Starting phenix.real_space_refine on Sun Sep 13 10:51:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xyb_33516/09_2026/7xyb_33516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xyb_33516/09_2026/7xyb_33516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xyb_33516/09_2026/7xyb_33516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xyb_33516/09_2026/7xyb_33516.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xyb_33516/09_2026/7xyb_33516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xyb_33516/09_2026/7xyb_33516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xyb_33516/09_2026/7xyb_33516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xyb_33516/09_2026/7xyb_33516.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 13839 2.51 5 N 4180 2.21 5 O 4374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22525 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1583 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1506 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 7672 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 445} Link IDs: {'PTRANS': 49, 'TRANS': 1140} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1682 Unresolved non-hydrogen angles: 2143 Unresolved non-hydrogen dihedrals: 1339 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'ASP:plan': 47, 'GLU:plan': 63, 'GLN:plan1': 19, 'PHE:plan': 18, 'ARG:plan': 38, 'TYR:plan': 14, 'ASN:plan1': 21, 'HIS:plan': 7, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 970 Chain: "D" Number of atoms: 9118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 9118 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 60, 'TRANS': 1277} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1673 Unresolved non-hydrogen dihedrals: 1055 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLU:plan': 58, 'ASN:plan1': 15, 'TYR:plan': 7, 'ARG:plan': 29, 'PHE:plan': 15, 'ASP:plan': 45, 'HIS:plan': 8, 'GLN:plan1': 12, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 767 Chain: "E" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 460 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 833 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 10, 'TYR:plan': 1, 'TRP:plan': 5, 'PHE:plan': 7, 'ARG:plan': 23, 'ASP:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 335 Chain: "R" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 310 Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "N" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 500 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "T" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.04, per 1000 atoms: 0.22 Number of scatterers: 22525 At special positions: 0 Unit cell: (142.29, 127.41, 147.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 65 15.00 Mg 1 11.99 O 4374 8.00 N 4180 7.00 C 13839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 888 " - pdb=" SG CYS D 895 " distance=2.24 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5886 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 47 sheets defined 41.0% alpha, 14.5% beta 25 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.426A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.517A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.924A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.701A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.782A pdb=" N LEU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.941A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.860A pdb=" N HIS C 169 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 350 through 357 Processing helix chain 'C' and resid 363 through 376 Processing helix chain 'C' and resid 382 through 396 removed outlier: 3.960A pdb=" N SER C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 Processing helix chain 'C' and resid 428 through 442 Processing helix chain 'C' and resid 460 through 484 removed outlier: 3.584A pdb=" N MET C 464 " --> pdb=" O CYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 removed outlier: 3.537A pdb=" N ILE C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.549A pdb=" N GLU C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 548 removed outlier: 3.945A pdb=" N ALA C 548 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 614 through 617 removed outlier: 3.565A pdb=" N ALA C 617 " --> pdb=" O ILE C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 614 through 617' Processing helix chain 'C' and resid 661 through 665 removed outlier: 3.644A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 708 through 717 removed outlier: 4.504A pdb=" N ASN C 712 " --> pdb=" O GLY C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 863 through 870 removed outlier: 3.525A pdb=" N LEU C 867 " --> pdb=" O GLY C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 984 Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.646A pdb=" N GLN C1055 " --> pdb=" O ARG C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 4.370A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C1123 " --> pdb=" O GLY C1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1118 through 1123' Processing helix chain 'C' and resid 1126 through 1151 Processing helix chain 'C' and resid 1154 through 1167 removed outlier: 3.529A pdb=" N LEU C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1192 removed outlier: 3.883A pdb=" N LEU C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1217 Processing helix chain 'C' and resid 1253 through 1257 removed outlier: 3.502A pdb=" N ASP C1256 " --> pdb=" O LEU C1253 " (cutoff:3.500A) Processing helix chain 'C' and resid 1286 through 1296 Processing helix chain 'C' and resid 1299 through 1308 Processing helix chain 'C' and resid 1312 through 1325 removed outlier: 3.952A pdb=" N THR C1317 " --> pdb=" O VAL C1313 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS C1318 " --> pdb=" O ASN C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1348 removed outlier: 3.581A pdb=" N ASN C1339 " --> pdb=" O PRO C1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.895A pdb=" N ILE D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 193 through 208 Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.710A pdb=" N VAL D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.525A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.900A pdb=" N TRP D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 410 " --> pdb=" O PRO D 406 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.730A pdb=" N GLN D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 635 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.295A pdb=" N ARG D 652 " --> pdb=" O ASP D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.865A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1051 through 1055 removed outlier: 3.653A pdb=" N THR D1054 " --> pdb=" O ASP D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.837A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.560A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.308A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.506A pdb=" N LEU D1292 " --> pdb=" O GLU D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.991A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.517A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.549A pdb=" N PHE G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 69 Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 105 through 120 Processing helix chain 'G' and resid 126 through 135 Processing helix chain 'G' and resid 137 through 171 removed outlier: 4.287A pdb=" N GLU G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Proline residue: G 166 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 6.429A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 170 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.567A pdb=" N ALA A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.665A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 6.808A pdb=" N LYS B 144 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 59 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 142 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.568A pdb=" N ALA B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.978A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 70 through 79 removed outlier: 5.312A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 76 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 103 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 119 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 70 through 79 removed outlier: 5.312A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 76 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 103 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.557A pdb=" N LEU C 188 " --> pdb=" O ILE C 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AB9, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC1, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC2, first strand: chain 'C' and resid 755 through 757 removed outlier: 6.941A pdb=" N ARG C 736 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL C 732 " --> pdb=" O ARG C 736 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 738 " --> pdb=" O ASP C 730 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC4, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC5, first strand: chain 'C' and resid 1083 through 1084 removed outlier: 4.699A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE C 821 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C1096 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 823 " --> pdb=" O ILE C1096 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1083 through 1084 Processing sheet with id=AC7, first strand: chain 'C' and resid 835 through 844 removed outlier: 4.074A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS C1074 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N GLY C 931 " --> pdb=" O LYS C1074 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 854 through 855 removed outlier: 3.919A pdb=" N GLU C 854 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 889 removed outlier: 6.235A pdb=" N LEU C 923 " --> pdb=" O LEU C 888 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.553A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.553A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1350 through 1351 Processing sheet with id=AD4, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.020A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.794A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 255 Processing sheet with id=AD9, first strand: chain 'D' and resid 316 through 317 removed outlier: 4.056A pdb=" N THR D 317 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.842A pdb=" N PHE D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ASN D 553 " --> pdb=" O PHE D 527 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY D 558 " --> pdb=" O GLN D 562 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLN D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.876A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AE6, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 3.578A pdb=" N GLY D1033 " --> pdb=" O VAL D1115 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1036 through 1038 Processing sheet with id=AE8, first strand: chain 'D' and resid 1046 through 1047 removed outlier: 3.712A pdb=" N ILE D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D1107 " --> pdb=" O ILE D1059 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1155 through 1156 Processing sheet with id=AF1, first strand: chain 'D' and resid 1172 through 1174 Processing sheet with id=AF2, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 7.027A pdb=" N LYS D1301 " --> pdb=" O SER D1267 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5054 1.33 - 1.45: 4674 1.45 - 1.57: 12960 1.57 - 1.69: 126 1.69 - 1.82: 115 Bond restraints: 22929 Sorted by residual: bond pdb=" O3' DG N 119 " pdb=" P DG N 120 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" C3' DT N 100 " pdb=" C2' DT N 100 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.76e+00 bond pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.44e+00 bond pdb=" C3' DC N 110 " pdb=" C2' DC N 110 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.63e+00 bond pdb=" N LEU G 45 " pdb=" CA LEU G 45 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.30e-02 5.92e+03 7.00e+00 ... (remaining 22924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 31206 2.94 - 5.88: 280 5.88 - 8.82: 28 8.82 - 11.76: 9 11.76 - 14.70: 1 Bond angle restraints: 31524 Sorted by residual: angle pdb=" C THR D 43 " pdb=" CA THR D 43 " pdb=" CB THR D 43 " ideal model delta sigma weight residual 116.53 101.83 14.70 1.47e+00 4.63e-01 1.00e+02 angle pdb=" N LYS C1277 " pdb=" CA LYS C1277 " pdb=" C LYS C1277 " ideal model delta sigma weight residual 111.28 103.79 7.49 1.09e+00 8.42e-01 4.72e+01 angle pdb=" N GLU G 35 " pdb=" CA GLU G 35 " pdb=" C GLU G 35 " ideal model delta sigma weight residual 113.41 105.70 7.71 1.22e+00 6.72e-01 3.99e+01 angle pdb=" N ARG G 34 " pdb=" CA ARG G 34 " pdb=" C ARG G 34 " ideal model delta sigma weight residual 113.20 106.07 7.13 1.21e+00 6.83e-01 3.48e+01 angle pdb=" O4' DG N 96 " pdb=" C4' DG N 96 " pdb=" C3' DG N 96 " ideal model delta sigma weight residual 106.00 102.66 3.34 6.00e-01 2.78e+00 3.10e+01 ... (remaining 31519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 12118 17.89 - 35.78: 1076 35.78 - 53.67: 358 53.67 - 71.56: 100 71.56 - 89.45: 15 Dihedral angle restraints: 13667 sinusoidal: 4564 harmonic: 9103 Sorted by residual: dihedral pdb=" C4' U R 61 " pdb=" C3' U R 61 " pdb=" C2' U R 61 " pdb=" C1' U R 61 " ideal model delta sinusoidal sigma weight residual 36.34 -44.38 80.73 1 3.10e+00 1.04e-01 8.38e+02 dihedral pdb=" C4' G R 59 " pdb=" C3' G R 59 " pdb=" C2' G R 59 " pdb=" C1' G R 59 " ideal model delta sinusoidal sigma weight residual 36.34 -36.69 73.04 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' G R 57 " pdb=" C3' G R 57 " pdb=" C2' G R 57 " pdb=" C1' G R 57 " ideal model delta sinusoidal sigma weight residual 36.34 -34.05 70.40 1 3.10e+00 1.04e-01 6.64e+02 ... (remaining 13664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3615 0.096 - 0.191: 204 0.191 - 0.287: 20 0.287 - 0.383: 2 0.383 - 0.479: 1 Chirality restraints: 3842 Sorted by residual: chirality pdb=" C2' U R 61 " pdb=" C3' U R 61 " pdb=" O2' U R 61 " pdb=" C1' U R 61 " both_signs ideal model delta sigma weight residual False -2.79 -2.31 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CA THR D 43 " pdb=" N THR D 43 " pdb=" C THR D 43 " pdb=" CB THR D 43 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LYS C1277 " pdb=" N LYS C1277 " pdb=" C LYS C1277 " pdb=" CB LYS C1277 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 3839 not shown) Planarity restraints: 3969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 42 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C GLU D 42 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU D 42 " -0.019 2.00e-02 2.50e+03 pdb=" N THR D 43 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 846 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C ARG C 846 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG C 846 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 847 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 48 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C THR D 48 " 0.048 2.00e-02 2.50e+03 pdb=" O THR D 48 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE D 49 " -0.017 2.00e-02 2.50e+03 ... (remaining 3966 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 248 2.55 - 3.13: 18935 3.13 - 3.72: 38051 3.72 - 4.31: 47327 4.31 - 4.90: 76985 Nonbonded interactions: 181546 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1601 " model vdw 1.956 2.170 nonbonded pdb=" O3' A R 70 " pdb="MG MG D1601 " model vdw 1.986 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1601 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1601 " model vdw 2.083 2.170 nonbonded pdb=" N GLN C 839 " pdb=" OE1 GLN C 839 " model vdw 2.192 3.120 ... (remaining 181541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 57 or (resid 58 throug \ h 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (re \ sid 64 through 66 and (name N or name CA or name C or name O or name CB )) or re \ sid 67 through 74 or (resid 75 and (name N or name CA or name C or name O or nam \ e CB )) or resid 76 through 79 or (resid 80 and (name N or name CA or name C or \ name O or name CB )) or resid 81 through 89 or (resid 90 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or resid 91 through 92 \ or (resid 93 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 4 or (resid 95 and (name N or name CA or name C or name O or name CB or name CG \ )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or nam \ e O or name CB )) or resid 109 through 113 or (resid 114 and (name N or name CA \ or name C or name O or name CB )) or resid 115 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 120 through 134 or re \ sid 139 through 141 or (resid 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 through 157 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 217 or (resid 21 \ 8 through 220 and (name N or name CA or name C or name O or name CB )) or resid \ 221 through 230)) selection = (chain 'B' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or resid 15 through 25 or (resid \ 26 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or resid 27 through 31 or (resid 32 and (name N or name CA or name C or name \ O or name CB )) or resid 33 through 71 or (resid 72 and (name N or name CA or n \ ame C or name O or name CB )) or resid 73 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or resid 118 through 126 or (resid \ 127 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 128 through 139 or (resid 140 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or resid 141 through 151 or (resid 152 and (name N or name CA \ or name C or name O or name CB )) or resid 153 through 193 or (resid 194 throug \ h 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 212 or (resid 213 through 215 and (name N or name CA or name C or name O or \ name CB )) or resid 216 through 230)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.760 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 0.005 0.209 22930 Z= 0.296 Angle : 0.771 14.698 31526 Z= 0.478 Chirality : 0.049 0.479 3842 Planarity : 0.004 0.052 3969 Dihedral : 16.611 89.453 7778 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.96 % Rotamer: Outliers : 0.62 % Allowed : 23.17 % Favored : 76.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 3157 helix: 1.23 (0.16), residues: 1182 sheet: -1.23 (0.25), residues: 401 loop : -1.31 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D1149 TYR 0.017 0.001 TYR D1241 PHE 0.031 0.001 PHE A 35 TRP 0.007 0.001 TRP C 812 HIS 0.014 0.002 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.29 (22929) covalent geometry : angle 0.76957 / 0.48 (31524) SS BOND : bond 0.20912 / 11.01 ( 1) SS BOND : angle 5.51597 / 2.97 ( 2) hydrogen bonds : bond 0.18373 / 12.98 ( 1156) hydrogen bonds : angle 6.96371 / 4.87 ( 3202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping REVERT: C 690 MET cc_start: 0.9091 (mpp) cc_final: 0.8712 (mpp) REVERT: C 810 MET cc_start: 0.8635 (ttp) cc_final: 0.8390 (ppp) REVERT: D 298 MET cc_start: 0.8631 (ptp) cc_final: 0.8373 (ptp) outliers start: 11 outliers final: 6 residues processed: 143 average time/residue: 0.1328 time to fit residues: 32.2924 Evaluate side-chains 132 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 46 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 140 ASN C 623 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 667 GLN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.035291 restraints weight = 211505.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036119 restraints weight = 123145.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036699 restraints weight = 83502.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037044 restraints weight = 62527.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037321 restraints weight = 51432.278| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22930 Z= 0.244 Angle : 0.708 21.706 31526 Z= 0.364 Chirality : 0.052 1.338 3842 Planarity : 0.004 0.047 3969 Dihedral : 13.868 138.251 4079 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.83 % Favored : 94.04 % Rotamer: Outliers : 3.27 % Allowed : 20.46 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3157 helix: 1.49 (0.15), residues: 1195 sheet: -1.30 (0.25), residues: 401 loop : -1.27 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 773 TYR 0.020 0.002 TYR C1244 PHE 0.016 0.001 PHE C 647 TRP 0.007 0.001 TRP C 812 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.24 (22929) covalent geometry : angle 0.70764 / 0.36 (31524) SS BOND : bond 0.01353 / 0.71 ( 1) SS BOND : angle 1.11143 / 0.59 ( 2) hydrogen bonds : bond 0.04753 / 3.21 ( 1156) hydrogen bonds : angle 5.44171 / 3.76 ( 3202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8947 (t80) cc_final: 0.8665 (t80) REVERT: A 142 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9247 (mmmt) REVERT: A 145 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8453 (p) REVERT: C 709 MET cc_start: 0.8700 (tpp) cc_final: 0.8491 (mpp) REVERT: C 810 MET cc_start: 0.8667 (ttp) cc_final: 0.8404 (ppp) REVERT: C 1148 MET cc_start: 0.9110 (ptp) cc_final: 0.8754 (ptp) REVERT: C 1247 MET cc_start: 0.9167 (mmm) cc_final: 0.8921 (mmm) REVERT: D 298 MET cc_start: 0.8661 (ptp) cc_final: 0.8315 (ptp) REVERT: D 816 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8696 (p) outliers start: 53 outliers final: 22 residues processed: 172 average time/residue: 0.1278 time to fit residues: 37.9988 Evaluate side-chains 149 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 61 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN C 467 ASN C 804 ASN ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.034126 restraints weight = 195442.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.034913 restraints weight = 118764.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.035463 restraints weight = 82250.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.035873 restraints weight = 62906.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.036166 restraints weight = 51376.739| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22930 Z= 0.209 Angle : 0.627 8.932 31526 Z= 0.326 Chirality : 0.044 0.401 3842 Planarity : 0.004 0.042 3969 Dihedral : 13.544 138.283 4073 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 4.31 % Allowed : 21.32 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3157 helix: 1.71 (0.15), residues: 1207 sheet: -1.34 (0.24), residues: 406 loop : -1.22 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 773 TYR 0.016 0.001 TYR C1244 PHE 0.014 0.001 PHE C 647 TRP 0.005 0.001 TRP D 868 HIS 0.009 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 (22929) covalent geometry : angle 0.62686 / 0.33 (31524) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 1.02294 / 0.57 ( 2) hydrogen bonds : bond 0.04048 / 2.77 ( 1156) hydrogen bonds : angle 4.93769 / 3.41 ( 3202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 131 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8641 (t80) REVERT: A 50 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8848 (p) REVERT: A 224 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8623 (tm-30) REVERT: B 102 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8654 (tt) REVERT: B 206 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8944 (p) REVERT: C 22 MET cc_start: 0.8877 (ppp) cc_final: 0.8660 (ppp) REVERT: C 134 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8720 (tmm) REVERT: C 810 MET cc_start: 0.8690 (ttp) cc_final: 0.8425 (ppp) REVERT: C 1247 MET cc_start: 0.9183 (mmm) cc_final: 0.8980 (mmm) REVERT: D 102 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7454 (mtp) REVERT: D 298 MET cc_start: 0.8740 (ptp) cc_final: 0.8350 (ptp) REVERT: D 466 MET cc_start: 0.8980 (tpt) cc_final: 0.8548 (tpt) REVERT: D 724 MET cc_start: 0.9216 (mpp) cc_final: 0.8736 (mpp) REVERT: E 30 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9053 (mm) REVERT: E 38 LYS cc_start: 0.9402 (mmtt) cc_final: 0.9196 (mmtt) outliers start: 70 outliers final: 34 residues processed: 190 average time/residue: 0.1317 time to fit residues: 42.5002 Evaluate side-chains 163 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 71 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 261 optimal weight: 50.0000 chunk 231 optimal weight: 10.0000 chunk 52 optimal weight: 50.0000 chunk 280 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 GLN B 140 ASN C 691 GLN C 771 ASN C 804 ASN C 837 HIS ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.034463 restraints weight = 213902.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.035258 restraints weight = 123227.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.035837 restraints weight = 83262.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.036192 restraints weight = 62530.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.036467 restraints weight = 51543.563| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 22930 Z= 0.258 Angle : 0.646 9.434 31526 Z= 0.336 Chirality : 0.043 0.389 3842 Planarity : 0.004 0.043 3969 Dihedral : 13.508 134.179 4072 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 5.30 % Allowed : 21.13 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3157 helix: 1.69 (0.15), residues: 1209 sheet: -1.48 (0.25), residues: 390 loop : -1.18 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 155 TYR 0.021 0.002 TYR C1244 PHE 0.014 0.001 PHE C 160 TRP 0.006 0.001 TRP D 868 HIS 0.009 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.26 (22929) covalent geometry : angle 0.64641 / 0.34 (31524) SS BOND : bond 0.00459 / 0.24 ( 1) SS BOND : angle 1.39536 / 0.77 ( 2) hydrogen bonds : bond 0.04156 / 2.81 ( 1156) hydrogen bonds : angle 4.90976 / 3.38 ( 3202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 128 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8680 (t80) REVERT: A 142 LYS cc_start: 0.9503 (mmmm) cc_final: 0.9179 (mmmt) REVERT: B 206 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8921 (p) REVERT: C 690 MET cc_start: 0.9177 (mtm) cc_final: 0.8876 (mtm) REVERT: C 810 MET cc_start: 0.8727 (ttp) cc_final: 0.8412 (ppp) REVERT: C 1148 MET cc_start: 0.9080 (ptm) cc_final: 0.8706 (ptp) REVERT: C 1247 MET cc_start: 0.9165 (mmm) cc_final: 0.8840 (mmm) REVERT: D 102 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7436 (mtp) REVERT: D 525 MET cc_start: 0.7853 (ppp) cc_final: 0.7549 (ppp) REVERT: D 724 MET cc_start: 0.9252 (mpp) cc_final: 0.8794 (mpp) REVERT: E 30 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9107 (mm) REVERT: E 38 LYS cc_start: 0.9421 (mmtt) cc_final: 0.9197 (mmtt) outliers start: 86 outliers final: 55 residues processed: 206 average time/residue: 0.1281 time to fit residues: 45.1537 Evaluate side-chains 184 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1266 VAL Chi-restraints excluded: chain D residue 1275 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 24 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 219 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 299 optimal weight: 50.0000 chunk 277 optimal weight: 20.0000 chunk 167 optimal weight: 50.0000 chunk 101 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN B 193 GLN C 623 GLN C 804 ASN C 837 HIS ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.033295 restraints weight = 201025.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.034060 restraints weight = 120703.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.034605 restraints weight = 82994.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034993 restraints weight = 63131.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035257 restraints weight = 51763.912| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 22930 Z= 0.298 Angle : 0.674 9.607 31526 Z= 0.351 Chirality : 0.044 0.349 3842 Planarity : 0.004 0.045 3969 Dihedral : 13.546 133.484 4072 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 5.48 % Allowed : 21.38 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3157 helix: 1.56 (0.15), residues: 1217 sheet: -1.44 (0.26), residues: 369 loop : -1.24 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 21 TYR 0.023 0.002 TYR C1244 PHE 0.015 0.002 PHE C 160 TRP 0.007 0.001 TRP D 868 HIS 0.010 0.002 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.30 (22929) covalent geometry : angle 0.67372 / 0.35 (31524) SS BOND : bond 0.00572 / 0.30 ( 1) SS BOND : angle 1.48927 / 0.83 ( 2) hydrogen bonds : bond 0.04372 / 2.95 ( 1156) hydrogen bonds : angle 4.96331 / 3.42 ( 3202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 124 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8612 (t80) REVERT: A 142 LYS cc_start: 0.9486 (mmmm) cc_final: 0.8875 (mmmt) REVERT: B 206 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8873 (p) REVERT: C 810 MET cc_start: 0.8729 (ttp) cc_final: 0.8436 (ppp) REVERT: C 1148 MET cc_start: 0.8984 (ptm) cc_final: 0.8646 (ptp) REVERT: C 1247 MET cc_start: 0.9152 (mmm) cc_final: 0.8805 (mmm) REVERT: C 1248 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9020 (mt) REVERT: D 102 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7751 (ttp) REVERT: D 724 MET cc_start: 0.9231 (mpp) cc_final: 0.8845 (mpp) REVERT: D 816 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8696 (p) REVERT: E 30 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9110 (mm) outliers start: 89 outliers final: 62 residues processed: 204 average time/residue: 0.1253 time to fit residues: 44.1204 Evaluate side-chains 190 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 122 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1266 VAL Chi-restraints excluded: chain D residue 1275 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 61 optimal weight: 30.0000 chunk 76 optimal weight: 7.9990 chunk 125 optimal weight: 40.0000 chunk 278 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 202 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 166 optimal weight: 50.0000 chunk 47 optimal weight: 20.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 140 ASN C 691 GLN C 804 ASN ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 GLN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.032552 restraints weight = 205880.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.033306 restraints weight = 121958.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.033801 restraints weight = 83263.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.034178 restraints weight = 63666.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.034408 restraints weight = 52180.241| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 22930 Z= 0.362 Angle : 0.764 11.892 31526 Z= 0.396 Chirality : 0.045 0.336 3842 Planarity : 0.005 0.075 3969 Dihedral : 13.674 133.056 4072 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 5.98 % Allowed : 21.07 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 3157 helix: 1.27 (0.15), residues: 1220 sheet: -1.46 (0.26), residues: 368 loop : -1.40 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 26 TYR 0.030 0.002 TYR D 631 PHE 0.023 0.002 PHE C 160 TRP 0.008 0.001 TRP C 812 HIS 0.010 0.002 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.36 (22929) covalent geometry : angle 0.76408 / 0.40 (31524) SS BOND : bond 0.00661 / 0.35 ( 1) SS BOND : angle 1.62287 / 0.90 ( 2) hydrogen bonds : bond 0.04913 / 3.32 ( 1156) hydrogen bonds : angle 5.18852 / 3.56 ( 3202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 123 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8647 (t80) REVERT: A 142 LYS cc_start: 0.9376 (mmmm) cc_final: 0.9171 (mmmm) REVERT: B 206 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8646 (p) REVERT: C 140 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8655 (p90) REVERT: C 810 MET cc_start: 0.8795 (ttp) cc_final: 0.8479 (ppp) REVERT: C 1247 MET cc_start: 0.9231 (mmm) cc_final: 0.8796 (mmm) REVERT: C 1248 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9019 (mt) REVERT: D 102 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7816 (ttp) REVERT: D 130 MET cc_start: 0.8988 (ppp) cc_final: 0.7784 (ppp) REVERT: D 298 MET cc_start: 0.8677 (ptp) cc_final: 0.8476 (ptp) REVERT: D 425 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8716 (ttt-90) REVERT: D 724 MET cc_start: 0.9277 (mpp) cc_final: 0.8880 (mpp) REVERT: D 816 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8651 (p) REVERT: D 1344 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9015 (pt) REVERT: E 30 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9163 (mm) outliers start: 97 outliers final: 68 residues processed: 212 average time/residue: 0.1267 time to fit residues: 45.9194 Evaluate side-chains 194 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 117 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1266 VAL Chi-restraints excluded: chain D residue 1275 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 24 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 181 optimal weight: 0.0970 chunk 296 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN C 804 ASN ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.042312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.033459 restraints weight = 196276.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.034243 restraints weight = 116992.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.034797 restraints weight = 80263.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035169 restraints weight = 60754.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.035463 restraints weight = 49757.984| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22930 Z= 0.157 Angle : 0.613 8.522 31526 Z= 0.320 Chirality : 0.043 0.332 3842 Planarity : 0.004 0.057 3969 Dihedral : 13.494 131.453 4072 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 4.56 % Allowed : 22.61 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 3157 helix: 1.62 (0.15), residues: 1209 sheet: -1.38 (0.26), residues: 374 loop : -1.26 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 773 TYR 0.018 0.002 TYR D 631 PHE 0.013 0.001 PHE C 511 TRP 0.009 0.001 TRP D 868 HIS 0.007 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (22929) covalent geometry : angle 0.61335 / 0.32 (31524) SS BOND : bond 0.00327 / 0.17 ( 1) SS BOND : angle 1.27356 / 0.69 ( 2) hydrogen bonds : bond 0.03726 / 2.52 ( 1156) hydrogen bonds : angle 4.84398 / 3.32 ( 3202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 127 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8499 (t80) REVERT: B 205 GLU cc_start: 0.8059 (tp30) cc_final: 0.7765 (tp30) REVERT: B 206 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.7947 (p) REVERT: C 134 MET cc_start: 0.8845 (tmm) cc_final: 0.8511 (tmm) REVERT: C 1247 MET cc_start: 0.9320 (mmm) cc_final: 0.8971 (mmm) REVERT: C 1248 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.8956 (mt) REVERT: D 102 MET cc_start: 0.8294 (mtp) cc_final: 0.7747 (ttp) REVERT: D 130 MET cc_start: 0.8942 (ppp) cc_final: 0.7676 (ppp) REVERT: D 298 MET cc_start: 0.8686 (ptp) cc_final: 0.8459 (ptp) REVERT: D 525 MET cc_start: 0.8049 (ppp) cc_final: 0.7847 (ppp) REVERT: D 724 MET cc_start: 0.9240 (mpp) cc_final: 0.8823 (mpp) REVERT: D 816 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8647 (p) REVERT: D 822 MET cc_start: 0.8949 (ptt) cc_final: 0.8520 (ppp) REVERT: E 30 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9108 (mm) outliers start: 74 outliers final: 51 residues processed: 195 average time/residue: 0.1319 time to fit residues: 44.4808 Evaluate side-chains 177 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1266 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 119 optimal weight: 50.0000 chunk 148 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 306 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 267 optimal weight: 0.6980 chunk 303 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN C 804 ASN ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034240 restraints weight = 209378.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035020 restraints weight = 119568.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.035595 restraints weight = 80415.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035950 restraints weight = 60060.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036211 restraints weight = 48901.343| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22930 Z= 0.181 Angle : 0.623 10.429 31526 Z= 0.320 Chirality : 0.043 0.310 3842 Planarity : 0.004 0.050 3969 Dihedral : 13.452 131.609 4072 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 3.94 % Allowed : 23.72 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 3157 helix: 1.68 (0.15), residues: 1210 sheet: -1.41 (0.27), residues: 366 loop : -1.14 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 21 TYR 0.017 0.001 TYR D1241 PHE 0.010 0.001 PHE C 394 TRP 0.007 0.001 TRP D 868 HIS 0.009 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (22929) covalent geometry : angle 0.62258 / 0.32 (31524) SS BOND : bond 0.00306 / 0.16 ( 1) SS BOND : angle 1.39189 / 0.77 ( 2) hydrogen bonds : bond 0.03699 / 2.50 ( 1156) hydrogen bonds : angle 4.78637 / 3.27 ( 3202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 123 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8518 (t80) REVERT: B 35 PHE cc_start: 0.9197 (m-80) cc_final: 0.8955 (m-80) REVERT: B 206 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8607 (p) REVERT: C 686 MET cc_start: 0.9399 (mtp) cc_final: 0.9189 (mtm) REVERT: C 1247 MET cc_start: 0.9243 (mmm) cc_final: 0.8955 (mmm) REVERT: C 1248 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9018 (mt) REVERT: D 102 MET cc_start: 0.8261 (mtp) cc_final: 0.7771 (ttp) REVERT: D 130 MET cc_start: 0.8902 (ppp) cc_final: 0.7690 (ppp) REVERT: D 525 MET cc_start: 0.8016 (ppp) cc_final: 0.7784 (ppp) REVERT: D 816 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8699 (p) REVERT: D 822 MET cc_start: 0.8989 (ptt) cc_final: 0.8536 (ppp) REVERT: E 30 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9144 (mm) REVERT: E 35 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.6187 (mttt) outliers start: 64 outliers final: 45 residues processed: 181 average time/residue: 0.1240 time to fit residues: 38.7954 Evaluate side-chains 174 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1275 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 128 optimal weight: 50.0000 chunk 302 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 chunk 99 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN C 804 ASN ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.033169 restraints weight = 199817.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.033941 restraints weight = 118665.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.034459 restraints weight = 81716.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.034843 restraints weight = 62240.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.035141 restraints weight = 50790.767| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22930 Z= 0.188 Angle : 0.620 9.655 31526 Z= 0.319 Chirality : 0.043 0.305 3842 Planarity : 0.004 0.049 3969 Dihedral : 13.419 131.467 4072 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 3.94 % Allowed : 23.23 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 3157 helix: 1.73 (0.16), residues: 1204 sheet: -1.35 (0.28), residues: 358 loop : -1.13 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 425 TYR 0.016 0.001 TYR D1241 PHE 0.010 0.001 PHE C 394 TRP 0.007 0.001 TRP D 868 HIS 0.009 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (22929) covalent geometry : angle 0.61966 / 0.32 (31524) SS BOND : bond 0.00321 / 0.17 ( 1) SS BOND : angle 1.31885 / 0.73 ( 2) hydrogen bonds : bond 0.03640 / 2.46 ( 1156) hydrogen bonds : angle 4.76565 / 3.26 ( 3202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8530 (t80) REVERT: B 35 PHE cc_start: 0.9194 (m-80) cc_final: 0.8923 (m-80) REVERT: B 206 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8596 (p) REVERT: C 686 MET cc_start: 0.9446 (mtp) cc_final: 0.9231 (mtp) REVERT: C 1247 MET cc_start: 0.9270 (mmm) cc_final: 0.8965 (mmm) REVERT: C 1248 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.8989 (mt) REVERT: D 102 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7766 (ttp) REVERT: D 130 MET cc_start: 0.8875 (ppp) cc_final: 0.7713 (ppp) REVERT: D 525 MET cc_start: 0.8103 (ppp) cc_final: 0.7874 (ppp) REVERT: D 724 MET cc_start: 0.9226 (mpp) cc_final: 0.8805 (mpp) REVERT: D 816 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8703 (p) REVERT: D 822 MET cc_start: 0.8958 (ptt) cc_final: 0.8568 (ppp) REVERT: E 30 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9119 (mm) REVERT: E 35 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6388 (mttt) outliers start: 64 outliers final: 52 residues processed: 179 average time/residue: 0.1241 time to fit residues: 38.5841 Evaluate side-chains 180 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1266 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 41 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 125 optimal weight: 8.9990 chunk 192 optimal weight: 40.0000 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 50.0000 chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 0.0050 chunk 288 optimal weight: 5.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN C 804 ASN ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 921 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.042515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.033667 restraints weight = 197830.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.034437 restraints weight = 116840.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034999 restraints weight = 80130.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035375 restraints weight = 60649.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.035656 restraints weight = 49447.096| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22930 Z= 0.140 Angle : 0.614 10.760 31526 Z= 0.314 Chirality : 0.043 0.298 3842 Planarity : 0.004 0.052 3969 Dihedral : 13.348 130.969 4072 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.08 % Rotamer: Outliers : 3.02 % Allowed : 24.09 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 3157 helix: 1.76 (0.16), residues: 1204 sheet: -1.36 (0.28), residues: 349 loop : -1.03 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 425 TYR 0.016 0.001 TYR D1241 PHE 0.034 0.001 PHE C 647 TRP 0.008 0.001 TRP D 868 HIS 0.008 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (22929) covalent geometry : angle 0.61413 / 0.31 (31524) SS BOND : bond 0.00181 / 0.10 ( 1) SS BOND : angle 1.21843 / 0.67 ( 2) hydrogen bonds : bond 0.03361 / 2.27 ( 1156) hydrogen bonds : angle 4.67610 / 3.19 ( 3202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8526 (t80) REVERT: A 75 GLN cc_start: 0.9173 (tp40) cc_final: 0.8958 (tp40) REVERT: A 76 GLU cc_start: 0.9215 (mp0) cc_final: 0.8924 (mp0) REVERT: A 142 LYS cc_start: 0.9322 (mmmm) cc_final: 0.8878 (mmmt) REVERT: B 35 PHE cc_start: 0.9150 (m-80) cc_final: 0.8875 (m-80) REVERT: B 206 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8563 (p) REVERT: C 1247 MET cc_start: 0.9270 (mmm) cc_final: 0.8953 (mmm) REVERT: C 1248 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.8995 (mt) REVERT: D 102 MET cc_start: 0.8236 (mtp) cc_final: 0.7788 (ttp) REVERT: D 130 MET cc_start: 0.8830 (ppp) cc_final: 0.7671 (ppp) REVERT: D 525 MET cc_start: 0.8104 (ppp) cc_final: 0.7896 (ppp) REVERT: D 724 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8832 (mpp) REVERT: D 816 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8668 (p) REVERT: D 822 MET cc_start: 0.8918 (ptt) cc_final: 0.8522 (ppp) REVERT: E 30 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9115 (mm) outliers start: 49 outliers final: 38 residues processed: 169 average time/residue: 0.1316 time to fit residues: 38.2324 Evaluate side-chains 169 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 41 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 278 optimal weight: 0.3980 chunk 137 optimal weight: 0.8980 chunk 190 optimal weight: 0.0980 chunk 154 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 68 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 GLN B 140 ASN ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.042955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.033956 restraints weight = 192536.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034750 restraints weight = 114500.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035341 restraints weight = 78542.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035718 restraints weight = 59289.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.035999 restraints weight = 48425.489| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22930 Z= 0.116 Angle : 0.623 14.838 31526 Z= 0.316 Chirality : 0.043 0.289 3842 Planarity : 0.004 0.061 3969 Dihedral : 13.294 130.682 4072 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.32 % Favored : 94.58 % Rotamer: Outliers : 2.90 % Allowed : 24.21 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 3157 helix: 1.73 (0.15), residues: 1210 sheet: -1.34 (0.28), residues: 364 loop : -0.98 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 425 TYR 0.016 0.001 TYR D1241 PHE 0.030 0.001 PHE C 647 TRP 0.008 0.001 TRP D 868 HIS 0.007 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (22929) covalent geometry : angle 0.62342 / 0.32 (31524) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 1.14177 / 0.62 ( 2) hydrogen bonds : bond 0.03247 / 2.19 ( 1156) hydrogen bonds : angle 4.62448 / 3.14 ( 3202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3408.38 seconds wall clock time: 59 minutes 59.16 seconds (3599.16 seconds total)