Starting phenix.real_space_refine on Fri Mar 6 05:59:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ri7_4885/03_2026/6ri7_4885.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ri7_4885/03_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_4885/03_2026/6ri7_4885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ri7_4885/03_2026/6ri7_4885.map" model { file = "/net/cci-nas-00/data/ceres_data/6ri7_4885/03_2026/6ri7_4885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ri7_4885/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 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: 5.91, per 1000 atoms: 0.21 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: 2.50 Conformation dependent library (CDL) restraints added in 930.2 milliseconds 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: 3.72 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: 6.26 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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=" 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=" 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=" C HIS D 419 " pdb=" N PRO D 420 " ideal model delta sigma weight residual 1.332 1.295 0.037 1.33e-02 5.65e+03 7.72e+00 bond pdb=" CA CYS A 176 " pdb=" CB CYS A 176 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.51e-02 4.39e+03 6.15e+00 bond pdb=" C LEU D1314 " pdb=" N ALA D1315 " ideal model delta sigma weight residual 1.333 1.290 0.043 1.73e-02 3.34e+03 6.09e+00 ... (remaining 29009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 38535 2.64 - 5.28: 822 5.28 - 7.93: 100 7.93 - 10.57: 31 10.57 - 13.21: 5 Bond angle restraints: 39493 Sorted by residual: angle pdb=" O3' DT N 34 " pdb=" C3' DT N 34 " pdb=" C2' DT N 34 " ideal model delta sigma weight residual 111.50 98.29 13.21 1.50e+00 4.44e-01 7.76e+01 angle pdb=" CA GLY D 344 " pdb=" C GLY D 344 " pdb=" N LYS D 345 " ideal model delta sigma weight residual 114.58 118.61 -4.03 8.60e-01 1.35e+00 2.19e+01 angle pdb=" C LEU D 472 " pdb=" N THR D 473 " pdb=" CA THR D 473 " ideal model delta sigma weight residual 122.67 115.46 7.21 1.73e+00 3.34e-01 1.74e+01 angle pdb=" C LEU D1314 " pdb=" N ALA D1315 " pdb=" CA ALA D1315 " ideal model delta sigma weight residual 122.55 114.95 7.60 2.03e+00 2.43e-01 1.40e+01 angle pdb=" C LYS D 321 " pdb=" N ARG D 322 " pdb=" CA ARG D 322 " ideal model delta sigma weight residual 122.31 113.69 8.62 2.34e+00 1.83e-01 1.36e+01 ... (remaining 39488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 17196 29.34 - 58.68: 442 58.68 - 88.02: 57 88.02 - 117.35: 0 117.35 - 146.69: 2 Dihedral angle restraints: 17697 sinusoidal: 7587 harmonic: 10110 Sorted by residual: dihedral pdb=" CA GLU A 29 " pdb=" C GLU A 29 " pdb=" N PRO A 30 " pdb=" CA PRO A 30 " ideal model delta harmonic sigma weight residual 180.00 -133.09 -46.91 0 5.00e+00 4.00e-02 8.80e+01 dihedral pdb=" CA ARG D 47 " pdb=" C ARG D 47 " pdb=" N THR D 48 " pdb=" CA THR D 48 " ideal model delta harmonic sigma weight residual 180.00 147.79 32.21 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual 180.00 -148.47 -31.53 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 17694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3718 0.068 - 0.137: 766 0.137 - 0.205: 29 0.205 - 0.273: 5 0.273 - 0.342: 1 Chirality restraints: 4519 Sorted by residual: 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 -2.66 -3.00 0.34 2.00e-01 2.50e+01 2.92e+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 chirality pdb=" CA LEU C1101 " pdb=" N LEU C1101 " pdb=" C LEU C1101 " pdb=" CB LEU C1101 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+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: 1.400 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.700 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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= 0.463 Angle : 1.036 51.234 39505 Z= 0.532 Chirality : 0.051 0.342 4519 Planarity : 0.006 0.103 4965 Dihedral : 12.636 146.693 11193 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 covalent geometry : bond 0.00944 (29014) covalent geometry : angle 0.97691 (39493) hydrogen bonds : bond 0.12232 ( 1250) hydrogen bonds : angle 7.22741 ( 3457) metal coordination : bond 0.10658 ( 8) metal coordination : angle 19.86862 ( 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 : 0.848 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: 0.2112 time to fit residues: 212.8339 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 : 0.739 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.084382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.063167 restraints weight = 95125.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064984 restraints weight = 52104.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066163 restraints weight = 34649.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066906 restraints weight = 26535.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067320 restraints weight = 22428.288| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29022 Z= 0.158 Angle : 0.728 13.419 39505 Z= 0.379 Chirality : 0.046 0.222 4519 Planarity : 0.005 0.096 4965 Dihedral : 14.560 140.629 4602 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.85 % Allowed : 9.67 % Favored : 88.48 % 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: -2.84 (0.13), residues: 3503 helix: -0.63 (0.14), residues: 1269 sheet: -2.17 (0.23), residues: 400 loop : -2.83 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 250 TYR 0.026 0.002 TYR D 349 PHE 0.022 0.002 PHE C 514 TRP 0.017 0.001 TRP C 183 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00339 (29014) covalent geometry : angle 0.72345 (39493) hydrogen bonds : bond 0.05262 ( 1250) hydrogen bonds : angle 5.40896 ( 3457) metal coordination : bond 0.01106 ( 8) metal coordination : angle 4.92980 ( 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 462 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 409 time to evaluate : 1.120 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: F 16 GLN cc_start: 0.9197 (tt0) cc_final: 0.8927 (pt0) REVERT: F 64 TYR cc_start: 0.8981 (t80) cc_final: 0.8739 (t80) REVERT: F 65 LEU cc_start: 0.9134 (mp) cc_final: 0.8932 (mp) REVERT: F 129 LEU cc_start: 0.8145 (tp) cc_final: 0.7761 (tp) REVERT: C 14 ASP cc_start: 0.7207 (t70) cc_final: 0.6964 (t0) REVERT: C 47 TYR cc_start: 0.7946 (p90) cc_final: 0.6958 (m-80) REVERT: C 221 LEU cc_start: 0.9136 (mt) cc_final: 0.8867 (tp) REVERT: C 233 ARG cc_start: 0.7496 (mtp85) cc_final: 0.7109 (ptm160) REVERT: C 241 LEU cc_start: 0.9353 (tt) cc_final: 0.8753 (mm) REVERT: C 403 MET cc_start: 0.9269 (tmm) cc_final: 0.8880 (tmm) REVERT: C 488 MET cc_start: 0.8644 (mmp) cc_final: 0.8321 (mmm) REVERT: C 549 ASP cc_start: 0.8488 (t0) cc_final: 0.8287 (t0) REVERT: C 922 ASN cc_start: 0.7659 (t0) cc_final: 0.7012 (p0) REVERT: C 1170 MET cc_start: 0.8824 (tpp) cc_final: 0.8527 (tpp) REVERT: C 1279 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8032 (mp0) REVERT: D 466 MET cc_start: 0.7406 (mtp) cc_final: 0.7198 (mtp) REVERT: D 913 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7601 (mt-10) REVERT: D 1059 LEU cc_start: 0.8353 (mp) cc_final: 0.7528 (tt) REVERT: D 1095 MET cc_start: 0.7449 (ttp) cc_final: 0.6988 (ppp) REVERT: D 1327 GLU cc_start: 0.8820 (pm20) cc_final: 0.8344 (pm20) REVERT: E 58 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7943 (pt) REVERT: E 68 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7356 (mt-10) outliers start: 53 outliers final: 22 residues processed: 448 average time/residue: 0.1777 time to fit residues: 127.6203 Evaluate side-chains 303 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 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 764 CYS 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 434 ILE Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL 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: 7.9990 chunk 158 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 333 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 296 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 19 ASN A 137 ASN B 186 ASN B 194 GLN C 273 HIS C 437 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1146 GLN C1209 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 430 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN 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 E 43 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055618 restraints weight = 99074.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.057385 restraints weight = 53209.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058508 restraints weight = 35236.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059294 restraints weight = 27026.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.059727 restraints weight = 22734.076| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 29022 Z= 0.320 Angle : 0.804 15.122 39505 Z= 0.414 Chirality : 0.047 0.191 4519 Planarity : 0.006 0.101 4965 Dihedral : 14.408 140.547 4602 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.04 % Allowed : 12.18 % Favored : 84.78 % 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: -2.18 (0.13), residues: 3503 helix: 0.08 (0.14), residues: 1278 sheet: -1.96 (0.23), residues: 431 loop : -2.54 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 838 TYR 0.026 0.002 TYR C1229 PHE 0.023 0.002 PHE F 112 TRP 0.024 0.003 TRP C 183 HIS 0.009 0.002 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00708 (29014) covalent geometry : angle 0.79890 (39493) hydrogen bonds : bond 0.05317 ( 1250) hydrogen bonds : angle 5.44079 ( 3457) metal coordination : bond 0.02010 ( 8) metal coordination : angle 5.05540 ( 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 356 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 269 time to evaluate : 1.174 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: 0.9204 (tt0) cc_final: 0.8860 (pt0) REVERT: F 72 LEU cc_start: 0.9021 (mm) cc_final: 0.8613 (mm) REVERT: A 177 TYR cc_start: 0.8099 (m-80) cc_final: 0.7184 (m-10) REVERT: B 18 GLN cc_start: 0.8633 (mp10) cc_final: 0.8355 (pp30) REVERT: B 51 MET cc_start: 0.8687 (mmm) cc_final: 0.8457 (mmm) REVERT: B 205 MET cc_start: 0.8176 (tmm) cc_final: 0.7492 (tmm) REVERT: C 47 TYR cc_start: 0.8319 (p90) cc_final: 0.7306 (m-80) REVERT: C 156 PHE cc_start: 0.8463 (m-10) cc_final: 0.8086 (m-10) REVERT: C 200 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.3795 (mtt180) REVERT: C 221 LEU cc_start: 0.9366 (mt) cc_final: 0.9037 (tp) REVERT: C 233 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7251 (ptm160) REVERT: C 237 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7435 (pp) REVERT: C 241 LEU cc_start: 0.9567 (tt) cc_final: 0.9018 (mm) REVERT: C 549 ASP cc_start: 0.8939 (t0) cc_final: 0.8659 (t70) REVERT: C 672 GLU cc_start: 0.8930 (pm20) cc_final: 0.8729 (pm20) REVERT: C 696 ASP cc_start: 0.8097 (t0) cc_final: 0.7566 (t0) REVERT: C 711 ASP cc_start: 0.8522 (m-30) cc_final: 0.8101 (m-30) REVERT: C 992 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6819 (mp) REVERT: C 1170 MET cc_start: 0.9234 (tpp) cc_final: 0.8993 (tpp) REVERT: C 1243 MET cc_start: 0.8887 (tmm) cc_final: 0.8440 (tmm) REVERT: C 1279 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8455 (mt-10) REVERT: D 298 MET cc_start: 0.8672 (tpp) cc_final: 0.8215 (tpp) REVERT: D 895 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7555 (p) REVERT: D 1051 ASP cc_start: 0.8694 (t0) cc_final: 0.8452 (t0) REVERT: D 1059 LEU cc_start: 0.8422 (mp) cc_final: 0.7869 (tt) REVERT: D 1239 ASP cc_start: 0.8480 (t0) cc_final: 0.7863 (t0) REVERT: D 1334 GLU cc_start: 0.8839 (tt0) cc_final: 0.8294 (tm-30) outliers start: 87 outliers final: 50 residues processed: 335 average time/residue: 0.1656 time to fit residues: 91.8317 Evaluate side-chains 289 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 74 ILE Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain A residue 65 LEU 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 39 ILE Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 237 LEU 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 562 GLU Chi-restraints excluded: chain C residue 657 THR 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 1105 SER Chi-restraints excluded: chain C residue 1176 LEU 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 1325 VAL 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 244 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 770 LEU 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 E residue 10 VAL Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 71 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 173 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 212 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 342 optimal weight: 30.0000 chunk 309 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 305 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN C 513 GLN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 ASN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.079657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057202 restraints weight = 96692.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058995 restraints weight = 51214.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.060210 restraints weight = 33793.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.060952 restraints weight = 25667.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.061337 restraints weight = 21613.180| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4373 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= 0.168 Angle : 0.659 14.618 39505 Z= 0.342 Chirality : 0.044 0.231 4519 Planarity : 0.005 0.094 4965 Dihedral : 14.240 137.626 4602 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.90 % Allowed : 13.61 % Favored : 83.49 % 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: -1.52 (0.14), residues: 3503 helix: 0.70 (0.15), residues: 1287 sheet: -1.61 (0.24), residues: 453 loop : -2.23 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 838 TYR 0.021 0.001 TYR D 46 PHE 0.013 0.001 PHE C1221 TRP 0.013 0.001 TRP C 183 HIS 0.004 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00374 (29014) covalent geometry : angle 0.65470 (39493) hydrogen bonds : bond 0.04600 ( 1250) hydrogen bonds : angle 4.98087 ( 3457) metal coordination : bond 0.01020 ( 8) metal coordination : angle 4.30001 ( 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 350 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 267 time to evaluate : 1.046 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: 0.9134 (tt0) cc_final: 0.8920 (pt0) REVERT: F 30 THR cc_start: 0.8576 (m) cc_final: 0.8223 (p) REVERT: F 31 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8363 (mmmt) REVERT: F 72 LEU cc_start: 0.9020 (mm) cc_final: 0.8669 (mm) REVERT: F 112 PHE cc_start: 0.6466 (m-80) cc_final: 0.6174 (m-80) REVERT: A 51 MET cc_start: 0.8918 (mmm) cc_final: 0.8666 (mmm) REVERT: A 93 GLN cc_start: 0.8358 (pt0) cc_final: 0.8091 (pp30) REVERT: A 137 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8762 (p0) REVERT: A 177 TYR cc_start: 0.8040 (m-80) cc_final: 0.6893 (m-10) REVERT: B 51 MET cc_start: 0.8595 (mmm) cc_final: 0.8310 (mmm) REVERT: B 186 ASN cc_start: 0.8858 (m-40) cc_final: 0.8534 (m-40) REVERT: B 205 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7926 (tmm) REVERT: C 47 TYR cc_start: 0.8272 (p90) cc_final: 0.7303 (m-80) REVERT: C 142 GLU cc_start: 0.8249 (pt0) cc_final: 0.8034 (pt0) REVERT: C 156 PHE cc_start: 0.8400 (m-10) cc_final: 0.8127 (m-10) REVERT: C 200 ARG cc_start: 0.5265 (OUTLIER) cc_final: 0.3881 (mtt180) REVERT: C 221 LEU cc_start: 0.9359 (mt) cc_final: 0.9006 (tp) REVERT: C 233 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7363 (ptm160) REVERT: C 237 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7327 (pp) REVERT: C 241 LEU cc_start: 0.9502 (tt) cc_final: 0.9062 (mm) REVERT: C 283 LYS cc_start: 0.7832 (pttt) cc_final: 0.7421 (mttm) REVERT: C 492 MET cc_start: 0.8698 (mtt) cc_final: 0.8117 (tpp) REVERT: C 696 ASP cc_start: 0.7669 (t0) cc_final: 0.6993 (t0) REVERT: C 711 ASP cc_start: 0.8523 (m-30) cc_final: 0.8101 (m-30) REVERT: C 922 ASN cc_start: 0.8285 (t0) cc_final: 0.7474 (p0) REVERT: C 992 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7186 (mp) REVERT: C 994 ARG cc_start: 0.8623 (mtp180) cc_final: 0.8272 (mmm160) REVERT: C 1170 MET cc_start: 0.9221 (tpp) cc_final: 0.8994 (tpp) REVERT: C 1279 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8397 (mt-10) REVERT: D 102 MET cc_start: 0.8269 (mtm) cc_final: 0.7899 (mtp) REVERT: D 298 MET cc_start: 0.8605 (tpp) cc_final: 0.8078 (tpp) REVERT: D 330 MET cc_start: 0.8556 (mtp) cc_final: 0.8104 (ttm) REVERT: D 811 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: D 895 CYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7508 (p) REVERT: D 913 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7692 (mt-10) REVERT: D 1051 ASP cc_start: 0.8678 (t0) cc_final: 0.8462 (t0) REVERT: D 1059 LEU cc_start: 0.8394 (mp) cc_final: 0.7780 (tt) REVERT: D 1239 ASP cc_start: 0.8423 (t0) cc_final: 0.7796 (t0) REVERT: D 1334 GLU cc_start: 0.8815 (tt0) cc_final: 0.8193 (tm-30) REVERT: E 29 GLN cc_start: 0.9290 (mt0) cc_final: 0.9038 (tt0) outliers start: 83 outliers final: 41 residues processed: 330 average time/residue: 0.1669 time to fit residues: 91.5991 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 : 1.158 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 39 ILE 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 237 LEU 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 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 1014 LEU 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 1105 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 128 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 472 LEU 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 1260 MET Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 66 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 326 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 339 optimal weight: 30.0000 chunk 130 optimal weight: 1.9990 chunk 322 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** C 517 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 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.081115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059228 restraints weight = 95519.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060898 restraints weight = 53423.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062014 restraints weight = 36233.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062760 restraints weight = 28046.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.063020 restraints weight = 23800.556| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29022 Z= 0.130 Angle : 0.621 12.172 39505 Z= 0.323 Chirality : 0.043 0.202 4519 Planarity : 0.005 0.091 4965 Dihedral : 14.089 139.326 4602 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.51 % Allowed : 14.66 % Favored : 82.83 % 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: -1.14 (0.14), residues: 3503 helix: 1.01 (0.15), residues: 1292 sheet: -1.30 (0.24), residues: 447 loop : -2.05 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 838 TYR 0.023 0.001 TYR D 46 PHE 0.014 0.001 PHE A 35 TRP 0.008 0.001 TRP C 183 HIS 0.007 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00276 (29014) covalent geometry : angle 0.61834 (39493) hydrogen bonds : bond 0.04276 ( 1250) hydrogen bonds : angle 4.74675 ( 3457) metal coordination : bond 0.00612 ( 8) metal coordination : angle 3.24653 ( 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 355 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 283 time to evaluate : 1.000 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 72 LEU cc_start: 0.8989 (mm) cc_final: 0.8593 (mm) REVERT: F 112 PHE cc_start: 0.6190 (m-80) cc_final: 0.5897 (m-80) REVERT: B 18 GLN cc_start: 0.8677 (mp-120) cc_final: 0.8278 (pp30) REVERT: B 186 ASN cc_start: 0.8796 (m-40) cc_final: 0.8574 (m-40) REVERT: C 47 TYR cc_start: 0.8037 (p90) cc_final: 0.7255 (m-80) REVERT: C 142 GLU cc_start: 0.7818 (pt0) cc_final: 0.7608 (pm20) REVERT: C 200 ARG cc_start: 0.5208 (OUTLIER) cc_final: 0.3731 (mtt180) REVERT: C 221 LEU cc_start: 0.9292 (mt) cc_final: 0.8972 (tp) REVERT: C 233 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7250 (ptm160) REVERT: C 237 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7206 (pp) REVERT: C 241 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9056 (mm) REVERT: C 492 MET cc_start: 0.8376 (mtt) cc_final: 0.7972 (tpp) REVERT: C 696 ASP cc_start: 0.7466 (t0) cc_final: 0.6876 (t70) REVERT: C 711 ASP cc_start: 0.8131 (m-30) cc_final: 0.7764 (m-30) REVERT: C 814 ASP cc_start: 0.8266 (m-30) cc_final: 0.8054 (m-30) REVERT: C 922 ASN cc_start: 0.8034 (t0) cc_final: 0.7400 (p0) REVERT: C 992 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6582 (mp) REVERT: C 994 ARG cc_start: 0.8532 (mtp180) cc_final: 0.8280 (mtp180) REVERT: C 1180 MET cc_start: 0.9431 (tpp) cc_final: 0.9137 (tpp) REVERT: C 1279 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8315 (mt-10) REVERT: D 102 MET cc_start: 0.7849 (mtm) cc_final: 0.7626 (mtp) REVERT: D 298 MET cc_start: 0.8415 (tpp) cc_final: 0.7972 (tpp) REVERT: D 330 MET cc_start: 0.8298 (mtp) cc_final: 0.7779 (ttm) REVERT: D 349 TYR cc_start: 0.8829 (m-80) cc_final: 0.8627 (m-80) REVERT: D 429 LEU cc_start: 0.9310 (mp) cc_final: 0.9087 (mp) REVERT: D 443 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: D 895 CYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7698 (p) REVERT: D 913 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7619 (mt-10) REVERT: D 1040 MET cc_start: 0.5966 (ttm) cc_final: 0.5397 (mtp) REVERT: D 1051 ASP cc_start: 0.8391 (t0) cc_final: 0.8121 (t0) REVERT: D 1059 LEU cc_start: 0.8282 (mp) cc_final: 0.7741 (tt) REVERT: D 1095 MET cc_start: 0.7224 (ttp) cc_final: 0.6776 (ppp) REVERT: D 1239 ASP cc_start: 0.8106 (t0) cc_final: 0.7504 (t0) REVERT: E 68 GLU cc_start: 0.8045 (pt0) cc_final: 0.7836 (pt0) outliers start: 72 outliers final: 39 residues processed: 332 average time/residue: 0.1743 time to fit residues: 94.6589 Evaluate side-chains 297 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 39 ILE 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 237 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 764 CYS 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 1105 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 92 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 785 ASP 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 1353 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 163 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 342 optimal weight: 50.0000 chunk 187 optimal weight: 4.9990 chunk 350 optimal weight: 30.0000 chunk 287 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN ** 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** 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 = 0.3387 r_free = 0.3387 target = 0.079635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057372 restraints weight = 96099.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.059218 restraints weight = 50432.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.060402 restraints weight = 32792.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061187 restraints weight = 24853.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.061589 restraints weight = 20751.454| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29022 Z= 0.178 Angle : 0.636 14.496 39505 Z= 0.328 Chirality : 0.042 0.200 4519 Planarity : 0.005 0.092 4965 Dihedral : 14.009 142.460 4602 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.69 % Allowed : 15.39 % Favored : 81.92 % 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: -0.95 (0.14), residues: 3503 helix: 1.16 (0.15), residues: 1280 sheet: -1.26 (0.24), residues: 448 loop : -1.88 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 838 TYR 0.026 0.001 TYR F 77 PHE 0.020 0.002 PHE C1025 TRP 0.025 0.001 TRP F 35 HIS 0.005 0.001 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00398 (29014) covalent geometry : angle 0.63343 (39493) hydrogen bonds : bond 0.04345 ( 1250) hydrogen bonds : angle 4.74503 ( 3457) metal coordination : bond 0.01004 ( 8) metal coordination : angle 3.11432 ( 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 335 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 1.075 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: F 72 LEU cc_start: 0.8669 (mm) cc_final: 0.8414 (mm) REVERT: A 177 TYR cc_start: 0.8231 (m-80) cc_final: 0.6841 (m-10) REVERT: B 18 GLN cc_start: 0.8793 (mp-120) cc_final: 0.8308 (pp30) REVERT: B 186 ASN cc_start: 0.8920 (m-40) cc_final: 0.8655 (m-40) REVERT: B 205 MET cc_start: 0.8151 (tmm) cc_final: 0.7585 (tmm) REVERT: C 47 TYR cc_start: 0.8232 (p90) cc_final: 0.7290 (m-80) REVERT: C 121 GLU cc_start: 0.8156 (pm20) cc_final: 0.7886 (pm20) REVERT: C 200 ARG cc_start: 0.5134 (OUTLIER) cc_final: 0.3664 (mtt180) REVERT: C 233 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7460 (ptm160) REVERT: C 237 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7333 (pp) REVERT: C 241 LEU cc_start: 0.9561 (tt) cc_final: 0.9055 (mm) REVERT: C 281 ASP cc_start: 0.7457 (t0) cc_final: 0.7121 (m-30) REVERT: C 315 MET cc_start: 0.7775 (mpp) cc_final: 0.7560 (mpp) REVERT: C 492 MET cc_start: 0.8744 (mtt) cc_final: 0.8203 (tpp) REVERT: C 517 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7900 (tm-30) REVERT: C 685 MET cc_start: 0.8092 (mtt) cc_final: 0.7276 (mtt) REVERT: C 696 ASP cc_start: 0.7623 (t0) cc_final: 0.7178 (t70) REVERT: C 711 ASP cc_start: 0.8530 (m-30) cc_final: 0.8114 (m-30) REVERT: C 922 ASN cc_start: 0.8451 (t0) cc_final: 0.7637 (p0) REVERT: C 992 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6761 (mp) REVERT: C 994 ARG cc_start: 0.8626 (mtp180) cc_final: 0.8366 (mtp180) REVERT: C 1073 LYS cc_start: 0.8776 (mttt) cc_final: 0.8573 (mtpp) REVERT: C 1279 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8439 (mt-10) REVERT: D 102 MET cc_start: 0.8409 (mtm) cc_final: 0.8042 (mtp) REVERT: D 298 MET cc_start: 0.8744 (tpp) cc_final: 0.8214 (tpp) REVERT: D 304 ASP cc_start: 0.8454 (m-30) cc_final: 0.7890 (p0) REVERT: D 330 MET cc_start: 0.8545 (mtp) cc_final: 0.7897 (ttm) REVERT: D 349 TYR cc_start: 0.9082 (m-80) cc_final: 0.8865 (m-80) REVERT: D 743 MET cc_start: 0.8602 (ptm) cc_final: 0.7212 (ppp) REVERT: D 895 CYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7500 (p) REVERT: D 913 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7679 (mt-10) REVERT: D 1059 LEU cc_start: 0.8407 (mp) cc_final: 0.7915 (tt) REVERT: D 1146 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8855 (mm-30) REVERT: D 1239 ASP cc_start: 0.8486 (t0) cc_final: 0.7830 (t0) REVERT: E 29 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.9071 (tt0) REVERT: E 43 ASN cc_start: 0.8737 (t0) cc_final: 0.8414 (t0) outliers start: 77 outliers final: 49 residues processed: 314 average time/residue: 0.1666 time to fit residues: 88.3774 Evaluate side-chains 288 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 39 ILE 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 237 LEU Chi-restraints excluded: chain C residue 289 VAL 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 742 TYR Chi-restraints excluded: chain C residue 764 CYS 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 1049 ILE Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1176 LEU 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 92 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 528 THR 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 29 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 59 optimal weight: 4.9990 chunk 288 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 348 optimal weight: 0.0970 chunk 196 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 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 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.057966 restraints weight = 95471.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.059803 restraints weight = 49855.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061013 restraints weight = 32492.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.061779 restraints weight = 24536.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.062307 restraints weight = 20597.012| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29022 Z= 0.145 Angle : 0.618 14.223 39505 Z= 0.319 Chirality : 0.042 0.201 4519 Planarity : 0.004 0.090 4965 Dihedral : 13.929 142.026 4602 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.62 % Allowed : 15.92 % Favored : 81.47 % 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: -0.84 (0.14), residues: 3503 helix: 1.22 (0.15), residues: 1282 sheet: -1.08 (0.25), residues: 442 loop : -1.83 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 838 TYR 0.020 0.001 TYR F 77 PHE 0.017 0.001 PHE D 461 TRP 0.014 0.001 TRP F 35 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00324 (29014) covalent geometry : angle 0.61651 (39493) hydrogen bonds : bond 0.04162 ( 1250) hydrogen bonds : angle 4.62861 ( 3457) metal coordination : bond 0.00752 ( 8) metal coordination : angle 2.87916 ( 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 336 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 261 time to evaluate : 1.056 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: F 72 LEU cc_start: 0.8602 (mm) cc_final: 0.8369 (mm) REVERT: F 124 MET cc_start: 0.8871 (mmm) cc_final: 0.8670 (tpp) REVERT: B 18 GLN cc_start: 0.8755 (mp-120) cc_final: 0.8352 (pp30) REVERT: B 186 ASN cc_start: 0.8937 (m-40) cc_final: 0.8509 (m-40) REVERT: B 205 MET cc_start: 0.8186 (tmm) cc_final: 0.7642 (tmm) REVERT: C 47 TYR cc_start: 0.8160 (p90) cc_final: 0.7355 (m-80) REVERT: C 121 GLU cc_start: 0.7987 (pm20) cc_final: 0.7781 (pm20) REVERT: C 200 ARG cc_start: 0.5136 (OUTLIER) cc_final: 0.3616 (mtt180) REVERT: C 233 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7441 (ptm160) REVERT: C 237 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7196 (pp) REVERT: C 241 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9097 (mm) REVERT: C 281 ASP cc_start: 0.7352 (t0) cc_final: 0.7066 (m-30) REVERT: C 492 MET cc_start: 0.8712 (mtt) cc_final: 0.8392 (mtp) REVERT: C 517 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 606 LEU cc_start: 0.9258 (mp) cc_final: 0.8901 (mt) REVERT: C 696 ASP cc_start: 0.7554 (t0) cc_final: 0.7092 (t70) REVERT: C 711 ASP cc_start: 0.8427 (m-30) cc_final: 0.8037 (m-30) REVERT: C 922 ASN cc_start: 0.8379 (t0) cc_final: 0.7634 (p0) REVERT: C 992 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6765 (mp) REVERT: C 994 ARG cc_start: 0.8538 (mtp180) cc_final: 0.8274 (mtp180) REVERT: C 1279 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8427 (mt-10) REVERT: C 1290 MET cc_start: 0.8889 (ttm) cc_final: 0.7946 (ttm) REVERT: D 102 MET cc_start: 0.8265 (mtm) cc_final: 0.7927 (mtp) REVERT: D 298 MET cc_start: 0.8720 (tpp) cc_final: 0.7967 (tpp) REVERT: D 304 ASP cc_start: 0.8431 (m-30) cc_final: 0.7887 (p0) REVERT: D 330 MET cc_start: 0.8467 (mtp) cc_final: 0.7830 (ttm) REVERT: D 497 GLU cc_start: 0.8346 (tp30) cc_final: 0.8057 (tm-30) REVERT: D 743 MET cc_start: 0.8631 (ptm) cc_final: 0.7304 (ppp) REVERT: D 895 CYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7572 (p) REVERT: D 1049 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8210 (pp30) REVERT: D 1059 LEU cc_start: 0.8401 (mp) cc_final: 0.7888 (tt) REVERT: D 1146 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8818 (mm-30) REVERT: D 1239 ASP cc_start: 0.8390 (t0) cc_final: 0.7743 (t0) REVERT: E 43 ASN cc_start: 0.8762 (t0) cc_final: 0.8387 (t0) outliers start: 75 outliers final: 44 residues processed: 311 average time/residue: 0.1602 time to fit residues: 83.6005 Evaluate side-chains 286 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 39 ILE 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 237 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 764 CYS 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 1105 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 92 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 639 VAL 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 1049 GLN Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 58 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 52 optimal weight: 0.0030 chunk 172 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.058065 restraints weight = 96009.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059717 restraints weight = 54129.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.060796 restraints weight = 36794.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.061506 restraints weight = 28553.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061753 restraints weight = 24390.873| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29022 Z= 0.159 Angle : 0.629 15.744 39505 Z= 0.323 Chirality : 0.042 0.161 4519 Planarity : 0.004 0.090 4965 Dihedral : 13.875 141.549 4602 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.55 % Allowed : 16.34 % Favored : 81.12 % 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: -0.79 (0.14), residues: 3503 helix: 1.23 (0.15), residues: 1288 sheet: -1.08 (0.24), residues: 463 loop : -1.78 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 838 TYR 0.017 0.001 TYR D 631 PHE 0.021 0.001 PHE B 8 TRP 0.014 0.001 TRP F 35 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00356 (29014) covalent geometry : angle 0.62723 (39493) hydrogen bonds : bond 0.04139 ( 1250) hydrogen bonds : angle 4.59150 ( 3457) metal coordination : bond 0.00839 ( 8) metal coordination : angle 2.61862 ( 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 327 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 254 time to evaluate : 1.082 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: A 125 LYS cc_start: 0.8767 (tttt) cc_final: 0.8546 (tptt) REVERT: A 152 TYR cc_start: 0.7909 (t80) cc_final: 0.7604 (t80) REVERT: B 18 GLN cc_start: 0.8690 (mp-120) cc_final: 0.8154 (pp30) REVERT: B 186 ASN cc_start: 0.8844 (m-40) cc_final: 0.8488 (m-40) REVERT: B 208 ASN cc_start: 0.9055 (p0) cc_final: 0.8802 (p0) REVERT: C 47 TYR cc_start: 0.8007 (p90) cc_final: 0.7340 (m-80) REVERT: C 200 ARG cc_start: 0.5205 (OUTLIER) cc_final: 0.3604 (mtt180) REVERT: C 233 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7866 (ptm160) REVERT: C 241 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9079 (mm) REVERT: C 281 ASP cc_start: 0.7266 (t0) cc_final: 0.7047 (m-30) REVERT: C 492 MET cc_start: 0.8501 (mtt) cc_final: 0.8210 (mtp) REVERT: C 517 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 653 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6723 (ptp) REVERT: C 672 GLU cc_start: 0.8707 (pm20) cc_final: 0.8230 (pt0) REVERT: C 696 ASP cc_start: 0.7454 (t0) cc_final: 0.7058 (t70) REVERT: C 711 ASP cc_start: 0.8192 (m-30) cc_final: 0.7800 (m-30) REVERT: C 922 ASN cc_start: 0.8269 (t0) cc_final: 0.7667 (p0) REVERT: C 992 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6535 (mp) REVERT: C 994 ARG cc_start: 0.8479 (mtp180) cc_final: 0.8229 (mtp180) REVERT: C 1290 MET cc_start: 0.8758 (ttm) cc_final: 0.7940 (ttm) REVERT: D 102 MET cc_start: 0.8051 (mtm) cc_final: 0.7775 (mtp) REVERT: D 298 MET cc_start: 0.8560 (tpp) cc_final: 0.7865 (tpp) REVERT: D 304 ASP cc_start: 0.8243 (m-30) cc_final: 0.7831 (p0) REVERT: D 330 MET cc_start: 0.8320 (mtp) cc_final: 0.7739 (ttm) REVERT: D 497 GLU cc_start: 0.8210 (tp30) cc_final: 0.7978 (tm-30) REVERT: D 743 MET cc_start: 0.8476 (ptm) cc_final: 0.7411 (ppp) REVERT: D 895 CYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7717 (p) REVERT: D 1059 LEU cc_start: 0.8354 (mp) cc_final: 0.7922 (tt) REVERT: D 1239 ASP cc_start: 0.8175 (t0) cc_final: 0.7577 (t0) REVERT: E 43 ASN cc_start: 0.8744 (t0) cc_final: 0.8244 (t0) outliers start: 73 outliers final: 49 residues processed: 303 average time/residue: 0.1659 time to fit residues: 84.4752 Evaluate side-chains 286 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 39 ILE 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 241 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 563 THR 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 742 TYR Chi-restraints excluded: chain C residue 764 CYS 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 1049 ILE Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 528 THR 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 44 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 99 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 302 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** 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 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057607 restraints weight = 95691.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.059449 restraints weight = 50200.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.060653 restraints weight = 32657.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061333 restraints weight = 24691.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061876 restraints weight = 20928.347| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29022 Z= 0.163 Angle : 0.644 14.712 39505 Z= 0.329 Chirality : 0.042 0.163 4519 Planarity : 0.004 0.090 4965 Dihedral : 13.843 140.788 4602 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.48 % Allowed : 16.75 % Favored : 80.77 % 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: -0.76 (0.14), residues: 3503 helix: 1.21 (0.15), residues: 1288 sheet: -0.90 (0.25), residues: 449 loop : -1.77 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 481 TYR 0.014 0.001 TYR D 631 PHE 0.019 0.001 PHE B 8 TRP 0.014 0.001 TRP F 35 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00369 (29014) covalent geometry : angle 0.64259 (39493) hydrogen bonds : bond 0.04132 ( 1250) hydrogen bonds : angle 4.56119 ( 3457) metal coordination : bond 0.00831 ( 8) metal coordination : angle 2.54769 ( 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 316 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 245 time to evaluate : 1.140 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: A 125 LYS cc_start: 0.8922 (tttt) cc_final: 0.8676 (ttmt) REVERT: A 127 GLN cc_start: 0.8796 (mp10) cc_final: 0.8548 (pm20) REVERT: A 152 TYR cc_start: 0.8317 (t80) cc_final: 0.7877 (t80) REVERT: B 18 GLN cc_start: 0.8747 (mp-120) cc_final: 0.8257 (pp30) REVERT: B 186 ASN cc_start: 0.8925 (m-40) cc_final: 0.8497 (m-40) REVERT: B 208 ASN cc_start: 0.9230 (p0) cc_final: 0.8912 (p0) REVERT: C 47 TYR cc_start: 0.8162 (p90) cc_final: 0.7359 (m-80) REVERT: C 200 ARG cc_start: 0.5263 (OUTLIER) cc_final: 0.3382 (mtt180) REVERT: C 233 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7756 (ptt-90) REVERT: C 241 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9120 (mm) REVERT: C 281 ASP cc_start: 0.7501 (t0) cc_final: 0.7183 (m-30) REVERT: C 429 MET cc_start: 0.9292 (mmt) cc_final: 0.9082 (mmt) REVERT: C 492 MET cc_start: 0.8742 (mtt) cc_final: 0.8531 (mtp) REVERT: C 517 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7543 (tm-30) REVERT: C 653 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7026 (ptp) REVERT: C 696 ASP cc_start: 0.7514 (t0) cc_final: 0.7075 (t70) REVERT: C 711 ASP cc_start: 0.8510 (m-30) cc_final: 0.8126 (m-30) REVERT: C 922 ASN cc_start: 0.8470 (t0) cc_final: 0.7787 (p0) REVERT: C 992 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6799 (mp) REVERT: C 994 ARG cc_start: 0.8507 (mtp180) cc_final: 0.8289 (mtp180) REVERT: C 1290 MET cc_start: 0.8867 (ttm) cc_final: 0.7971 (ttm) REVERT: D 298 MET cc_start: 0.8805 (tpp) cc_final: 0.8033 (tpp) REVERT: D 304 ASP cc_start: 0.8468 (m-30) cc_final: 0.8082 (p0) REVERT: D 330 MET cc_start: 0.8493 (mtp) cc_final: 0.7850 (ttm) REVERT: D 484 MET cc_start: 0.9063 (mmm) cc_final: 0.8824 (mmt) REVERT: D 743 MET cc_start: 0.8717 (ptm) cc_final: 0.7247 (ppp) REVERT: D 772 TYR cc_start: 0.9087 (t80) cc_final: 0.8820 (t80) REVERT: D 821 MET cc_start: 0.8381 (tpp) cc_final: 0.7553 (tpp) REVERT: D 822 MET cc_start: 0.9390 (tpp) cc_final: 0.9121 (tpp) REVERT: D 895 CYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7417 (p) REVERT: D 1059 LEU cc_start: 0.8437 (mp) cc_final: 0.7969 (tt) REVERT: D 1146 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8871 (mm-30) REVERT: D 1239 ASP cc_start: 0.8455 (t0) cc_final: 0.7802 (t0) REVERT: E 43 ASN cc_start: 0.8828 (t0) cc_final: 0.8354 (t0) REVERT: E 55 GLU cc_start: 0.8579 (tt0) cc_final: 0.8273 (tp30) outliers start: 71 outliers final: 52 residues processed: 292 average time/residue: 0.1629 time to fit residues: 80.1854 Evaluate side-chains 287 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 39 ILE 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 241 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 563 THR 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 681 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 764 CYS 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 1049 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 528 THR 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 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 200 optimal weight: 0.5980 chunk 293 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 351 optimal weight: 50.0000 chunk 17 optimal weight: 7.9990 chunk 306 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 HIS ** 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.080783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058895 restraints weight = 94799.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060522 restraints weight = 53593.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.061628 restraints weight = 36591.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062314 restraints weight = 28506.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062691 restraints weight = 24423.370| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29022 Z= 0.138 Angle : 0.638 15.152 39505 Z= 0.325 Chirality : 0.042 0.167 4519 Planarity : 0.004 0.088 4965 Dihedral : 13.796 139.293 4602 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.85 % Allowed : 17.77 % Favored : 80.38 % 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: -0.69 (0.14), residues: 3503 helix: 1.28 (0.15), residues: 1282 sheet: -0.92 (0.25), residues: 439 loop : -1.71 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 233 TYR 0.020 0.001 TYR D 631 PHE 0.017 0.001 PHE D 461 TRP 0.014 0.001 TRP F 35 HIS 0.004 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00314 (29014) covalent geometry : angle 0.63654 (39493) hydrogen bonds : bond 0.03988 ( 1250) hydrogen bonds : angle 4.48385 ( 3457) metal coordination : bond 0.00615 ( 8) metal coordination : angle 2.34476 ( 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 309 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 1.026 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 77 TYR cc_start: 0.7799 (t80) cc_final: 0.7494 (t80) REVERT: A 51 MET cc_start: 0.8599 (mmm) cc_final: 0.8287 (mmm) REVERT: A 152 TYR cc_start: 0.7872 (t80) cc_final: 0.7623 (t80) REVERT: B 18 GLN cc_start: 0.8658 (mp-120) cc_final: 0.8191 (pp30) REVERT: B 51 MET cc_start: 0.8571 (mmm) cc_final: 0.8298 (mmm) REVERT: B 186 ASN cc_start: 0.8867 (m-40) cc_final: 0.8505 (m-40) REVERT: B 208 ASN cc_start: 0.9069 (p0) cc_final: 0.8742 (p0) REVERT: C 47 TYR cc_start: 0.7939 (p90) cc_final: 0.7358 (m-80) REVERT: C 200 ARG cc_start: 0.5356 (OUTLIER) cc_final: 0.3385 (mtt180) REVERT: C 233 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7422 (ptt-90) REVERT: C 241 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9104 (mm) REVERT: C 281 ASP cc_start: 0.7571 (t0) cc_final: 0.7263 (m-30) REVERT: C 492 MET cc_start: 0.8465 (mtt) cc_final: 0.8187 (tpp) REVERT: C 517 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 632 ASP cc_start: 0.7513 (p0) cc_final: 0.7210 (p0) REVERT: C 672 GLU cc_start: 0.8651 (pm20) cc_final: 0.8275 (pt0) REVERT: C 696 ASP cc_start: 0.7346 (t0) cc_final: 0.6980 (t70) REVERT: C 711 ASP cc_start: 0.8163 (m-30) cc_final: 0.7797 (m-30) REVERT: C 922 ASN cc_start: 0.8270 (t0) cc_final: 0.7720 (p0) REVERT: C 992 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6532 (mp) REVERT: C 1080 ASN cc_start: 0.9039 (t0) cc_final: 0.8321 (t0) REVERT: C 1180 MET cc_start: 0.9440 (tpp) cc_final: 0.9207 (tpp) REVERT: D 102 MET cc_start: 0.7893 (mtm) cc_final: 0.7657 (mtp) REVERT: D 180 MET cc_start: 0.6982 (mmm) cc_final: 0.6732 (mmm) REVERT: D 298 MET cc_start: 0.8561 (tpp) cc_final: 0.7877 (tpp) REVERT: D 330 MET cc_start: 0.8238 (mtp) cc_final: 0.7875 (ttm) REVERT: D 472 LEU cc_start: 0.8744 (mm) cc_final: 0.8530 (mm) REVERT: D 718 SER cc_start: 0.9109 (t) cc_final: 0.8898 (m) REVERT: D 743 MET cc_start: 0.8492 (ptm) cc_final: 0.7453 (ppp) REVERT: D 772 TYR cc_start: 0.9061 (t80) cc_final: 0.8847 (t80) REVERT: D 821 MET cc_start: 0.8194 (tpp) cc_final: 0.7373 (tpp) REVERT: D 895 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7707 (p) REVERT: D 1059 LEU cc_start: 0.8320 (mp) cc_final: 0.7879 (tt) REVERT: D 1095 MET cc_start: 0.7102 (ttp) cc_final: 0.6635 (ppp) REVERT: D 1239 ASP cc_start: 0.8121 (t0) cc_final: 0.7523 (t0) REVERT: E 43 ASN cc_start: 0.8728 (t0) cc_final: 0.8238 (t0) REVERT: E 55 GLU cc_start: 0.8291 (tt0) cc_final: 0.8031 (tp30) outliers start: 53 outliers final: 41 residues processed: 288 average time/residue: 0.1690 time to fit residues: 80.8591 Evaluate side-chains 282 residues out of total 3002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 39 ILE 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 241 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 LEU 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 681 MET Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 764 CYS 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 1105 SER Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 639 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 207 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 HIS ** 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 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 = 0.3386 r_free = 0.3386 target = 0.079668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.057904 restraints weight = 95515.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059542 restraints weight = 53759.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060624 restraints weight = 36483.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061261 restraints weight = 28353.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061736 restraints weight = 24296.988| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 29022 Z= 0.182 Angle : 0.660 15.245 39505 Z= 0.336 Chirality : 0.042 0.193 4519 Planarity : 0.004 0.089 4965 Dihedral : 13.787 139.022 4602 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.06 % Allowed : 17.66 % Favored : 80.28 % 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: -0.67 (0.14), residues: 3503 helix: 1.29 (0.15), residues: 1283 sheet: -0.85 (0.25), residues: 443 loop : -1.71 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 312 TYR 0.022 0.001 TYR A 68 PHE 0.020 0.002 PHE C1025 TRP 0.016 0.001 TRP F 35 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00412 (29014) covalent geometry : angle 0.65924 (39493) hydrogen bonds : bond 0.04137 ( 1250) hydrogen bonds : angle 4.55899 ( 3457) metal coordination : bond 0.00932 ( 8) metal coordination : angle 2.36866 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.35 seconds wall clock time: 83 minutes 10.45 seconds (4990.45 seconds total)