Starting phenix.real_space_refine on Mon Sep 14 06:24:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ri7_4885/09_2026/6ri7_4885.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ri7_4885/09_2026/6ri7_4885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ri7_4885/09_2026/6ri7_4885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ri7_4885/09_2026/6ri7_4885.map" model { file = "/net/cci-nas-00/data/ceres_data/6ri7_4885/09_2026/6ri7_4885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ri7_4885/09_2026/6ri7_4885.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ri7_4885/09_2026/6ri7_4885.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ri7_4885/09_2026/6ri7_4885.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.107 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 64 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17612 2.51 5 N 5057 2.21 5 O 5615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28461 Number of models: 1 Model: "" Number of chains: 11 Chain: "N" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "T" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "F" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1292 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "C" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "D" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "R" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 771 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 549 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 16, 'TYR:plan': 10, 'GLN:plan1': 4, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 10, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 331 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16792 SG CYS D 70 104.170 113.778 82.690 1.00125.80 S ATOM 16806 SG CYS D 72 104.682 117.024 82.731 1.00129.42 S ATOM 16914 SG CYS D 85 106.479 115.478 85.469 1.00123.50 S ATOM 16938 SG CYS D 88 103.025 114.341 85.847 1.00131.18 S ATOM 22626 SG CYS D 814 100.771 46.707 88.528 1.00 77.22 S ATOM 23191 SG CYS D 888 99.269 50.268 89.134 1.00 82.94 S ATOM 23242 SG CYS D 895 99.525 48.841 86.136 1.00 76.09 S ATOM 23263 SG CYS D 898 97.195 47.090 87.708 1.00 67.76 S Time building chain proxies: 5.58, per 1000 atoms: 0.20 Number of scatterers: 28461 At special positions: 0 Unit cell: (136.109, 168.318, 164.162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 64 15.00 Mg 1 11.99 O 5615 8.00 N 5057 7.00 C 17612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 12 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 48 sheets defined 39.8% alpha, 14.0% beta 23 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'F' and resid 7 through 24 Processing helix chain 'F' and resid 24 through 37 Processing helix chain 'F' and resid 45 through 72 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 88 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 154 through 162 removed outlier: 3.892A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.985A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 88 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 154 through 162 removed outlier: 3.974A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.784A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.727A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.163A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.834A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.602A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.814A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.846A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 819 through 826 removed outlier: 4.033A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 removed outlier: 4.171A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 979 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 1006 through 1038 Processing helix chain 'C' and resid 1081 through 1084 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.705A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.022A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 113 through 118 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 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 195 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.522A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.984A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (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 452 through 457 removed outlier: 4.283A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 593 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.488A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.784A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.532A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.078A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 937 through 949 removed outlier: 4.374A pdb=" N SER D 942 " --> pdb=" O GLY D 938 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 948 " --> pdb=" O ALA D 944 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 949 " --> pdb=" O ALA D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.555A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.553A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 74 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 24 through 38 removed outlier: 3.509A pdb=" N GLU G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 71 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.720A pdb=" N GLN G 81 " --> pdb=" O SER G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 Processing sheet with id=AA1, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.544A pdb=" N ALA F 152 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU F 94 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL F 150 " --> pdb=" O GLU F 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 13 through 17 removed outlier: 6.686A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 104 removed outlier: 7.407A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA6, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.096A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.577A pdb=" N LEU B 102 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.931A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.237A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.788A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.788A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB7, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.134A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB9, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AC1, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.001A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 303 removed outlier: 7.322A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.377A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.190A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.759A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 817 through 818 removed outlier: 4.506A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 834 through 838 removed outlier: 6.382A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.930A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD2, first strand: chain 'C' and resid 1086 through 1087 removed outlier: 3.860A pdb=" N GLU C1219 " --> pdb=" O ASP C1214 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.639A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD7, first strand: chain 'D' and resid 106 through 112 removed outlier: 10.818A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD9, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.727A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.964A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 951 through 952 removed outlier: 3.680A pdb=" N GLU D1015 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.175A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1035 Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1048 Processing sheet with id=AE8, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE9, first strand: chain 'D' and resid 1176 through 1178 Processing sheet with id=AF1, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 5.349A pdb=" N ILE D1266 " --> pdb=" O SER D1303 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER D1303 " --> pdb=" O ILE D1266 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN D1268 " --> pdb=" O THR D1301 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AF3, first strand: chain 'G' and resid 101 through 103 removed outlier: 5.576A pdb=" N GLU G 94 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL G 150 " --> pdb=" O GLU G 94 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8386 1.33 - 1.45: 4540 1.45 - 1.57: 15773 1.57 - 1.69: 124 1.69 - 1.81: 191 Bond restraints: 29014 Sorted by residual: bond pdb=" C3' DG T 17 " pdb=" O3' DG T 17 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.00e+01 bond pdb=" CA LEU D 541 " pdb=" C LEU D 541 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.80e-02 3.09e+03 1.95e+01 bond pdb=" C3' DC T 18 " pdb=" O3' DC T 18 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.94e+01 bond pdb=" C SER A 178 " pdb=" N PRO A 179 " ideal model delta sigma weight residual 1.335 1.285 0.050 1.19e-02 7.06e+03 1.73e+01 bond pdb=" N9 DA N 27 " pdb=" C4 DA N 27 " ideal model delta sigma weight residual 1.374 1.349 0.025 6.00e-03 2.78e+04 1.69e+01 ... (remaining 29009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 38091 2.30 - 4.60: 1198 4.60 - 6.89: 147 6.89 - 9.19: 43 9.19 - 11.49: 14 Bond angle restraints: 39493 Sorted by residual: angle pdb=" O4' DC T 14 " pdb=" C4' DC T 14 " pdb=" C3' DC T 14 " ideal model delta sigma weight residual 106.00 102.64 3.36 6.00e-01 2.78e+00 3.13e+01 angle pdb=" O4' DC T 15 " pdb=" C4' DC T 15 " pdb=" C3' DC T 15 " ideal model delta sigma weight residual 106.00 102.90 3.10 6.00e-01 2.78e+00 2.67e+01 angle pdb=" O4' DA N 32 " pdb=" C1' DA N 32 " pdb=" N9 DA N 32 " ideal model delta sigma weight residual 108.00 111.56 -3.56 7.00e-01 2.04e+00 2.58e+01 angle pdb=" O4' DC N 24 " pdb=" C4' DC N 24 " pdb=" C3' DC N 24 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.45e+01 angle pdb=" C3' DA N 32 " pdb=" C2' DA N 32 " pdb=" C1' DA N 32 " ideal model delta sigma weight residual 102.50 96.71 5.79 1.20e+00 6.94e-01 2.33e+01 ... (remaining 39488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 17162 29.34 - 58.68: 441 58.68 - 88.02: 46 88.02 - 117.35: 0 117.35 - 146.69: 2 Dihedral angle restraints: 17651 sinusoidal: 7541 harmonic: 10110 Sorted by residual: dihedral pdb=" C4' G R 5 " pdb=" C3' G R 5 " pdb=" C2' G R 5 " pdb=" C1' G R 5 " ideal model delta sinusoidal sigma weight residual 36.35 -35.43 71.78 1 3.10e+00 1.04e-01 6.87e+02 dihedral pdb=" O4' G R 5 " pdb=" C4' G R 5 " pdb=" C3' G R 5 " pdb=" C2' G R 5 " ideal model delta sinusoidal sigma weight residual -35.15 30.84 -65.99 1 4.00e+00 6.25e-02 3.56e+02 dihedral pdb=" O4' G R 5 " pdb=" C2' G R 5 " pdb=" C1' G R 5 " pdb=" C3' G R 5 " ideal model delta sinusoidal sigma weight residual 25.59 -28.58 54.18 3 3.80e+00 6.93e-02 1.44e+02 ... (remaining 17648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3394 0.057 - 0.113: 971 0.113 - 0.170: 127 0.170 - 0.227: 22 0.227 - 0.284: 5 Chirality restraints: 4519 Sorted by residual: chirality pdb=" C2' G R 5 " pdb=" C3' G R 5 " pdb=" O2' G R 5 " pdb=" C1' G R 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' DT N 34 " pdb=" C4' DT N 34 " pdb=" O3' DT N 34 " pdb=" C2' DT N 34 " both_signs ideal model delta sigma weight residual False -2.73 -3.00 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE D 754 " pdb=" CA ILE D 754 " pdb=" CG1 ILE D 754 " pdb=" CG2 ILE D 754 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4516 not shown) Planarity restraints: 4965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 30 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1229 " 0.018 2.00e-02 2.50e+03 1.96e-02 7.66e+00 pdb=" CG TYR C1229 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR C1229 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C1229 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C1229 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C1229 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C1229 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C1229 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 78 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO F 79 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 79 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 79 " -0.035 5.00e-02 4.00e+02 ... (remaining 4962 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 296 2.49 - 3.09: 23984 3.09 - 3.69: 42983 3.69 - 4.30: 60414 4.30 - 4.90: 93968 Nonbonded interactions: 221645 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1503 " model vdw 1.885 2.170 nonbonded pdb=" O2 DC N 12 " pdb=" N2 DG T 28 " model vdw 1.960 2.496 nonbonded pdb=" N2 DG N 10 " pdb=" O2 DC T 30 " model vdw 1.997 2.496 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.000 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.034 2.170 ... (remaining 221640 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 7 through 232) selection = (chain 'B' and resid 7 through 232) } ncs_group { reference = (chain 'F' and ((resid 1 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 through 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 or (resid 41 through 82 and (name N or name \ CA or name C or name O or name CB )) or resid 83 or (resid 84 through 87 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 88 through 97 and ( \ name N or name CA or name C or name O or name CB )) or resid 98 or (resid 99 thr \ ough 106 and (name N or name CA or name C or name O or name CB )) or resid 107 o \ r (resid 108 through 112 and (name N or name CA or name C or name O or name CB ) \ ) or resid 113 or (resid 114 through 133 and (name N or name CA or name C or nam \ e O or name CB )) or resid 134 or (resid 135 through 143 and (name N or name CA \ or name C or name O or name CB )) or resid 144 or (resid 145 through 156 and (na \ me N or name CA or name C or name O or name CB )))) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 30.480 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.010 0.199 29022 Z= 0.513 Angle : 1.046 51.234 39505 Z= 0.564 Chirality : 0.052 0.284 4519 Planarity : 0.006 0.103 4965 Dihedral : 12.486 146.693 11147 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.39 % Favored : 85.61 % Rotamer: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.11), residues: 3503 helix: -2.99 (0.10), residues: 1248 sheet: -2.86 (0.21), residues: 440 loop : -3.74 (0.12), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1304 TYR 0.044 0.003 TYR C1229 PHE 0.030 0.003 PHE F 112 TRP 0.029 0.003 TRP C 183 HIS 0.010 0.002 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.51 (29014) covalent geometry : angle 0.98668 / 0.56 (39493) hydrogen bonds : bond 0.12232 / 12.72 ( 1250) hydrogen bonds : angle 7.22741 / 7.78 ( 3457) metal coordination : bond 0.10658 / 9.19 ( 8) metal coordination : angle 19.86862 / 38.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 668 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 GLN cc_start: 0.9167 (tt0) cc_final: 0.8951 (tt0) REVERT: F 72 LEU cc_start: 0.8921 (mp) cc_final: 0.8544 (mm) REVERT: F 109 ASP cc_start: 0.8134 (m-30) cc_final: 0.7532 (m-30) REVERT: F 129 LEU cc_start: 0.8205 (tp) cc_final: 0.7798 (tp) REVERT: A 145 LYS cc_start: 0.8792 (tttt) cc_final: 0.8416 (ttmt) REVERT: B 95 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8303 (mttt) REVERT: C 14 ASP cc_start: 0.7322 (t70) cc_final: 0.7092 (t0) REVERT: C 47 TYR cc_start: 0.8022 (p90) cc_final: 0.6842 (m-80) REVERT: C 221 LEU cc_start: 0.9209 (mt) cc_final: 0.8944 (tp) REVERT: C 233 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7272 (ptm160) REVERT: C 515 MET cc_start: 0.7047 (ttp) cc_final: 0.6704 (ttm) REVERT: C 549 ASP cc_start: 0.8418 (t0) cc_final: 0.8092 (t0) REVERT: C 711 ASP cc_start: 0.7900 (m-30) cc_final: 0.7481 (m-30) REVERT: C 815 SER cc_start: 0.8647 (m) cc_final: 0.8386 (t) REVERT: D 355 ILE cc_start: 0.9174 (pt) cc_final: 0.8837 (pt) REVERT: D 369 PRO cc_start: 0.8670 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: D 458 ASN cc_start: 0.8450 (t0) cc_final: 0.8248 (t0) REVERT: D 591 ILE cc_start: 0.9124 (tt) cc_final: 0.8877 (tt) REVERT: D 1034 PHE cc_start: 0.6826 (m-10) cc_final: 0.6261 (m-80) REVERT: D 1205 GLU cc_start: 0.8162 (tp30) cc_final: 0.7869 (tp30) REVERT: D 1251 LYS cc_start: 0.8145 (mttp) cc_final: 0.7810 (mtpt) REVERT: D 1327 GLU cc_start: 0.8922 (pm20) cc_final: 0.8308 (pm20) REVERT: D 1337 VAL cc_start: 0.9256 (m) cc_final: 0.9034 (p) outliers start: 3 outliers final: 0 residues processed: 670 average time/residue: 0.2085 time to fit residues: 210.2079 Evaluate side-chains 320 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 137 ASN B 23 HIS B 132 HIS B 186 ASN C 65 ASN C 69 GLN C 150 HIS C 387 ASN C 573 ASN C 628 HIS C 688 GLN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C 856 ASN C1116 HIS C1256 GLN C1257 GLN C1268 GLN C1313 HIS D 232 ASN D 266 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 365 GLN D 424 ASN D 488 ASN D 489 ASN D 771 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D 929 GLN D 936 HIS D1010 GLN D1108 GLN D1114 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062828 restraints weight = 95057.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064658 restraints weight = 51900.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065850 restraints weight = 34421.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.066613 restraints weight = 26187.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067004 restraints weight = 22141.935| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29022 Z= 0.176 Angle : 0.790 12.909 39505 Z= 0.409 Chirality : 0.050 0.452 4519 Planarity : 0.006 0.097 4965 Dihedral : 14.245 145.518 4556 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.95 % Allowed : 9.70 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.13), residues: 3503 helix: -0.86 (0.13), residues: 1262 sheet: -2.26 (0.23), residues: 414 loop : -2.90 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 250 TYR 0.031 0.002 TYR C1229 PHE 0.026 0.002 PHE C 514 TRP 0.018 0.002 TRP C 183 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (29014) covalent geometry : angle 0.78437 / 0.41 (39493) hydrogen bonds : bond 0.05690 / 6.30 ( 1250) hydrogen bonds : angle 5.63538 / 5.96 ( 3457) metal coordination : bond 0.01232 / 1.11 ( 8) metal coordination : angle 5.40536 / 9.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 403 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 GLN cc_start: 0.9165 (tt0) cc_final: 0.8914 (tt0) REVERT: F 129 LEU cc_start: 0.8041 (tp) cc_final: 0.7621 (tp) REVERT: C 14 ASP cc_start: 0.7286 (t70) cc_final: 0.7031 (t0) REVERT: C 47 TYR cc_start: 0.7947 (p90) cc_final: 0.6862 (m-80) REVERT: C 142 GLU cc_start: 0.7658 (tt0) cc_final: 0.7435 (pt0) REVERT: C 221 LEU cc_start: 0.9154 (mt) cc_final: 0.8852 (tp) REVERT: C 233 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7132 (ptm160) REVERT: C 237 LEU cc_start: 0.8300 (mp) cc_final: 0.7612 (pp) REVERT: C 241 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8731 (mm) REVERT: C 403 MET cc_start: 0.9320 (tmm) cc_final: 0.8931 (tmm) REVERT: C 549 ASP cc_start: 0.8495 (t0) cc_final: 0.8258 (t0) REVERT: C 685 MET cc_start: 0.7836 (mtm) cc_final: 0.7606 (mtt) REVERT: C 798 GLN cc_start: 0.7096 (mt0) cc_final: 0.6338 (mt0) REVERT: C 922 ASN cc_start: 0.7766 (t0) cc_final: 0.7054 (p0) REVERT: C 1170 MET cc_start: 0.8896 (tpp) cc_final: 0.8578 (tpp) REVERT: C 1273 MET cc_start: 0.7922 (mtm) cc_final: 0.7670 (mtt) REVERT: C 1279 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8016 (mp0) REVERT: D 355 ILE cc_start: 0.9192 (pt) cc_final: 0.8619 (pt) REVERT: D 466 MET cc_start: 0.7414 (mtp) cc_final: 0.7099 (mtp) REVERT: D 805 GLN cc_start: 0.7663 (tt0) cc_final: 0.6381 (tt0) REVERT: D 913 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7597 (mt-10) REVERT: D 1059 LEU cc_start: 0.8360 (mp) cc_final: 0.7547 (tt) REVERT: D 1095 MET cc_start: 0.7354 (ttp) cc_final: 0.6841 (ppp) REVERT: D 1327 GLU cc_start: 0.8861 (pm20) cc_final: 0.8339 (pm20) REVERT: E 58 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7910 (pt) REVERT: E 68 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7377 (mt-10) outliers start: 56 outliers final: 24 residues processed: 442 average time/residue: 0.1776 time to fit residues: 126.4348 Evaluate side-chains 299 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 258 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 296 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 19 ASN F 81 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN B 18 GLN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS D1049 GLN D1279 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.079409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.057036 restraints weight = 98839.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.058836 restraints weight = 52759.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.060015 restraints weight = 34822.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.060779 restraints weight = 26557.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.061259 restraints weight = 22401.242| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 29022 Z= 0.268 Angle : 0.794 13.267 39505 Z= 0.410 Chirality : 0.049 0.341 4519 Planarity : 0.006 0.100 4965 Dihedral : 14.052 144.473 4556 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.90 % Allowed : 11.48 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 3503 helix: -0.01 (0.14), residues: 1279 sheet: -1.90 (0.24), residues: 403 loop : -2.57 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 838 TYR 0.032 0.002 TYR F 77 PHE 0.019 0.002 PHE C 389 TRP 0.029 0.002 TRP F 35 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.27 (29014) covalent geometry : angle 0.79056 / 0.41 (39493) hydrogen bonds : bond 0.05410 / 5.94 ( 1250) hydrogen bonds : angle 5.41494 / 5.82 ( 3457) metal coordination : bond 0.01908 / 1.84 ( 8) metal coordination : angle 4.53295 / 7.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 277 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 GLN cc_start: 0.9186 (tt0) cc_final: 0.8863 (pt0) REVERT: F 72 LEU cc_start: 0.8935 (mm) cc_final: 0.8450 (mm) REVERT: B 18 GLN cc_start: 0.8677 (mp-120) cc_final: 0.8181 (pp30) REVERT: B 51 MET cc_start: 0.8669 (mmm) cc_final: 0.8412 (mmm) REVERT: B 205 MET cc_start: 0.7641 (tmm) cc_final: 0.7317 (tmm) REVERT: C 14 ASP cc_start: 0.7526 (t70) cc_final: 0.7314 (t0) REVERT: C 47 TYR cc_start: 0.8345 (p90) cc_final: 0.7246 (m-80) REVERT: C 221 LEU cc_start: 0.9305 (mt) cc_final: 0.8979 (tp) REVERT: C 233 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7356 (ptm160) REVERT: C 241 LEU cc_start: 0.9569 (tt) cc_final: 0.8988 (mm) REVERT: C 403 MET cc_start: 0.9446 (tmm) cc_final: 0.9073 (tmm) REVERT: C 517 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 549 ASP cc_start: 0.8883 (t0) cc_final: 0.8520 (t70) REVERT: C 654 ASP cc_start: 0.7300 (m-30) cc_final: 0.7047 (m-30) REVERT: C 696 ASP cc_start: 0.8128 (m-30) cc_final: 0.7660 (t0) REVERT: C 711 ASP cc_start: 0.8472 (m-30) cc_final: 0.7777 (m-30) REVERT: C 805 MET cc_start: 0.8909 (ptm) cc_final: 0.8597 (ptm) REVERT: C 922 ASN cc_start: 0.8224 (t0) cc_final: 0.7269 (p0) REVERT: C 992 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6763 (mp) REVERT: C 1243 MET cc_start: 0.8728 (tmm) cc_final: 0.8422 (tmm) REVERT: C 1273 MET cc_start: 0.8943 (mtm) cc_final: 0.8730 (mtt) REVERT: C 1279 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8334 (mt-10) REVERT: D 92 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.6409 (p) REVERT: D 133 ARG cc_start: 0.7953 (ptt90) cc_final: 0.7739 (ptt90) REVERT: D 298 MET cc_start: 0.8607 (tpp) cc_final: 0.8264 (tpp) REVERT: D 458 ASN cc_start: 0.9097 (t0) cc_final: 0.8773 (t0) REVERT: D 860 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7941 (tmm-80) REVERT: D 895 CYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7484 (p) REVERT: D 913 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 1059 LEU cc_start: 0.8334 (mp) cc_final: 0.7832 (tt) REVERT: D 1095 MET cc_start: 0.7181 (ttp) cc_final: 0.6616 (ppp) outliers start: 83 outliers final: 40 residues processed: 341 average time/residue: 0.1676 time to fit residues: 93.8627 Evaluate side-chains 285 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 860 ARG Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 173 optimal weight: 1.9990 chunk 312 optimal weight: 0.0170 chunk 62 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 342 optimal weight: 50.0000 chunk 309 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 305 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 137 ASN B 194 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.079793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.057287 restraints weight = 97215.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.059127 restraints weight = 51697.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.060323 restraints weight = 33962.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061074 restraints weight = 25873.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061570 restraints weight = 21848.733| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29022 Z= 0.196 Angle : 0.704 14.990 39505 Z= 0.364 Chirality : 0.047 0.348 4519 Planarity : 0.005 0.095 4965 Dihedral : 13.890 143.024 4556 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.04 % Allowed : 13.12 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3503 helix: 0.51 (0.15), residues: 1276 sheet: -1.71 (0.24), residues: 438 loop : -2.31 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 88 TYR 0.027 0.002 TYR F 77 PHE 0.017 0.002 PHE C 38 TRP 0.032 0.002 TRP F 35 HIS 0.006 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (29014) covalent geometry : angle 0.69977 / 0.36 (39493) hydrogen bonds : bond 0.04888 / 5.42 ( 1250) hydrogen bonds : angle 5.08652 / 5.47 ( 3457) metal coordination : bond 0.01207 / 1.15 ( 8) metal coordination : angle 4.40522 / 7.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 GLN cc_start: 0.9163 (tt0) cc_final: 0.8848 (pt0) REVERT: F 30 THR cc_start: 0.8579 (m) cc_final: 0.8291 (p) REVERT: F 72 LEU cc_start: 0.9023 (mm) cc_final: 0.8635 (mm) REVERT: A 51 MET cc_start: 0.8934 (mmm) cc_final: 0.8667 (mmm) REVERT: A 177 TYR cc_start: 0.8060 (m-80) cc_final: 0.7203 (m-80) REVERT: B 18 GLN cc_start: 0.8731 (mp-120) cc_final: 0.8109 (pp30) REVERT: B 51 MET cc_start: 0.8618 (mmm) cc_final: 0.8290 (mmm) REVERT: B 186 ASN cc_start: 0.8790 (m-40) cc_final: 0.8251 (m-40) REVERT: B 205 MET cc_start: 0.7792 (tmm) cc_final: 0.7255 (tmm) REVERT: C 47 TYR cc_start: 0.8325 (p90) cc_final: 0.7290 (m-80) REVERT: C 156 PHE cc_start: 0.8528 (m-80) cc_final: 0.8305 (m-10) REVERT: C 160 ASP cc_start: 0.8368 (t0) cc_final: 0.8102 (t0) REVERT: C 221 LEU cc_start: 0.9357 (mt) cc_final: 0.9006 (tp) REVERT: C 233 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7191 (ptm160) REVERT: C 241 LEU cc_start: 0.9505 (tt) cc_final: 0.8974 (mm) REVERT: C 283 LYS cc_start: 0.7865 (pttt) cc_final: 0.7509 (mttm) REVERT: C 403 MET cc_start: 0.9383 (tmm) cc_final: 0.8971 (tmm) REVERT: C 488 MET cc_start: 0.8465 (tpp) cc_final: 0.8171 (tpp) REVERT: C 517 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 549 ASP cc_start: 0.8936 (t0) cc_final: 0.8709 (t70) REVERT: C 696 ASP cc_start: 0.8046 (m-30) cc_final: 0.7694 (t70) REVERT: C 711 ASP cc_start: 0.8450 (m-30) cc_final: 0.7804 (m-30) REVERT: C 805 MET cc_start: 0.8886 (ptm) cc_final: 0.8678 (ptm) REVERT: C 922 ASN cc_start: 0.8228 (t0) cc_final: 0.7273 (p0) REVERT: C 992 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6790 (mp) REVERT: C 994 ARG cc_start: 0.8631 (mtp180) cc_final: 0.8332 (mtt-85) REVERT: C 1279 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8349 (mt-10) REVERT: C 1329 GLU cc_start: 0.8641 (tt0) cc_final: 0.8215 (tt0) REVERT: D 130 MET cc_start: 0.8468 (mtp) cc_final: 0.8125 (mtt) REVERT: D 298 MET cc_start: 0.8622 (tpp) cc_final: 0.8178 (tpp) REVERT: D 330 MET cc_start: 0.8541 (mtp) cc_final: 0.7997 (ttm) REVERT: D 472 LEU cc_start: 0.8940 (mm) cc_final: 0.8691 (mm) REVERT: D 504 GLN cc_start: 0.8047 (pt0) cc_final: 0.7455 (pt0) REVERT: D 610 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8599 (ptt-90) REVERT: D 644 MET cc_start: 0.9058 (mtm) cc_final: 0.8691 (mtm) REVERT: D 811 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: D 822 MET cc_start: 0.8722 (mmm) cc_final: 0.8313 (mmm) REVERT: D 895 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7455 (p) REVERT: D 913 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7854 (mt-10) REVERT: D 932 MET cc_start: 0.8444 (tpt) cc_final: 0.8212 (tpt) REVERT: D 1051 ASP cc_start: 0.8640 (t0) cc_final: 0.8411 (t0) REVERT: D 1059 LEU cc_start: 0.8288 (mp) cc_final: 0.7808 (tt) REVERT: D 1334 GLU cc_start: 0.8812 (tt0) cc_final: 0.8156 (tm-30) REVERT: D 1353 VAL cc_start: 0.9477 (p) cc_final: 0.9269 (p) REVERT: E 43 ASN cc_start: 0.8477 (t0) cc_final: 0.8245 (t0) outliers start: 87 outliers final: 48 residues processed: 348 average time/residue: 0.1743 time to fit residues: 98.7933 Evaluate side-chains 291 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 610 ARG Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 66 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 79 optimal weight: 0.0370 chunk 326 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 339 optimal weight: 30.0000 chunk 130 optimal weight: 0.9990 chunk 322 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 194 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 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 = 0.3415 r_free = 0.3415 target = 0.080770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058427 restraints weight = 96040.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060257 restraints weight = 50705.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061490 restraints weight = 33267.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.062274 restraints weight = 25160.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.062696 restraints weight = 21156.089| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29022 Z= 0.138 Angle : 0.660 12.942 39505 Z= 0.341 Chirality : 0.045 0.356 4519 Planarity : 0.005 0.093 4965 Dihedral : 13.780 142.701 4556 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.62 % Allowed : 14.38 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3503 helix: 0.76 (0.15), residues: 1287 sheet: -1.53 (0.24), residues: 424 loop : -2.12 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 799 TYR 0.024 0.001 TYR D 46 PHE 0.013 0.001 PHE D 172 TRP 0.029 0.001 TRP F 35 HIS 0.006 0.001 HIS D 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (29014) covalent geometry : angle 0.65675 / 0.34 (39493) hydrogen bonds : bond 0.04656 / 5.17 ( 1250) hydrogen bonds : angle 4.89432 / 5.24 ( 3457) metal coordination : bond 0.00729 / 0.69 ( 8) metal coordination : angle 3.67716 / 6.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 GLN cc_start: 0.9172 (tt0) cc_final: 0.8866 (pt0) REVERT: F 30 THR cc_start: 0.8538 (m) cc_final: 0.8306 (p) REVERT: F 72 LEU cc_start: 0.9018 (mm) cc_final: 0.8591 (mm) REVERT: F 112 PHE cc_start: 0.6243 (m-80) cc_final: 0.5867 (m-80) REVERT: B 18 GLN cc_start: 0.8775 (mp-120) cc_final: 0.8191 (pp30) REVERT: B 186 ASN cc_start: 0.8760 (m-40) cc_final: 0.8228 (m-40) REVERT: B 205 MET cc_start: 0.7931 (tmm) cc_final: 0.7288 (tmm) REVERT: C 47 TYR cc_start: 0.8253 (p90) cc_final: 0.7202 (m-80) REVERT: C 160 ASP cc_start: 0.8402 (t0) cc_final: 0.8116 (t0) REVERT: C 200 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.3495 (mtt180) REVERT: C 221 LEU cc_start: 0.9343 (mt) cc_final: 0.9000 (tp) REVERT: C 233 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7311 (ptm160) REVERT: C 241 LEU cc_start: 0.9508 (tt) cc_final: 0.9138 (mm) REVERT: C 285 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7484 (mp) REVERT: C 315 MET cc_start: 0.7744 (ptp) cc_final: 0.7443 (mpp) REVERT: C 403 MET cc_start: 0.9399 (tmm) cc_final: 0.8966 (tmm) REVERT: C 488 MET cc_start: 0.8454 (tpp) cc_final: 0.7860 (mmm) REVERT: C 492 MET cc_start: 0.8768 (ttm) cc_final: 0.8177 (tpp) REVERT: C 653 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7020 (ptp) REVERT: C 696 ASP cc_start: 0.7976 (m-30) cc_final: 0.7624 (t0) REVERT: C 711 ASP cc_start: 0.8421 (m-30) cc_final: 0.7704 (m-30) REVERT: C 805 MET cc_start: 0.8873 (ptm) cc_final: 0.8619 (ptm) REVERT: C 922 ASN cc_start: 0.8154 (t0) cc_final: 0.7247 (p0) REVERT: C 992 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6982 (mp) REVERT: C 994 ARG cc_start: 0.8609 (mtp180) cc_final: 0.8269 (mmm160) REVERT: C 1279 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8321 (mt-10) REVERT: D 130 MET cc_start: 0.8450 (mtp) cc_final: 0.8052 (mtt) REVERT: D 298 MET cc_start: 0.8642 (tpp) cc_final: 0.8237 (tpp) REVERT: D 330 MET cc_start: 0.8531 (mtp) cc_final: 0.8018 (ttm) REVERT: D 472 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8567 (mm) REVERT: D 811 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: D 822 MET cc_start: 0.8665 (mmm) cc_final: 0.8258 (mmm) REVERT: D 895 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7446 (p) REVERT: D 913 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7710 (mt-10) REVERT: D 1059 LEU cc_start: 0.8263 (mp) cc_final: 0.7742 (tt) REVERT: D 1095 MET cc_start: 0.7030 (ttp) cc_final: 0.6615 (ppp) REVERT: E 68 GLU cc_start: 0.8039 (pt0) cc_final: 0.7771 (pt0) outliers start: 75 outliers final: 39 residues processed: 318 average time/residue: 0.1657 time to fit residues: 87.6174 Evaluate side-chains 286 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 163 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 94 optimal weight: 0.0060 chunk 325 optimal weight: 0.0970 chunk 342 optimal weight: 50.0000 chunk 187 optimal weight: 0.0000 chunk 350 optimal weight: 40.0000 chunk 287 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 80 GLN A 137 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.080996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058580 restraints weight = 96180.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.060441 restraints weight = 50715.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.061620 restraints weight = 33128.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062436 restraints weight = 25150.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062909 restraints weight = 21132.861| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29022 Z= 0.134 Angle : 0.646 13.197 39505 Z= 0.334 Chirality : 0.045 0.355 4519 Planarity : 0.004 0.091 4965 Dihedral : 13.710 143.811 4556 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.41 % Allowed : 14.90 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3503 helix: 0.91 (0.15), residues: 1283 sheet: -1.34 (0.25), residues: 425 loop : -2.00 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.017 0.001 TYR F 77 PHE 0.013 0.001 PHE A 35 TRP 0.029 0.001 TRP F 35 HIS 0.006 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (29014) covalent geometry : angle 0.64390 / 0.33 (39493) hydrogen bonds : bond 0.04485 / 4.98 ( 1250) hydrogen bonds : angle 4.79788 / 5.15 ( 3457) metal coordination : bond 0.00669 / 0.63 ( 8) metal coordination : angle 3.19130 / 5.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 GLN cc_start: 0.9144 (tt0) cc_final: 0.8943 (pt0) REVERT: F 30 THR cc_start: 0.8515 (m) cc_final: 0.8088 (p) REVERT: F 31 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8361 (mmmt) REVERT: F 34 THR cc_start: 0.9025 (m) cc_final: 0.8585 (p) REVERT: F 72 LEU cc_start: 0.8882 (mm) cc_final: 0.8569 (mm) REVERT: F 112 PHE cc_start: 0.6183 (m-80) cc_final: 0.5826 (m-80) REVERT: B 18 GLN cc_start: 0.8801 (mp-120) cc_final: 0.8255 (pp30) REVERT: B 51 MET cc_start: 0.8494 (mmm) cc_final: 0.8280 (mmm) REVERT: B 186 ASN cc_start: 0.8762 (m-40) cc_final: 0.8245 (m-40) REVERT: B 205 MET cc_start: 0.7906 (tmm) cc_final: 0.7545 (tmm) REVERT: C 47 TYR cc_start: 0.8225 (p90) cc_final: 0.7212 (m-80) REVERT: C 142 GLU cc_start: 0.8020 (pt0) cc_final: 0.7733 (pm20) REVERT: C 160 ASP cc_start: 0.8433 (t0) cc_final: 0.8141 (t0) REVERT: C 200 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.3486 (mtt180) REVERT: C 221 LEU cc_start: 0.9351 (mt) cc_final: 0.9010 (tp) REVERT: C 233 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7347 (ptm160) REVERT: C 241 LEU cc_start: 0.9529 (tt) cc_final: 0.9110 (mm) REVERT: C 247 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.7275 (tpm170) REVERT: C 315 MET cc_start: 0.7707 (ptp) cc_final: 0.7395 (mpp) REVERT: C 488 MET cc_start: 0.8529 (tpp) cc_final: 0.7986 (mmm) REVERT: C 492 MET cc_start: 0.8768 (ttm) cc_final: 0.8184 (tpp) REVERT: C 672 GLU cc_start: 0.8714 (pm20) cc_final: 0.8415 (pt0) REVERT: C 696 ASP cc_start: 0.7960 (m-30) cc_final: 0.7596 (t0) REVERT: C 711 ASP cc_start: 0.8430 (m-30) cc_final: 0.7724 (m-30) REVERT: C 805 MET cc_start: 0.8879 (ptm) cc_final: 0.8601 (ptm) REVERT: C 922 ASN cc_start: 0.8179 (t0) cc_final: 0.7287 (p0) REVERT: C 992 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6985 (mp) REVERT: C 994 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8278 (mmm160) REVERT: C 1279 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8359 (mt-10) REVERT: D 130 MET cc_start: 0.8517 (mtp) cc_final: 0.8090 (mtt) REVERT: D 298 MET cc_start: 0.8678 (tpp) cc_final: 0.8315 (tpp) REVERT: D 304 ASP cc_start: 0.8424 (m-30) cc_final: 0.7752 (p0) REVERT: D 330 MET cc_start: 0.8532 (mtp) cc_final: 0.7915 (ttm) REVERT: D 443 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8663 (tp30) REVERT: D 472 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8564 (mm) REVERT: D 822 MET cc_start: 0.8695 (mmm) cc_final: 0.8295 (mmm) REVERT: D 895 CYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7434 (p) REVERT: D 913 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7678 (mt-10) REVERT: D 1040 MET cc_start: 0.6095 (ptp) cc_final: 0.5724 (ptp) REVERT: D 1059 LEU cc_start: 0.8384 (mp) cc_final: 0.7912 (tt) REVERT: D 1095 MET cc_start: 0.7032 (ttp) cc_final: 0.6628 (ppp) outliers start: 69 outliers final: 43 residues processed: 310 average time/residue: 0.1636 time to fit residues: 84.9648 Evaluate side-chains 289 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 59 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 348 optimal weight: 50.0000 chunk 196 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 194 GLN C 573 ASN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.079947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.057759 restraints weight = 96264.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059594 restraints weight = 50623.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060758 restraints weight = 32974.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061585 restraints weight = 25041.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061902 restraints weight = 20931.583| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29022 Z= 0.174 Angle : 0.666 13.826 39505 Z= 0.341 Chirality : 0.045 0.346 4519 Planarity : 0.005 0.092 4965 Dihedral : 13.663 145.339 4556 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.69 % Allowed : 15.53 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3503 helix: 1.00 (0.15), residues: 1283 sheet: -1.30 (0.24), residues: 446 loop : -1.93 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 827 TYR 0.022 0.001 TYR D 46 PHE 0.028 0.002 PHE C 156 TRP 0.029 0.001 TRP F 35 HIS 0.006 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (29014) covalent geometry : angle 0.66388 / 0.34 (39493) hydrogen bonds : bond 0.04472 / 4.98 ( 1250) hydrogen bonds : angle 4.78949 / 5.14 ( 3457) metal coordination : bond 0.01026 / 0.98 ( 8) metal coordination : angle 3.07429 / 5.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 246 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 GLN cc_start: 0.9138 (tt0) cc_final: 0.8938 (pt0) REVERT: F 34 THR cc_start: 0.9030 (m) cc_final: 0.8562 (p) REVERT: F 72 LEU cc_start: 0.8802 (mm) cc_final: 0.8524 (mm) REVERT: A 51 MET cc_start: 0.8988 (mmm) cc_final: 0.8624 (mmm) REVERT: A 127 GLN cc_start: 0.8858 (mp10) cc_final: 0.8600 (pm20) REVERT: B 18 GLN cc_start: 0.8806 (mp-120) cc_final: 0.8324 (pp30) REVERT: B 186 ASN cc_start: 0.8840 (m-40) cc_final: 0.8347 (m-40) REVERT: B 205 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7683 (ppp) REVERT: C 47 TYR cc_start: 0.8171 (p90) cc_final: 0.7223 (m-80) REVERT: C 121 GLU cc_start: 0.8077 (pm20) cc_final: 0.7747 (pm20) REVERT: C 160 ASP cc_start: 0.8563 (t0) cc_final: 0.8362 (t0) REVERT: C 200 ARG cc_start: 0.5294 (OUTLIER) cc_final: 0.3539 (mtt180) REVERT: C 233 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7397 (ptm160) REVERT: C 239 MET cc_start: 0.7582 (mtm) cc_final: 0.6980 (mmm) REVERT: C 241 LEU cc_start: 0.9539 (tt) cc_final: 0.9151 (mm) REVERT: C 247 ARG cc_start: 0.7681 (tpp-160) cc_final: 0.7309 (tpm170) REVERT: C 488 MET cc_start: 0.8598 (tpp) cc_final: 0.8262 (tpp) REVERT: C 492 MET cc_start: 0.8746 (ttm) cc_final: 0.8151 (tpp) REVERT: C 653 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7029 (ptp) REVERT: C 696 ASP cc_start: 0.8040 (m-30) cc_final: 0.7622 (t0) REVERT: C 711 ASP cc_start: 0.8533 (m-30) cc_final: 0.7824 (m-30) REVERT: C 922 ASN cc_start: 0.8282 (t0) cc_final: 0.7426 (p0) REVERT: C 992 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6788 (mp) REVERT: C 994 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8324 (mtp180) REVERT: C 1279 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8375 (mt-10) REVERT: D 130 MET cc_start: 0.8550 (mtp) cc_final: 0.8095 (mtt) REVERT: D 298 MET cc_start: 0.8650 (tpp) cc_final: 0.8257 (tpp) REVERT: D 330 MET cc_start: 0.8540 (mtp) cc_final: 0.7898 (ttm) REVERT: D 472 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8596 (mm) REVERT: D 707 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8549 (tp) REVERT: D 743 MET cc_start: 0.8140 (ptt) cc_final: 0.7731 (ppp) REVERT: D 895 CYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7158 (p) REVERT: D 913 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 1040 MET cc_start: 0.6175 (ptp) cc_final: 0.5747 (ptp) REVERT: D 1051 ASP cc_start: 0.8602 (t0) cc_final: 0.8323 (t0) REVERT: D 1059 LEU cc_start: 0.8427 (mp) cc_final: 0.7991 (tt) REVERT: D 1095 MET cc_start: 0.7048 (ttp) cc_final: 0.6640 (ppp) REVERT: D 1239 ASP cc_start: 0.8464 (t0) cc_final: 0.7775 (t0) outliers start: 77 outliers final: 46 residues processed: 298 average time/residue: 0.1640 time to fit residues: 82.5644 Evaluate side-chains 290 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 58 optimal weight: 0.4980 chunk 301 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 40.0000 chunk 206 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 172 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.058452 restraints weight = 96033.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.060308 restraints weight = 50024.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061536 restraints weight = 32512.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.062325 restraints weight = 24485.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.062768 restraints weight = 20457.829| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29022 Z= 0.138 Angle : 0.648 13.246 39505 Z= 0.333 Chirality : 0.045 0.347 4519 Planarity : 0.004 0.090 4965 Dihedral : 13.599 145.134 4556 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.09 % Allowed : 16.37 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3503 helix: 1.14 (0.15), residues: 1276 sheet: -1.08 (0.25), residues: 428 loop : -1.81 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1345 TYR 0.023 0.001 TYR D 46 PHE 0.015 0.001 PHE C1025 TRP 0.031 0.001 TRP F 35 HIS 0.007 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (29014) covalent geometry : angle 0.64482 / 0.33 (39493) hydrogen bonds : bond 0.04311 / 4.83 ( 1250) hydrogen bonds : angle 4.68070 / 5.04 ( 3457) metal coordination : bond 0.01156 / 1.10 ( 8) metal coordination : angle 3.48061 / 6.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 30 THR cc_start: 0.8586 (m) cc_final: 0.8137 (p) REVERT: F 34 THR cc_start: 0.8985 (m) cc_final: 0.8551 (p) REVERT: F 72 LEU cc_start: 0.8716 (mm) cc_final: 0.8468 (mm) REVERT: A 51 MET cc_start: 0.8923 (mmm) cc_final: 0.8524 (mmm) REVERT: A 127 GLN cc_start: 0.8896 (mp10) cc_final: 0.8561 (pm20) REVERT: B 18 GLN cc_start: 0.8791 (mp-120) cc_final: 0.8179 (pp30) REVERT: B 51 MET cc_start: 0.8549 (mmm) cc_final: 0.8328 (mmm) REVERT: B 186 ASN cc_start: 0.8854 (m-40) cc_final: 0.8369 (m-40) REVERT: B 205 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7746 (ppp) REVERT: C 47 TYR cc_start: 0.8242 (p90) cc_final: 0.7327 (m-80) REVERT: C 121 GLU cc_start: 0.8094 (pm20) cc_final: 0.7827 (pm20) REVERT: C 160 ASP cc_start: 0.8716 (t0) cc_final: 0.8297 (t70) REVERT: C 200 ARG cc_start: 0.5271 (OUTLIER) cc_final: 0.3469 (mtt180) REVERT: C 233 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7624 (ptm160) REVERT: C 239 MET cc_start: 0.7555 (mtm) cc_final: 0.7048 (mmm) REVERT: C 241 LEU cc_start: 0.9564 (tt) cc_final: 0.9160 (mm) REVERT: C 247 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.7326 (tpm170) REVERT: C 429 MET cc_start: 0.9328 (mmt) cc_final: 0.8822 (mmt) REVERT: C 459 MET cc_start: 0.9150 (mmm) cc_final: 0.8904 (mpp) REVERT: C 488 MET cc_start: 0.8610 (tpp) cc_final: 0.8291 (tpp) REVERT: C 492 MET cc_start: 0.8741 (ttm) cc_final: 0.8170 (tpp) REVERT: C 653 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7134 (ptp) REVERT: C 654 ASP cc_start: 0.7276 (m-30) cc_final: 0.6921 (m-30) REVERT: C 696 ASP cc_start: 0.8018 (m-30) cc_final: 0.7503 (t0) REVERT: C 711 ASP cc_start: 0.8528 (m-30) cc_final: 0.7824 (m-30) REVERT: C 922 ASN cc_start: 0.8284 (t0) cc_final: 0.7415 (p0) REVERT: C 992 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6864 (mp) REVERT: C 994 ARG cc_start: 0.8592 (mtp180) cc_final: 0.8319 (mtp180) REVERT: C 1107 MET cc_start: 0.7609 (mtm) cc_final: 0.7365 (mtt) REVERT: C 1279 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8371 (mt-10) REVERT: D 130 MET cc_start: 0.8518 (mtp) cc_final: 0.8075 (mtt) REVERT: D 298 MET cc_start: 0.8665 (tpp) cc_final: 0.8349 (tpp) REVERT: D 304 ASP cc_start: 0.8463 (m-30) cc_final: 0.7872 (p0) REVERT: D 330 MET cc_start: 0.8506 (mtp) cc_final: 0.7872 (ttm) REVERT: D 472 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8506 (mm) REVERT: D 513 MET cc_start: 0.8744 (mmm) cc_final: 0.8324 (mmm) REVERT: D 743 MET cc_start: 0.8123 (ptt) cc_final: 0.7854 (ppp) REVERT: D 895 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7158 (p) REVERT: D 913 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 1040 MET cc_start: 0.6228 (ptp) cc_final: 0.5925 (ptp) REVERT: D 1059 LEU cc_start: 0.8426 (mp) cc_final: 0.7976 (tt) REVERT: D 1095 MET cc_start: 0.6870 (ttp) cc_final: 0.6471 (ppp) REVERT: D 1146 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8524 (mp0) REVERT: D 1239 ASP cc_start: 0.8445 (t0) cc_final: 0.7752 (t0) outliers start: 60 outliers final: 38 residues processed: 305 average time/residue: 0.1725 time to fit residues: 87.4436 Evaluate side-chains 285 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 99 optimal weight: 5.9990 chunk 117 optimal weight: 0.0370 chunk 317 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 302 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 200 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 0.0020 overall best weight: 0.5270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1049 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059488 restraints weight = 95317.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.061396 restraints weight = 49551.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062625 restraints weight = 32052.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.063451 restraints weight = 24057.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063717 restraints weight = 20137.091| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29022 Z= 0.123 Angle : 0.656 12.667 39505 Z= 0.335 Chirality : 0.044 0.348 4519 Planarity : 0.004 0.088 4965 Dihedral : 13.548 144.031 4556 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 2.16 % Allowed : 17.24 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3503 helix: 1.21 (0.15), residues: 1271 sheet: -0.93 (0.25), residues: 433 loop : -1.76 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 233 TYR 0.021 0.001 TYR D 46 PHE 0.033 0.001 PHE C 156 TRP 0.032 0.001 TRP F 35 HIS 0.007 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (29014) covalent geometry : angle 0.65415 / 0.33 (39493) hydrogen bonds : bond 0.04168 / 4.66 ( 1250) hydrogen bonds : angle 4.60531 / 4.95 ( 3457) metal coordination : bond 0.00729 / 0.69 ( 8) metal coordination : angle 3.18361 / 5.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 30 THR cc_start: 0.8591 (m) cc_final: 0.8102 (p) REVERT: F 34 THR cc_start: 0.8987 (m) cc_final: 0.8542 (p) REVERT: F 72 LEU cc_start: 0.8621 (mm) cc_final: 0.8383 (mm) REVERT: F 124 MET cc_start: 0.8768 (mmm) cc_final: 0.8540 (tpp) REVERT: A 51 MET cc_start: 0.8855 (mmm) cc_final: 0.8388 (mmm) REVERT: A 127 GLN cc_start: 0.8893 (mp10) cc_final: 0.8573 (pm20) REVERT: A 152 TYR cc_start: 0.8169 (t80) cc_final: 0.7779 (t80) REVERT: B 18 GLN cc_start: 0.8741 (mp-120) cc_final: 0.8167 (pp30) REVERT: B 186 ASN cc_start: 0.8782 (m-40) cc_final: 0.8343 (m-40) REVERT: C 47 TYR cc_start: 0.8185 (p90) cc_final: 0.7329 (m-80) REVERT: C 121 GLU cc_start: 0.7993 (pm20) cc_final: 0.7757 (pm20) REVERT: C 160 ASP cc_start: 0.8630 (t0) cc_final: 0.8429 (t70) REVERT: C 200 ARG cc_start: 0.5201 (OUTLIER) cc_final: 0.3402 (mtt180) REVERT: C 233 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7822 (ptt-90) REVERT: C 239 MET cc_start: 0.8017 (mtm) cc_final: 0.7789 (mmt) REVERT: C 241 LEU cc_start: 0.9539 (tt) cc_final: 0.9163 (mm) REVERT: C 247 ARG cc_start: 0.7571 (tpp-160) cc_final: 0.7262 (tpm170) REVERT: C 315 MET cc_start: 0.7571 (ptp) cc_final: 0.7209 (mpp) REVERT: C 488 MET cc_start: 0.8615 (tpp) cc_final: 0.8339 (tpp) REVERT: C 492 MET cc_start: 0.8723 (ttm) cc_final: 0.8125 (tpp) REVERT: C 653 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7092 (ptp) REVERT: C 668 ILE cc_start: 0.9518 (mm) cc_final: 0.9208 (tp) REVERT: C 672 GLU cc_start: 0.8823 (pm20) cc_final: 0.8447 (pt0) REVERT: C 696 ASP cc_start: 0.7957 (m-30) cc_final: 0.7427 (t0) REVERT: C 711 ASP cc_start: 0.8491 (m-30) cc_final: 0.7766 (m-30) REVERT: C 796 LEU cc_start: 0.9284 (mp) cc_final: 0.8944 (mp) REVERT: C 865 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8804 (tp) REVERT: C 922 ASN cc_start: 0.8230 (t0) cc_final: 0.7386 (p0) REVERT: C 992 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6876 (mp) REVERT: C 994 ARG cc_start: 0.8569 (mtp180) cc_final: 0.8341 (mmm160) REVERT: C 1107 MET cc_start: 0.7725 (mtm) cc_final: 0.7367 (mtt) REVERT: C 1273 MET cc_start: 0.8755 (mtm) cc_final: 0.8364 (mpp) REVERT: C 1279 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8397 (mt-10) REVERT: D 130 MET cc_start: 0.8469 (mtp) cc_final: 0.8058 (mtt) REVERT: D 180 MET cc_start: 0.6990 (mtp) cc_final: 0.6677 (mmm) REVERT: D 298 MET cc_start: 0.8679 (tpp) cc_final: 0.8094 (tpp) REVERT: D 304 ASP cc_start: 0.8418 (m-30) cc_final: 0.7825 (p0) REVERT: D 330 MET cc_start: 0.8410 (mtp) cc_final: 0.7800 (ttm) REVERT: D 472 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8426 (mm) REVERT: D 513 MET cc_start: 0.8695 (mmm) cc_final: 0.8166 (mmm) REVERT: D 822 MET cc_start: 0.8758 (mmm) cc_final: 0.8344 (mmm) REVERT: D 895 CYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7265 (p) REVERT: D 913 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7692 (mt-10) REVERT: D 1040 MET cc_start: 0.6035 (ptp) cc_final: 0.5716 (ptp) REVERT: D 1059 LEU cc_start: 0.8402 (mp) cc_final: 0.7986 (tt) REVERT: D 1095 MET cc_start: 0.6866 (ttp) cc_final: 0.6485 (ppp) REVERT: D 1239 ASP cc_start: 0.8415 (t0) cc_final: 0.7741 (t0) outliers start: 62 outliers final: 38 residues processed: 323 average time/residue: 0.1691 time to fit residues: 90.9687 Evaluate side-chains 294 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 200 optimal weight: 0.9980 chunk 293 optimal weight: 8.9990 chunk 224 optimal weight: 0.0570 chunk 50 optimal weight: 4.9990 chunk 351 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 chunk 306 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059873 restraints weight = 95169.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061552 restraints weight = 53474.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062641 restraints weight = 36321.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.063378 restraints weight = 28215.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063764 restraints weight = 24034.002| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 29022 Z= 0.179 Angle : 0.773 59.168 39505 Z= 0.417 Chirality : 0.045 0.414 4519 Planarity : 0.005 0.088 4965 Dihedral : 13.551 144.007 4556 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.61 % Allowed : 17.98 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3503 helix: 1.20 (0.15), residues: 1271 sheet: -0.91 (0.25), residues: 433 loop : -1.76 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 91 TYR 0.037 0.002 TYR B 68 PHE 0.026 0.001 PHE C 156 TRP 0.028 0.001 TRP F 35 HIS 0.015 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (29014) covalent geometry : angle 0.77109 / 0.42 (39493) hydrogen bonds : bond 0.04177 / 4.68 ( 1250) hydrogen bonds : angle 4.60001 / 4.95 ( 3457) metal coordination : bond 0.00763 / 0.71 ( 8) metal coordination : angle 3.14578 / 5.48 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 30 THR cc_start: 0.8562 (m) cc_final: 0.8126 (p) REVERT: F 34 THR cc_start: 0.8989 (m) cc_final: 0.8530 (p) REVERT: F 72 LEU cc_start: 0.8617 (mm) cc_final: 0.8387 (mm) REVERT: F 124 MET cc_start: 0.8588 (mmm) cc_final: 0.8338 (tpp) REVERT: A 51 MET cc_start: 0.8607 (mmm) cc_final: 0.8273 (mmm) REVERT: A 152 TYR cc_start: 0.7798 (t80) cc_final: 0.7515 (t80) REVERT: B 18 GLN cc_start: 0.8658 (mp-120) cc_final: 0.8074 (pp30) REVERT: B 186 ASN cc_start: 0.8723 (m-40) cc_final: 0.8378 (m-40) REVERT: B 205 MET cc_start: 0.7591 (ppp) cc_final: 0.7321 (tmm) REVERT: C 47 TYR cc_start: 0.8003 (p90) cc_final: 0.7334 (m-80) REVERT: C 160 ASP cc_start: 0.8410 (t0) cc_final: 0.8200 (t70) REVERT: C 200 ARG cc_start: 0.5318 (OUTLIER) cc_final: 0.3465 (mtt180) REVERT: C 239 MET cc_start: 0.7879 (mtm) cc_final: 0.7619 (mmp) REVERT: C 241 LEU cc_start: 0.9442 (tt) cc_final: 0.9109 (mm) REVERT: C 247 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.7217 (tpm170) REVERT: C 315 MET cc_start: 0.7194 (ptp) cc_final: 0.6946 (mpp) REVERT: C 488 MET cc_start: 0.8790 (tpp) cc_final: 0.8512 (tpp) REVERT: C 492 MET cc_start: 0.8477 (ttm) cc_final: 0.8044 (tpp) REVERT: C 668 ILE cc_start: 0.9457 (mm) cc_final: 0.9124 (tp) REVERT: C 672 GLU cc_start: 0.8671 (pm20) cc_final: 0.8218 (pt0) REVERT: C 696 ASP cc_start: 0.7761 (m-30) cc_final: 0.7445 (t0) REVERT: C 711 ASP cc_start: 0.8190 (m-30) cc_final: 0.7414 (m-30) REVERT: C 796 LEU cc_start: 0.9176 (mp) cc_final: 0.8925 (mp) REVERT: C 865 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8573 (tp) REVERT: C 922 ASN cc_start: 0.8016 (t0) cc_final: 0.7326 (p0) REVERT: C 992 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6556 (mp) REVERT: C 1107 MET cc_start: 0.7536 (mtm) cc_final: 0.7330 (mtt) REVERT: C 1273 MET cc_start: 0.8599 (mtm) cc_final: 0.8339 (mpp) REVERT: C 1279 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8251 (mt-10) REVERT: D 130 MET cc_start: 0.8257 (mtp) cc_final: 0.7943 (mtt) REVERT: D 180 MET cc_start: 0.6818 (mtp) cc_final: 0.6547 (mmm) REVERT: D 298 MET cc_start: 0.8435 (tpp) cc_final: 0.7967 (tpp) REVERT: D 304 ASP cc_start: 0.8263 (m-30) cc_final: 0.7715 (p0) REVERT: D 330 MET cc_start: 0.8225 (mtp) cc_final: 0.7699 (ttm) REVERT: D 472 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8398 (mm) REVERT: D 513 MET cc_start: 0.8271 (mmm) cc_final: 0.7925 (mmm) REVERT: D 697 MET cc_start: 0.8412 (ttp) cc_final: 0.7857 (tmm) REVERT: D 822 MET cc_start: 0.8617 (mmm) cc_final: 0.8251 (mmm) REVERT: D 895 CYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7461 (p) REVERT: D 913 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7640 (mt-10) REVERT: D 1040 MET cc_start: 0.5962 (ptp) cc_final: 0.5711 (ptp) REVERT: D 1059 LEU cc_start: 0.8275 (mp) cc_final: 0.7918 (tt) REVERT: D 1095 MET cc_start: 0.7073 (ttp) cc_final: 0.6636 (ppp) REVERT: D 1239 ASP cc_start: 0.8113 (t0) cc_final: 0.7505 (t0) outliers start: 46 outliers final: 36 residues processed: 279 average time/residue: 0.1655 time to fit residues: 77.4212 Evaluate side-chains 284 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 207 optimal weight: 6.9990 chunk 287 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 162 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059358 restraints weight = 96234.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061241 restraints weight = 50580.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062487 restraints weight = 33072.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.063297 restraints weight = 24965.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063731 restraints weight = 20904.462| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 29022 Z= 0.179 Angle : 0.773 59.168 39505 Z= 0.417 Chirality : 0.045 0.414 4519 Planarity : 0.005 0.088 4965 Dihedral : 13.551 144.007 4556 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.43 % Allowed : 18.25 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3503 helix: 1.20 (0.15), residues: 1271 sheet: -0.91 (0.25), residues: 433 loop : -1.76 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 91 TYR 0.037 0.002 TYR B 68 PHE 0.026 0.001 PHE C 156 TRP 0.028 0.001 TRP F 35 HIS 0.015 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (29014) covalent geometry : angle 0.77109 / 0.42 (39493) hydrogen bonds : bond 0.04177 / 4.68 ( 1250) hydrogen bonds : angle 4.60001 / 4.95 ( 3457) metal coordination : bond 0.00763 / 0.71 ( 8) metal coordination : angle 3.14578 / 5.48 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4694.27 seconds wall clock time: 81 minutes 58.77 seconds (4918.77 seconds total)