Starting phenix.real_space_refine on Mon Jun 23 02:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xya_33515/06_2025/7xya_33515.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xya_33515/06_2025/7xya_33515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xya_33515/06_2025/7xya_33515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xya_33515/06_2025/7xya_33515.map" model { file = "/net/cci-nas-00/data/ceres_data/7xya_33515/06_2025/7xya_33515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xya_33515/06_2025/7xya_33515.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 126 5.49 5 Mg 1 5.21 5 S 84 5.16 5 C 16219 2.51 5 N 4891 2.21 5 O 5229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26550 Number of models: 1 Model: "" Number of chains: 11 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, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1499 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 7936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 7936 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 369} Link IDs: {'PTRANS': 49, 'TRANS': 1140} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1406 Unresolved non-hydrogen angles: 1792 Unresolved non-hydrogen dihedrals: 1109 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 10, 'ASN:plan1': 18, 'TRP:plan': 1, 'ASP:plan': 42, 'PHE:plan': 16, 'GLU:plan': 56, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 814 Chain: "D" Number of atoms: 9270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 9270 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 60, 'TRANS': 1277} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1154 Unresolved non-hydrogen angles: 1470 Unresolved non-hydrogen dihedrals: 917 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 24, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 55, 'ASP:plan': 43} Unresolved non-hydrogen planarities: 690 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: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "F" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2418 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Chain: "N" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1196 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "R" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "T" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1195 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 783 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 647 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 1, 'TRP:plan': 5, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 301 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: 14.38, per 1000 atoms: 0.54 Number of scatterers: 26550 At special positions: 0 Unit cell: (147.87, 159.96, 159.96, 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 84 16.00 P 126 15.00 Mg 1 11.99 O 5229 8.00 N 4891 7.00 C 16219 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=2.30 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: 6.47 Conformation dependent library (CDL) restraints added in 3.5 seconds 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6442 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 45 sheets defined 44.1% alpha, 13.2% beta 53 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 9.94 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.181A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.712A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.572A 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 211 through 227 removed outlier: 3.820A 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: 4.089A 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 210 through 217 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: 4.064A 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 426 through 443 removed outlier: 4.023A pdb=" N ILE C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 484 Processing helix chain 'C' and resid 493 through 498 removed outlier: 3.671A pdb=" N ILE C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 removed outlier: 3.615A pdb=" N SER C 514 " --> pdb=" O PHE C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'C' and resid 544 through 548 removed outlier: 3.608A pdb=" N ALA C 548 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 removed outlier: 3.545A pdb=" N TYR C 560 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 617 removed outlier: 3.708A 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: 3.838A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 673 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: 4.471A pdb=" N ASN C 712 " --> pdb=" O GLY C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 863 through 870 Processing helix chain 'C' and resid 947 through 984 Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.606A pdb=" N GLN C1055 " --> pdb=" O ARG C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 4.138A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) removed outlier: 3.745A 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 Processing helix chain 'C' and resid 1182 through 1192 Processing helix chain 'C' and resid 1206 through 1217 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 1326 removed outlier: 3.819A pdb=" N THR C1317 " --> pdb=" O VAL C1313 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS C1318 " --> pdb=" O ASN C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1348 removed outlier: 3.756A 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 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 205 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 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 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.922A pdb=" N TRP D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP D 410 " --> pdb=" O PRO D 406 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (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 483 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 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.503A pdb=" N VAL D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) 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: 4.360A pdb=" N ARG D 652 " --> pdb=" O ASP D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.582A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.645A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.780A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.576A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) 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: 3.573A 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: 3.738A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.510A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.340A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.630A pdb=" N LEU D1292 " --> pdb=" O GLU D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.988A 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 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 8 through 14 Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.804A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'F' and resid 98 through 109 removed outlier: 3.837A pdb=" N THR F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 138 removed outlier: 3.684A pdb=" N GLN F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 155 Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.617A pdb=" N VAL F 163 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 238 removed outlier: 3.785A pdb=" N ALA F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 261 Processing helix chain 'F' and resid 266 through 300 removed outlier: 3.558A pdb=" N ARG F 300 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 310 Processing helix chain 'F' and resid 317 through 327 removed outlier: 3.738A pdb=" N LYS F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 removed outlier: 3.516A pdb=" N GLU F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 356 Processing helix chain 'F' and resid 358 through 396 removed outlier: 4.905A pdb=" N ARG F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU F 390 " --> pdb=" O ALA F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 404 through 422 Processing helix chain 'F' and resid 430 through 450 removed outlier: 4.134A pdb=" N TYR F 434 " --> pdb=" O LYS F 430 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP F 437 " --> pdb=" O THR F 433 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP F 438 " --> pdb=" O TYR F 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 25 through 35 Processing helix chain 'G' and resid 50 through 69 Processing helix chain 'G' and resid 72 through 84 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 170 removed outlier: 4.276A 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 removed outlier: 7.097A pdb=" N ASP A 198 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 6.085A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (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 111 removed outlier: 3.554A 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 18 removed outlier: 3.762A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP B 198 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 6.785A pdb=" N LYS B 144 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA B 59 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS B 142 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE B 61 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN B 140 " --> pdb=" O ILE B 61 " (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 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: 6.061A 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 74 removed outlier: 4.045A pdb=" N LYS C 119 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 78 through 79 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: 3.717A pdb=" N CYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB9, first strand: chain 'C' and resid 585 through 586 removed outlier: 5.097A pdb=" N GLU C 607 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC2, first strand: chain 'C' and resid 721 through 722 removed outlier: 6.619A pdb=" N VAL C 721 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 755 through 757 removed outlier: 6.873A pdb=" N ARG C 736 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL C 732 " --> pdb=" O ARG C 736 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 738 " --> pdb=" O ASP C 730 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC5, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC6, first strand: chain 'C' and resid 1083 through 1084 removed outlier: 4.548A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N ILE C1113 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG C 806 " --> pdb=" O ILE C1113 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU C1115 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA C 808 " --> pdb=" O LEU C1115 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE C 821 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C1096 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 823 " --> pdb=" O ILE C1096 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1083 through 1084 Processing sheet with id=AC8, first strand: chain 'C' and resid 835 through 846 removed outlier: 4.342A pdb=" N LYS C1065 " --> pdb=" O ALA C 845 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N LYS C1074 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N GLY C 931 " --> pdb=" O LYS C1074 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD1, first strand: chain 'C' and resid 892 through 893 Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.562A pdb=" N CYS D 366 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 7.380A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1350 through 1353 removed outlier: 3.684A pdb=" N GLU C1353 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.329A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N SER D 109 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VAL D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.722A pdb=" N GLY D 558 " --> pdb=" O GLN D 562 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.429A pdb=" N VAL D 848 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.789A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AE4, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 3.746A pdb=" N GLY D1033 " --> pdb=" O VAL D1115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1036 through 1038 Processing sheet with id=AE6, first strand: chain 'D' and resid 1046 through 1047 Processing sheet with id=AE7, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.706A pdb=" N ILE D1155 " --> pdb=" O ILE D1210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1172 through 1174 Processing sheet with id=AE9, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 7.218A pdb=" N LYS D1301 " --> pdb=" O SER D1267 " (cutoff:3.500A) 1285 hydrogen bonds defined for protein. 3645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 15.18 Time building geometry restraints manager: 7.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4936 1.33 - 1.45: 6707 1.45 - 1.57: 15114 1.57 - 1.70: 250 1.70 - 1.82: 150 Bond restraints: 27157 Sorted by residual: bond pdb=" N VAL D 253 " pdb=" CA VAL D 253 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.92e+01 bond pdb=" N ILE C 887 " pdb=" CA ILE C 887 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.23e-02 6.61e+03 1.17e+01 bond pdb=" N VAL C 889 " pdb=" CA VAL C 889 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N LEU C 18 " pdb=" CA LEU C 18 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.18e-02 7.18e+03 9.00e+00 bond pdb=" N LYS C 919 " pdb=" CA LYS C 919 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 8.92e+00 ... (remaining 27152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 36624 1.99 - 3.97: 719 3.97 - 5.96: 82 5.96 - 7.95: 19 7.95 - 9.93: 6 Bond angle restraints: 37450 Sorted by residual: angle pdb=" C PRO C 350 " pdb=" CA PRO C 350 " pdb=" CB PRO C 350 " ideal model delta sigma weight residual 112.64 104.82 7.82 1.43e+00 4.89e-01 2.99e+01 angle pdb=" N THR C 921 " pdb=" CA THR C 921 " pdb=" C THR C 921 " ideal model delta sigma weight residual 112.59 106.00 6.59 1.22e+00 6.72e-01 2.92e+01 angle pdb=" CA GLY C1281 " pdb=" C GLY C1281 " pdb=" O GLY C1281 " ideal model delta sigma weight residual 122.23 118.59 3.64 6.90e-01 2.10e+00 2.78e+01 angle pdb=" CA LYS C1277 " pdb=" C LYS C1277 " pdb=" O LYS C1277 " ideal model delta sigma weight residual 120.70 114.78 5.92 1.15e+00 7.56e-01 2.65e+01 angle pdb=" C LEU C1274 " pdb=" N GLY C1275 " pdb=" CA GLY C1275 " ideal model delta sigma weight residual 121.46 116.75 4.71 9.50e-01 1.11e+00 2.46e+01 ... (remaining 37445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 14752 27.09 - 54.18: 1203 54.18 - 81.27: 202 81.27 - 108.36: 11 108.36 - 135.45: 2 Dihedral angle restraints: 16170 sinusoidal: 6212 harmonic: 9958 Sorted by residual: dihedral pdb=" CB CYS D 888 " pdb=" SG CYS D 888 " pdb=" SG CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sinusoidal sigma weight residual 93.00 -177.48 -89.52 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CA LYS F 327 " pdb=" C LYS F 327 " pdb=" N PRO F 328 " pdb=" CA PRO F 328 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA CYS D 898 " pdb=" C CYS D 898 " pdb=" N TYR D 899 " pdb=" CA TYR D 899 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 16167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3860 0.060 - 0.120: 566 0.120 - 0.180: 45 0.180 - 0.240: 7 0.240 - 0.300: 5 Chirality restraints: 4483 Sorted by residual: 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 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA GLN C1279 " pdb=" N GLN C1279 " pdb=" C GLN C1279 " pdb=" CB GLN C1279 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA THR C 921 " pdb=" N THR C 921 " pdb=" C THR C 921 " pdb=" CB THR C 921 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4480 not shown) Planarity restraints: 4495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 651 " 0.065 5.00e-02 4.00e+02 9.54e-02 1.45e+01 pdb=" N PRO C 652 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 652 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 652 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 845 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C ALA C 845 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA C 845 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 846 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 16 " 0.013 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C SER C 16 " -0.048 2.00e-02 2.50e+03 pdb=" O SER C 16 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS C 17 " 0.016 2.00e-02 2.50e+03 ... (remaining 4492 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 193 2.55 - 3.14: 20815 3.14 - 3.72: 43690 3.72 - 4.31: 55778 4.31 - 4.90: 92275 Nonbonded interactions: 212751 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1601 " model vdw 1.962 2.170 nonbonded pdb=" O3' A R 18 " pdb="MG MG D1601 " model vdw 1.989 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1601 " model vdw 2.016 2.170 nonbonded pdb=" NZ LYS C1082 " pdb=" O ASP D 462 " model vdw 2.201 3.120 nonbonded pdb=" NE2 HIS C1087 " pdb=" OE1 GLU C1131 " model vdw 2.203 3.120 ... (remaining 212746 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 or (resid 68 and (name N or name CA or name C or name O or name CB )) or \ resid 69 through 74 or (resid 75 and (name N or name CA or name C or name O or n \ ame CB )) or resid 76 through 79 or (resid 80 and (name N or name CA or name C o \ r name O or name CB )) or resid 81 through 89 or (resid 90 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2)) or resid 91 through 9 \ 2 or (resid 93 and (name N or name CA or name C or name O or name CB )) or resid \ 94 or (resid 95 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or n \ ame O or name CB )) or resid 109 through 113 or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 through 118 or (resid 119 and ( \ name N or name CA or name C or name O or name CB )) or resid 120 through 134 or \ resid 139 through 141 or (resid 142 and (name N or name CA or name C or name O o \ r name CB )) or resid 143 through 157 or (resid 169 and (name N or name CA or na \ me 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 \ 218 through 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.030 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 70.320 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.004 0.272 27158 Z= 0.222 Angle : 0.679 9.933 37452 Z= 0.410 Chirality : 0.043 0.300 4483 Planarity : 0.004 0.095 4495 Dihedral : 19.124 135.446 9725 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 1.00 % Allowed : 19.63 % Favored : 79.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3441 helix: 1.34 (0.14), residues: 1422 sheet: -0.54 (0.27), residues: 401 loop : -1.39 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 41 HIS 0.009 0.001 HIS D 430 PHE 0.020 0.002 PHE F 306 TYR 0.014 0.001 TYR D 679 ARG 0.011 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.15985 ( 1410) hydrogen bonds : angle 6.05744 ( 3911) SS BOND : bond 0.27171 ( 1) SS BOND : angle 6.35597 ( 2) covalent geometry : bond 0.00385 (27157) covalent geometry : angle 0.67756 (37450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 261 MET cc_start: 0.4331 (tmm) cc_final: 0.4102 (tmm) REVERT: F 383 MET cc_start: 0.8895 (tpp) cc_final: 0.8534 (ttt) outliers start: 20 outliers final: 10 residues processed: 199 average time/residue: 0.3817 time to fit residues: 129.4750 Evaluate side-chains 183 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain E residue 22 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 0.7980 chunk 269 optimal weight: 0.0030 chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 278 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 overall best weight: 2.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN B 188 ASN C 524 ASN C 837 HIS ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1322 ASN D 477 GLN D 566 ASN D 921 GLN D1218 HIS D1235 ASN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.096217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.068727 restraints weight = 77309.694| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.43 r_work: 0.3077 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27158 Z= 0.188 Angle : 0.579 8.315 37452 Z= 0.312 Chirality : 0.042 0.160 4483 Planarity : 0.004 0.052 4495 Dihedral : 18.616 143.700 5139 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 3.51 % Allowed : 17.57 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3441 helix: 1.42 (0.14), residues: 1454 sheet: -0.62 (0.27), residues: 386 loop : -1.31 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 41 HIS 0.014 0.001 HIS C 556 PHE 0.019 0.002 PHE F 306 TYR 0.020 0.002 TYR D 679 ARG 0.005 0.001 ARG C 547 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 1410) hydrogen bonds : angle 4.56705 ( 3911) SS BOND : bond 0.00031 ( 1) SS BOND : angle 1.01371 ( 2) covalent geometry : bond 0.00431 (27157) covalent geometry : angle 0.57864 (37450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 191 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8063 (tp40) REVERT: C 1285 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: D 239 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9021 (pp) REVERT: F 356 GLU cc_start: 0.6531 (mm-30) cc_final: 0.6111 (pt0) outliers start: 70 outliers final: 37 residues processed: 245 average time/residue: 0.3402 time to fit residues: 139.2112 Evaluate side-chains 218 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1067 VAL Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 359 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 35 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 312 optimal weight: 20.0000 chunk 339 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 258 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 260 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN ** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1175 ASN D 266 ASN D 921 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.092697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065255 restraints weight = 76374.767| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.68 r_work: 0.2966 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 27158 Z= 0.298 Angle : 0.677 9.942 37452 Z= 0.363 Chirality : 0.045 0.214 4483 Planarity : 0.005 0.067 4495 Dihedral : 18.646 138.660 5130 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 4.97 % Allowed : 18.47 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3441 helix: 1.13 (0.14), residues: 1467 sheet: -0.98 (0.25), residues: 395 loop : -1.42 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 41 HIS 0.008 0.002 HIS D 430 PHE 0.025 0.003 PHE F 225 TYR 0.019 0.002 TYR D 679 ARG 0.009 0.001 ARG D 901 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 1410) hydrogen bonds : angle 4.62042 ( 3911) SS BOND : bond 0.00340 ( 1) SS BOND : angle 2.26690 ( 2) covalent geometry : bond 0.00680 (27157) covalent geometry : angle 0.67664 (37450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 180 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7958 (tp40) REVERT: B 25 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8689 (mtmt) REVERT: B 213 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 224 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 192 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7581 (t80) REVERT: C 1285 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: D 20 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8904 (mt) REVERT: D 140 TYR cc_start: 0.8117 (m-10) cc_final: 0.7661 (m-10) REVERT: D 239 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9043 (pp) REVERT: D 312 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5761 (ptm160) REVERT: D 504 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: D 545 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.8934 (p90) REVERT: F 356 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6388 (pt0) REVERT: F 429 TYR cc_start: 0.8715 (m-80) cc_final: 0.8495 (m-80) outliers start: 99 outliers final: 57 residues processed: 266 average time/residue: 0.3441 time to fit residues: 153.7665 Evaluate side-chains 229 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 163 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 1067 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1187 LEU Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 110 optimal weight: 3.9990 chunk 335 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 263 optimal weight: 0.0470 chunk 137 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 276 optimal weight: 30.0000 chunk 331 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 309 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.094561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067175 restraints weight = 76915.746| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.36 r_work: 0.3043 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27158 Z= 0.146 Angle : 0.539 7.444 37452 Z= 0.292 Chirality : 0.041 0.155 4483 Planarity : 0.004 0.046 4495 Dihedral : 18.460 137.368 5130 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 4.22 % Allowed : 19.53 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3441 helix: 1.55 (0.14), residues: 1447 sheet: -0.80 (0.26), residues: 380 loop : -1.19 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 41 HIS 0.005 0.001 HIS D 430 PHE 0.020 0.002 PHE F 225 TYR 0.017 0.001 TYR D 679 ARG 0.004 0.000 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1410) hydrogen bonds : angle 4.26783 ( 3911) SS BOND : bond 0.00235 ( 1) SS BOND : angle 1.21263 ( 2) covalent geometry : bond 0.00327 (27157) covalent geometry : angle 0.53884 (37450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 179 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7972 (tp40) REVERT: B 224 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7938 (tp40) REVERT: C 192 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7670 (t80) REVERT: C 740 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8094 (tpt90) REVERT: C 1285 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: D 239 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9062 (pp) REVERT: D 504 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8703 (pt0) REVERT: D 715 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8054 (t0) REVERT: F 301 MET cc_start: 0.2304 (tmm) cc_final: 0.1856 (tmm) REVERT: F 356 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6476 (pt0) REVERT: F 429 TYR cc_start: 0.8675 (m-80) cc_final: 0.8330 (m-80) outliers start: 84 outliers final: 50 residues processed: 248 average time/residue: 0.3359 time to fit residues: 140.7214 Evaluate side-chains 226 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1337 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 114 optimal weight: 20.0000 chunk 298 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 chunk 167 optimal weight: 50.0000 chunk 336 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 340 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN C 623 GLN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1272 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN ** F 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.093854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066602 restraints weight = 76793.480| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.68 r_work: 0.3003 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27158 Z= 0.174 Angle : 0.543 7.172 37452 Z= 0.294 Chirality : 0.041 0.166 4483 Planarity : 0.004 0.048 4495 Dihedral : 18.346 135.810 5130 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 4.47 % Allowed : 19.73 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3441 helix: 1.60 (0.14), residues: 1458 sheet: -0.86 (0.26), residues: 392 loop : -1.19 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 41 HIS 0.005 0.001 HIS D 104 PHE 0.023 0.002 PHE F 306 TYR 0.018 0.001 TYR D 679 ARG 0.003 0.000 ARG D 417 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 1410) hydrogen bonds : angle 4.19428 ( 3911) SS BOND : bond 0.00177 ( 1) SS BOND : angle 1.32155 ( 2) covalent geometry : bond 0.00396 (27157) covalent geometry : angle 0.54269 (37450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 174 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7930 (tp40) REVERT: B 224 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: C 3 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.5364 (t80) REVERT: C 192 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7431 (t80) REVERT: C 1285 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: D 20 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8808 (mt) REVERT: D 239 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9032 (pp) REVERT: D 715 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7822 (t0) REVERT: D 1247 LYS cc_start: 0.8539 (tptp) cc_final: 0.8282 (mtpp) REVERT: F 301 MET cc_start: 0.2551 (tmm) cc_final: 0.2323 (tmm) outliers start: 89 outliers final: 61 residues processed: 250 average time/residue: 0.3640 time to fit residues: 151.0481 Evaluate side-chains 233 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 164 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1067 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1187 LEU Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1124 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 174 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 30.0000 chunk 344 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 205 optimal weight: 0.6980 chunk 258 optimal weight: 20.0000 chunk 328 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** E 15 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 = 0.3743 r_free = 0.3743 target = 0.093819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066682 restraints weight = 76136.686| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.65 r_work: 0.3006 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27158 Z= 0.167 Angle : 0.536 7.580 37452 Z= 0.290 Chirality : 0.041 0.158 4483 Planarity : 0.004 0.049 4495 Dihedral : 18.264 134.772 5128 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 4.52 % Allowed : 20.23 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3441 helix: 1.63 (0.14), residues: 1463 sheet: -0.95 (0.25), residues: 403 loop : -1.11 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 41 HIS 0.008 0.001 HIS D 777 PHE 0.024 0.002 PHE F 310 TYR 0.019 0.001 TYR D 679 ARG 0.008 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 1410) hydrogen bonds : angle 4.14664 ( 3911) SS BOND : bond 0.00208 ( 1) SS BOND : angle 1.21280 ( 2) covalent geometry : bond 0.00380 (27157) covalent geometry : angle 0.53637 (37450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 174 time to evaluate : 3.033 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7917 (tp40) REVERT: B 224 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: C 3 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.5150 (t80) REVERT: C 140 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.6942 (p90) REVERT: C 192 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7381 (t80) REVERT: C 1285 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: D 20 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8824 (mt) REVERT: D 239 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9019 (pp) REVERT: D 715 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7855 (t0) REVERT: D 1247 LYS cc_start: 0.8571 (tptp) cc_final: 0.8316 (mtpp) REVERT: E 19 LEU cc_start: 0.8876 (tt) cc_final: 0.8670 (tp) REVERT: F 356 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6270 (pt0) REVERT: F 429 TYR cc_start: 0.8585 (m-80) cc_final: 0.8263 (m-80) outliers start: 91 outliers final: 63 residues processed: 251 average time/residue: 0.3735 time to fit residues: 160.8478 Evaluate side-chains 242 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1187 LEU Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 298 optimal weight: 0.3980 chunk 328 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 chunk 274 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 320 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 ASN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.096039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069444 restraints weight = 76600.397| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.63 r_work: 0.3075 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27158 Z= 0.108 Angle : 0.499 7.187 37452 Z= 0.272 Chirality : 0.039 0.147 4483 Planarity : 0.004 0.048 4495 Dihedral : 18.061 133.491 5128 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 3.01 % Allowed : 21.84 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3441 helix: 1.90 (0.14), residues: 1444 sheet: -0.71 (0.26), residues: 389 loop : -0.98 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 236 HIS 0.004 0.001 HIS D 104 PHE 0.018 0.001 PHE F 260 TYR 0.019 0.001 TYR D 679 ARG 0.004 0.000 ARG F 101 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 1410) hydrogen bonds : angle 3.92624 ( 3911) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.46157 ( 2) covalent geometry : bond 0.00230 (27157) covalent geometry : angle 0.49877 (37450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 3.025 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7990 (tp40) REVERT: B 97 GLU cc_start: 0.8356 (tp30) cc_final: 0.8139 (tp30) REVERT: C 3 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.5335 (t80) REVERT: C 192 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7375 (t80) REVERT: D 20 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8769 (mt) REVERT: D 504 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: D 822 MET cc_start: 0.8742 (ttm) cc_final: 0.8475 (mtp) REVERT: F 261 MET cc_start: 0.4564 (tmm) cc_final: 0.4042 (tmm) REVERT: F 356 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6242 (tm-30) outliers start: 61 outliers final: 36 residues processed: 239 average time/residue: 0.4145 time to fit residues: 168.8497 Evaluate side-chains 208 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1124 ILE Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 187 optimal weight: 0.9980 chunk 121 optimal weight: 0.0170 chunk 323 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 315 optimal weight: 0.0270 chunk 344 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 ASN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** E 15 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 = 0.3758 r_free = 0.3758 target = 0.094589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.067694 restraints weight = 76556.873| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.69 r_work: 0.3031 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27158 Z= 0.150 Angle : 0.525 7.879 37452 Z= 0.283 Chirality : 0.040 0.204 4483 Planarity : 0.004 0.047 4495 Dihedral : 18.036 133.352 5127 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 3.16 % Allowed : 21.99 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3441 helix: 1.91 (0.14), residues: 1455 sheet: -0.69 (0.26), residues: 398 loop : -0.97 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 41 HIS 0.005 0.001 HIS D 777 PHE 0.026 0.001 PHE F 306 TYR 0.027 0.001 TYR F 150 ARG 0.004 0.000 ARG C 642 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 1410) hydrogen bonds : angle 3.94341 ( 3911) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.82721 ( 2) covalent geometry : bond 0.00339 (27157) covalent geometry : angle 0.52448 (37450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 2.685 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7745 (tp40) REVERT: B 97 GLU cc_start: 0.8377 (tp30) cc_final: 0.8158 (tp30) REVERT: B 224 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: C 3 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.5089 (t80) REVERT: C 192 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7391 (t80) REVERT: D 20 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8779 (mt) REVERT: D 504 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: D 672 LEU cc_start: 0.8147 (mt) cc_final: 0.7775 (tp) REVERT: D 822 MET cc_start: 0.8791 (ttm) cc_final: 0.8500 (mtp) REVERT: F 261 MET cc_start: 0.4647 (tmm) cc_final: 0.4418 (tmm) REVERT: F 356 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6303 (tm-30) REVERT: F 383 MET cc_start: 0.8830 (tpp) cc_final: 0.8573 (ttt) REVERT: F 429 TYR cc_start: 0.8712 (m-80) cc_final: 0.8402 (m-80) outliers start: 64 outliers final: 54 residues processed: 226 average time/residue: 0.3440 time to fit residues: 133.5322 Evaluate side-chains 225 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1187 LEU Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1124 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 332 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 322 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 804 ASN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.094197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.067362 restraints weight = 76620.484| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.58 r_work: 0.3026 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27158 Z= 0.160 Angle : 0.528 8.706 37452 Z= 0.285 Chirality : 0.040 0.189 4483 Planarity : 0.004 0.048 4495 Dihedral : 18.046 133.258 5127 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 3.36 % Allowed : 21.69 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3441 helix: 1.85 (0.14), residues: 1461 sheet: -0.65 (0.26), residues: 397 loop : -0.98 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 41 HIS 0.005 0.001 HIS D 104 PHE 0.022 0.001 PHE F 306 TYR 0.021 0.001 TYR F 150 ARG 0.003 0.000 ARG C1231 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1410) hydrogen bonds : angle 3.96968 ( 3911) SS BOND : bond 0.00178 ( 1) SS BOND : angle 0.93759 ( 2) covalent geometry : bond 0.00365 (27157) covalent geometry : angle 0.52796 (37450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 3.249 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7729 (tp40) REVERT: B 224 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: C 3 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.5158 (t80) REVERT: C 192 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7289 (t80) REVERT: C 805 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8256 (mtm) REVERT: C 1285 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: D 20 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8780 (mt) REVERT: D 504 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8486 (pt0) REVERT: D 822 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8473 (mtp) REVERT: F 261 MET cc_start: 0.4796 (tmm) cc_final: 0.4593 (tmm) REVERT: F 356 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6312 (tm-30) REVERT: F 383 MET cc_start: 0.8829 (tpp) cc_final: 0.8519 (ttt) REVERT: F 429 TYR cc_start: 0.8683 (m-80) cc_final: 0.8305 (m-80) outliers start: 68 outliers final: 55 residues processed: 223 average time/residue: 0.3823 time to fit residues: 148.8001 Evaluate side-chains 227 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1067 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1124 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 152 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 chunk 330 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 56 optimal weight: 0.0060 chunk 75 optimal weight: 1.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 ASN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** E 15 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 = 0.3753 r_free = 0.3753 target = 0.094311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067699 restraints weight = 75908.813| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.60 r_work: 0.3023 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27158 Z= 0.145 Angle : 0.523 9.062 37452 Z= 0.282 Chirality : 0.040 0.190 4483 Planarity : 0.004 0.048 4495 Dihedral : 18.028 132.807 5127 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 3.16 % Allowed : 22.09 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3441 helix: 1.88 (0.14), residues: 1458 sheet: -0.68 (0.26), residues: 401 loop : -0.95 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 41 HIS 0.005 0.001 HIS D 104 PHE 0.029 0.001 PHE C1285 TYR 0.021 0.001 TYR D 679 ARG 0.003 0.000 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 1410) hydrogen bonds : angle 3.95886 ( 3911) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.88069 ( 2) covalent geometry : bond 0.00329 (27157) covalent geometry : angle 0.52303 (37450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 167 time to evaluate : 2.865 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping revert: symmetry clash REVERT: C 3 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.5073 (t80) REVERT: C 192 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.7322 (t80) REVERT: C 1285 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: D 20 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8795 (mt) REVERT: D 239 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8994 (pp) REVERT: D 504 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: D 822 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8478 (mtp) REVERT: F 261 MET cc_start: 0.4831 (tmm) cc_final: 0.4557 (tmm) REVERT: F 356 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6355 (tm-30) REVERT: F 429 TYR cc_start: 0.8677 (m-80) cc_final: 0.8305 (m-80) outliers start: 64 outliers final: 55 residues processed: 224 average time/residue: 0.3310 time to fit residues: 127.7425 Evaluate side-chains 223 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain C residue 1285 PHE Chi-restraints excluded: chain C residue 1304 GLU Chi-restraints excluded: chain C residue 1308 VAL Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 984 VAL Chi-restraints excluded: chain D residue 1124 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain E residue 46 PRO Chi-restraints excluded: chain F residue 167 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 323 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 263 optimal weight: 50.0000 chunk 288 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 272 optimal weight: 50.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 ASN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** E 15 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 = 0.3739 r_free = 0.3739 target = 0.093641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066813 restraints weight = 76583.820| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.62 r_work: 0.3005 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27158 Z= 0.173 Angle : 0.543 9.123 37452 Z= 0.292 Chirality : 0.040 0.188 4483 Planarity : 0.004 0.047 4495 Dihedral : 18.037 132.438 5127 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.41 % Allowed : 21.74 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3441 helix: 1.85 (0.14), residues: 1457 sheet: -0.64 (0.26), residues: 392 loop : -0.96 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 41 HIS 0.005 0.001 HIS D 104 PHE 0.037 0.002 PHE C1285 TYR 0.021 0.001 TYR D 679 ARG 0.003 0.000 ARG C1231 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1410) hydrogen bonds : angle 4.02364 ( 3911) SS BOND : bond 0.00209 ( 1) SS BOND : angle 1.11102 ( 2) covalent geometry : bond 0.00397 (27157) covalent geometry : angle 0.54254 (37450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14543.07 seconds wall clock time: 257 minutes 7.71 seconds (15427.71 seconds total)