 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7543 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7468 (pp30) cc_final: 0.7225 (pp30) REVERT: B 255 ASP cc_start: 0.8402 (t0) cc_final: 0.8165 (t70) REVERT: B 283 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7782 (ttt-90) REVERT: B 313 ASP cc_start: 0.8358 (t0) cc_final: 0.7617 (m-30) REVERT: B 386 TRP cc_start: 0.5956 (p-90) cc_final: 0.5726 (p-90) outliers start: 12 outliers final: 10 residues processed: 140 average time/residue: 0.2733 time to fit residues: 51.7779 Evaluate side-chains 133 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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: 0.7980 chunk 103 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 125 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 112 optimal weight: 0.0470 chunk 107 optimal weight: 0.0470 chunk 116 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.2176 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.211424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.169336 restraints weight = 12145.909| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.64 r_work: 0.3814 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10284 Z= 0.139 Angle : 0.519 7.984 14066 Z= 0.273 Chirality : 0.045 0.158 1670 Planarity : 0.004 0.051 1880 Dihedral : 3.843 20.143 1554 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 1.56 % Allowed : 10.67 % Favored : 87.77 % 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: -1.72 (0.22), residues: 1476 helix: 0.89 (0.43), residues: 158 sheet: -1.18 (0.23), residues: 536 loop : -1.51 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.002 0.001 HIS A 805 PHE 0.012 0.001 PHE B 208 TYR 0.010 0.001 TYR B 221 ARG 0.010 0.001 ARG A 947 *********************** 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 151 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 25 SER cc_start: 0.9033 (t) cc_final: 0.8809 (p) REVERT: A 151 GLU cc_start: 0.7890 (tp30) cc_final: 0.7398 (tp30) REVERT: A 183 GLN cc_start: 0.8736 (tp40) cc_final: 0.8262 (tt0) REVERT: A 784 GLU cc_start: 0.7691 (tp30) cc_final: 0.7399 (tp30) REVERT: A 900 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7522 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7460 (pp30) cc_final: 0.7142 (pp30) REVERT: B 255 ASP cc_start: 0.8410 (t0) cc_final: 0.8177 (t70) REVERT: B 260 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 283 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7586 (ttt-90) REVERT: B 313 ASP cc_start: 0.8333 (t0) cc_final: 0.7473 (m-30) REVERT: B 386 TRP cc_start: 0.5772 (p-90) cc_final: 0.5408 (p-90) outliers start: 13 outliers final: 9 residues processed: 142 average time/residue: 0.2515 time to fit residues: 49.1973 Evaluate side-chains 136 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 877 ASN 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 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: 2.9990 chunk 97 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN B 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.204181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161937 restraints weight = 12000.424| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.58 r_work: 0.3728 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10284 Z= 0.318 Angle : 0.594 7.608 14066 Z= 0.307 Chirality : 0.046 0.166 1670 Planarity : 0.004 0.051 1880 Dihedral : 4.116 20.754 1554 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 1.92 % Allowed : 11.63 % Favored : 86.45 % 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: -1.87 (0.22), residues: 1476 helix: 0.72 (0.42), residues: 160 sheet: -1.32 (0.22), residues: 554 loop : -1.56 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 224 HIS 0.004 0.001 HIS A 22 PHE 0.019 0.002 PHE A 169 TYR 0.018 0.002 TYR A 346 ARG 0.005 0.000 ARG B 262 *********************** 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 137 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.124 Fit side-chains REVERT: A 57 MET cc_start: 0.7995 (ttm) cc_final: 0.7579 (ttt) REVERT: A 151 GLU cc_start: 0.7848 (tp30) cc_final: 0.7373 (tp30) REVERT: A 784 GLU cc_start: 0.7744 (tp30) cc_final: 0.7519 (tp30) REVERT: A 900 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7487 (ptm-80) REVERT: A 989 ARG cc_start: 0.8554 (ptp-170) cc_final: 0.8163 (ptp90) REVERT: A 1015 GLN cc_start: 0.7510 (pp30) cc_final: 0.7124 (pp30) REVERT: B 255 ASP cc_start: 0.8455 (t0) cc_final: 0.8224 (t70) REVERT: B 283 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7799 (ttt-90) REVERT: B 314 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8281 (mt) REVERT: B 386 TRP cc_start: 0.5931 (p-90) cc_final: 0.5470 (p-90) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.2561 time to fit residues: 45.2959 Evaluate side-chains 133 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 887 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 0.0770 chunk 146 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.189608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147390 restraints weight = 12235.445| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.64 r_work: 0.3560 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10284 Z= 0.308 Angle : 0.579 7.666 14066 Z= 0.301 Chirality : 0.046 0.158 1670 Planarity : 0.004 0.050 1880 Dihedral : 4.153 21.226 1554 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.50 % Rotamer: Outliers : 2.16 % Allowed : 13.19 % Favored : 84.65 % 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: -1.90 (0.21), residues: 1476 helix: 0.73 (0.42), residues: 158 sheet: -1.30 (0.22), residues: 550 loop : -1.62 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 207 HIS 0.004 0.001 HIS A1070 PHE 0.014 0.002 PHE A 829 TYR 0.017 0.002 TYR A 346 ARG 0.006 0.000 ARG B 262 *********************** 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 143 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8108 (ttm) cc_final: 0.7586 (ttt) REVERT: A 151 GLU cc_start: 0.7717 (tp30) cc_final: 0.7467 (tp30) REVERT: A 312 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 784 GLU cc_start: 0.7661 (tp30) cc_final: 0.7404 (tp30) REVERT: A 876 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: A 900 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7466 (ptm-80) REVERT: A 912 LEU cc_start: 0.9102 (tp) cc_final: 0.8879 (tp) REVERT: A 989 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.8171 (ptp90) REVERT: A 1015 GLN cc_start: 0.7564 (pp30) cc_final: 0.7149 (pp30) REVERT: B 260 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 283 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7754 (ttt-90) REVERT: B 314 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 386 TRP cc_start: 0.6054 (p-90) cc_final: 0.5498 (p-90) outliers start: 18 outliers final: 15 residues processed: 136 average time/residue: 0.2562 time to fit residues: 48.0063 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 379 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 136 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 122 optimal weight: 50.0000 chunk 68 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 49 optimal weight: 0.0670 overall best weight: 1.3522 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.190002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147379 restraints weight = 12293.646| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.75 r_work: 0.3551 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10284 Z= 0.269 Angle : 0.563 7.469 14066 Z= 0.292 Chirality : 0.046 0.164 1670 Planarity : 0.004 0.051 1880 Dihedral : 4.098 21.163 1554 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.76 % Allowed : 13.31 % Favored : 83.93 % 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: -1.90 (0.21), residues: 1476 helix: 0.76 (0.42), residues: 158 sheet: -1.31 (0.22), residues: 550 loop : -1.63 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 207 HIS 0.002 0.001 HIS A1070 PHE 0.013 0.002 PHE A 829 TYR 0.014 0.002 TYR A 346 ARG 0.007 0.000 ARG B 262 *********************** 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 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8106 (ttm) cc_final: 0.7555 (ttt) REVERT: A 151 GLU cc_start: 0.7679 (tp30) cc_final: 0.7419 (tp30) REVERT: A 156 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8557 (m-40) REVERT: A 312 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 784 GLU cc_start: 0.7504 (tp30) cc_final: 0.7285 (tp30) REVERT: A 876 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: A 900 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7457 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7535 (pp30) cc_final: 0.7124 (pp30) REVERT: B 260 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 314 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8222 (mt) REVERT: B 386 TRP cc_start: 0.6150 (p-90) cc_final: 0.5576 (p-90) outliers start: 23 outliers final: 17 residues processed: 138 average time/residue: 0.2451 time to fit residues: 46.6278 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 761 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 133 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 81 optimal weight: 0.0170 chunk 142 optimal weight: 40.0000 chunk 122 optimal weight: 40.0000 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 chunk 73 optimal weight: 0.5980 overall best weight: 1.5224 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.189174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.146539 restraints weight = 12411.460| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.74 r_work: 0.3537 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10284 Z= 0.297 Angle : 0.576 7.506 14066 Z= 0.299 Chirality : 0.046 0.169 1670 Planarity : 0.004 0.051 1880 Dihedral : 4.135 21.240 1554 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.76 % Allowed : 13.67 % 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: -1.92 (0.21), residues: 1476 helix: 0.74 (0.42), residues: 158 sheet: -1.31 (0.22), residues: 557 loop : -1.64 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.003 0.001 HIS A1070 PHE 0.014 0.002 PHE A 829 TYR 0.015 0.002 TYR A 346 ARG 0.008 0.000 ARG B 262 *********************** 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 150 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8134 (ttm) cc_final: 0.7625 (ttt) REVERT: A 156 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8548 (m-40) REVERT: A 178 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8427 (pt) REVERT: A 193 TYR cc_start: 0.8770 (m-80) cc_final: 0.8484 (m-80) REVERT: A 248 ILE cc_start: 0.7530 (mm) cc_final: 0.7260 (mm) REVERT: A 312 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 876 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: A 900 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7160 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7570 (pp30) cc_final: 0.7159 (pp30) REVERT: B 260 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 313 ASP cc_start: 0.8179 (t0) cc_final: 0.7976 (t0) REVERT: B 386 TRP cc_start: 0.6069 (p-90) cc_final: 0.5480 (p-90) outliers start: 23 outliers final: 17 residues processed: 141 average time/residue: 0.2475 time to fit residues: 48.4877 Evaluate side-chains 141 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 379 SER Chi-restraints excluded: chain A residue 761 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.191946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149178 restraints weight = 12348.801| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.78 r_work: 0.3582 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10284 Z= 0.194 Angle : 0.528 7.348 14066 Z= 0.277 Chirality : 0.045 0.172 1670 Planarity : 0.004 0.052 1880 Dihedral : 3.938 21.121 1554 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.40 % Allowed : 15.23 % Favored : 82.37 % 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: -1.81 (0.21), residues: 1476 helix: 0.85 (0.42), residues: 158 sheet: -1.18 (0.22), residues: 538 loop : -1.63 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 207 HIS 0.003 0.001 HIS A1070 PHE 0.011 0.001 PHE A 829 TYR 0.012 0.001 TYR B 221 ARG 0.007 0.000 ARG B 262 *********************** 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 151 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8074 (ttm) cc_final: 0.7751 (ttt) REVERT: A 151 GLU cc_start: 0.7651 (tp30) cc_final: 0.7355 (tp30) REVERT: A 156 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8579 (m-40) REVERT: A 312 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 876 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: A 900 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7456 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7739 (pp30) cc_final: 0.7314 (pp30) REVERT: A 1022 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8001 (p) REVERT: B 260 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7414 (tm-30) REVERT: B 386 TRP cc_start: 0.6128 (p-90) cc_final: 0.5568 (p-90) outliers start: 20 outliers final: 14 residues processed: 143 average time/residue: 0.2580 time to fit residues: 50.7680 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 220 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 761 LEU 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 1022 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 122 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 124 optimal weight: 50.0000 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.192803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150808 restraints weight = 12205.462| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.62 r_work: 0.3598 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10284 Z= 0.188 Angle : 0.535 8.972 14066 Z= 0.279 Chirality : 0.045 0.178 1670 Planarity : 0.004 0.052 1880 Dihedral : 3.841 20.824 1554 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.28 % Allowed : 15.71 % Favored : 82.01 % 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: -1.79 (0.21), residues: 1476 helix: 0.84 (0.43), residues: 160 sheet: -1.11 (0.22), residues: 538 loop : -1.67 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.002 0.001 HIS A1070 PHE 0.012 0.001 PHE A 829 TYR 0.012 0.001 TYR B 221 ARG 0.005 0.000 ARG B 262 *********************** 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 144 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8035 (ttm) cc_final: 0.7706 (ttt) REVERT: A 151 GLU cc_start: 0.7578 (tp30) cc_final: 0.7249 (tp30) REVERT: A 178 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8496 (pt) REVERT: A 213 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: A 312 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 876 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: A 900 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7446 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7754 (pp30) cc_final: 0.7364 (pp30) REVERT: A 1022 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8022 (p) REVERT: B 260 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7466 (tm-30) REVERT: B 386 TRP cc_start: 0.6070 (p-90) cc_final: 0.5566 (p-90) outliers start: 19 outliers final: 14 residues processed: 136 average time/residue: 0.2601 time to fit residues: 48.8162 Evaluate side-chains 143 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 761 LEU 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 957 VAL Chi-restraints excluded: chain A residue 1022 THR 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: 30.0000 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 66 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.189092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146328 restraints weight = 12367.650| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.75 r_work: 0.3555 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10284 Z= 0.287 Angle : 0.571 7.999 14066 Z= 0.296 Chirality : 0.046 0.182 1670 Planarity : 0.004 0.052 1880 Dihedral : 4.034 21.016 1554 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.52 % Allowed : 15.83 % Favored : 81.65 % 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: -1.87 (0.21), residues: 1476 helix: 0.74 (0.42), residues: 160 sheet: -1.17 (0.22), residues: 542 loop : -1.71 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.003 0.001 HIS A1009 PHE 0.015 0.002 PHE A 799 TYR 0.019 0.002 TYR A 837 ARG 0.005 0.000 ARG B 262 ********************** 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 145 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8175 (ttm) cc_final: 0.7664 (ttt) REVERT: A 151 GLU cc_start: 0.7610 (tp30) cc_final: 0.7263 (tp30) REVERT: A 178 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8533 (pt) REVERT: A 248 ILE cc_start: 0.7644 (mm) cc_final: 0.7372 (mm) REVERT: A 312 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 900 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7434 (ptm-80) REVERT: A 1015 GLN cc_start: 0.7710 (pp30) cc_final: 0.7299 (pp30) REVERT: A 1022 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 260 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 386 TRP cc_start: 0.6119 (p-90) cc_final: 0.5578 (p-90) outliers start: 21 outliers final: 19 residues processed: 136 average time/residue: 0.2538 time to fit residues: 47.7792 Evaluate side-chains 144 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 218 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 761 LEU 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 957 VAL Chi-restraints excluded: chain A residue 1022 THR 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: 1.9990 chunk 113 optimal weight: 30.0000 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN 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 = 0.189720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146933 restraints weight = 12236.907| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.74 r_work: 0.3549 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10284 Z= 0.291 Angle : 0.577 8.071 14066 Z= 0.299 Chirality : 0.046 0.181 1670 Planarity : 0.004 0.052 1880 Dihedral : 4.075 21.377 1554 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.00 % Allowed : 15.35 % Favored : 81.65 % 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: -1.90 (0.21), residues: 1476 helix: 0.71 (0.42), residues: 160 sheet: -1.20 (0.22), residues: 540 loop : -1.71 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.004 0.001 HIS A1009 PHE 0.015 0.002 PHE A 799 TYR 0.017 0.002 TYR A 837 ARG 0.005 0.000 ARG B 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.90 seconds wall clock time: 102 minutes 34.59 seconds (6154.59 seconds total)