Starting phenix.real_space_refine on Tue Feb 20 16:48:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri7_4885/02_2024/6ri7_4885.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri7_4885/02_2024/6ri7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri7_4885/02_2024/6ri7_4885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri7_4885/02_2024/6ri7_4885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri7_4885/02_2024/6ri7_4885.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri7_4885/02_2024/6ri7_4885.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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 Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 13} 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: 15.44, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 12.82 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 12 7006 Ramachandran restraints generated. 3503 Oldfield, 0 Emsley, 3503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 48 sheets defined 39.8% alpha, 14.0% beta 23 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 10.23 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: 13.70 Time building geometry restraints manager: 13.67 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: 96.11 - 103.69: 533 103.69 - 111.27: 12882 111.27 - 118.85: 10961 118.85 - 126.43: 14706 126.43 - 134.01: 411 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 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.890 Check model and map are aligned: 0.420 Set scattering table: 0.290 Process input model: 91.450 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.940 ------------------------------------------------------------------------------- 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 : 0.009 0.090 29014 Z= 0.616 Angle : 0.977 13.212 39493 Z= 0.529 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 : 23.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.003 TRP C 183 HIS 0.010 0.002 HIS C 673 PHE 0.030 0.003 PHE F 112 TYR 0.044 0.003 TYR C1229 ARG 0.013 0.001 ARG D1304 *********************** 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 fitting. rotamer outliers: 3 poor density : 668 time to evaluate : 3.328 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: 0.8646 (m) cc_final: 0.8386 (t) REVERT: D 355 ILE cc_start: 0.9174 (pt) cc_final: 0.8838 (pt) REVERT: D 369 PRO cc_start: 0.8670 (Cg_exo) cc_final: 0.8385 (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: 0.8144 (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: 0.4876 time to fit residues: 486.0736 Evaluate side-chains 320 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 0.5980 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 320 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 137 ASN B 132 HIS B 186 ASN C 65 ASN C 69 GLN C 150 HIS C 387 ASN C 437 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 688 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1256 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 266 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D1010 GLN D1049 GLN D1108 GLN ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29014 Z= 0.223 Angle : 0.708 13.613 39493 Z= 0.369 Chirality : 0.046 0.215 4519 Planarity : 0.005 0.096 4965 Dihedral : 14.496 139.575 4602 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.30 % Allowed : 9.77 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.13), residues: 3503 helix: -0.55 (0.14), residues: 1275 sheet: -2.11 (0.24), residues: 391 loop : -2.80 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 183 HIS 0.007 0.001 HIS D 936 PHE 0.019 0.002 PHE C 514 TYR 0.029 0.002 TYR D 382 ARG 0.010 0.001 ARG C 936 *********************** 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 453 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 387 time to evaluate : 3.616 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: 0.9201 (tt0) cc_final: 0.8906 (pt0) REVERT: F 129 LEU cc_start: 0.8242 (tp) cc_final: 0.7883 (tp) REVERT: B 95 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8379 (mttt) REVERT: C 14 ASP cc_start: 0.7152 (t70) cc_final: 0.6853 (t0) REVERT: C 47 TYR cc_start: 0.8002 (p90) cc_final: 0.7014 (m-80) REVERT: C 221 LEU cc_start: 0.9143 (mt) cc_final: 0.8878 (tp) REVERT: C 233 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7086 (ptm160) REVERT: C 241 LEU cc_start: 0.9399 (tt) cc_final: 0.8808 (mm) REVERT: C 403 MET cc_start: 0.9193 (tmm) cc_final: 0.8810 (tmm) REVERT: C 488 MET cc_start: 0.8625 (mmt) cc_final: 0.8241 (mmm) REVERT: C 549 ASP cc_start: 0.8556 (t0) cc_final: 0.8338 (t0) REVERT: C 922 ASN cc_start: 0.7630 (t0) cc_final: 0.7022 (p0) REVERT: C 1170 MET cc_start: 0.8923 (tpp) cc_final: 0.8636 (tpp) REVERT: C 1180 MET cc_start: 0.9209 (tpp) cc_final: 0.8872 (tpp) REVERT: C 1279 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8066 (mp0) REVERT: D 458 ASN cc_start: 0.8469 (t0) cc_final: 0.8251 (t0) REVERT: D 643 ASP cc_start: 0.7908 (m-30) cc_final: 0.7577 (m-30) REVERT: D 895 CYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7625 (p) REVERT: D 913 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7535 (mt-10) REVERT: D 1059 LEU cc_start: 0.8517 (mp) cc_final: 0.7723 (tt) REVERT: D 1095 MET cc_start: 0.7486 (ttp) cc_final: 0.7031 (ppp) REVERT: D 1327 GLU cc_start: 0.8773 (pm20) cc_final: 0.8382 (pm20) REVERT: E 68 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7521 (mt-10) outliers start: 66 outliers final: 28 residues processed: 433 average time/residue: 0.4505 time to fit residues: 312.2634 Evaluate side-chains 312 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 283 time to evaluate : 3.378 ------------------------------------------------------------------------------- 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 F residue 100 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 196 VAL 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 498 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 770 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 C residue 1299 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 895 CYS 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 61 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 218 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 346 optimal weight: 50.0000 chunk 286 optimal weight: 0.4980 chunk 318 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN B 186 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 824 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1307 ASN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29014 Z= 0.187 Angle : 0.641 11.651 39493 Z= 0.333 Chirality : 0.044 0.187 4519 Planarity : 0.005 0.095 4965 Dihedral : 14.248 138.467 4602 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.02 % Allowed : 12.43 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3503 helix: 0.40 (0.14), residues: 1290 sheet: -1.73 (0.24), residues: 412 loop : -2.41 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 115 HIS 0.005 0.001 HIS C1070 PHE 0.018 0.001 PHE C 514 TYR 0.020 0.001 TYR D 46 ARG 0.005 0.000 ARG B 143 *********************** 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 378 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 320 time to evaluate : 3.570 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: F 16 GLN cc_start: 0.9111 (tt0) cc_final: 0.8840 (pt0) REVERT: F 72 LEU cc_start: 0.8913 (mm) cc_final: 0.8478 (mm) REVERT: B 18 GLN cc_start: 0.8410 (mp10) cc_final: 0.8123 (pp30) REVERT: B 205 MET cc_start: 0.7905 (tmm) cc_final: 0.7540 (tmm) REVERT: C 14 ASP cc_start: 0.7065 (t70) cc_final: 0.6827 (t0) REVERT: C 47 TYR cc_start: 0.7918 (p90) cc_final: 0.7137 (m-80) REVERT: C 221 LEU cc_start: 0.9130 (mt) cc_final: 0.8862 (tp) REVERT: C 233 ARG cc_start: 0.7580 (mtp85) cc_final: 0.7075 (ptm160) REVERT: C 237 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7212 (pp) REVERT: C 241 LEU cc_start: 0.9395 (tt) cc_final: 0.8895 (mm) REVERT: C 403 MET cc_start: 0.9209 (tmm) cc_final: 0.8786 (tmm) REVERT: C 454 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8270 (mtt180) REVERT: C 488 MET cc_start: 0.8619 (mmt) cc_final: 0.8146 (mmm) REVERT: C 492 MET cc_start: 0.8268 (ttm) cc_final: 0.7801 (tpp) REVERT: C 517 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 922 ASN cc_start: 0.7523 (t0) cc_final: 0.6950 (p0) REVERT: C 992 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6636 (mp) REVERT: C 994 ARG cc_start: 0.8589 (mtp180) cc_final: 0.8304 (mtt-85) REVERT: C 1170 MET cc_start: 0.8877 (tpp) cc_final: 0.8594 (tpp) REVERT: C 1180 MET cc_start: 0.9216 (tpp) cc_final: 0.8954 (tpp) REVERT: D 24 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7923 (mt) REVERT: D 298 MET cc_start: 0.8178 (tpp) cc_final: 0.7844 (tpp) REVERT: D 458 ASN cc_start: 0.8491 (t0) cc_final: 0.8258 (t0) REVERT: D 643 ASP cc_start: 0.7844 (m-30) cc_final: 0.7540 (m-30) REVERT: D 822 MET cc_start: 0.8182 (mmm) cc_final: 0.7832 (mmm) REVERT: D 913 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7459 (mt-10) REVERT: D 1059 LEU cc_start: 0.8364 (mp) cc_final: 0.7844 (tt) REVERT: D 1095 MET cc_start: 0.7485 (ttp) cc_final: 0.7045 (ppp) outliers start: 58 outliers final: 27 residues processed: 361 average time/residue: 0.4137 time to fit residues: 241.7009 Evaluate side-chains 302 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 272 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 237 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 677 ASN Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 764 CYS 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 1254 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 252 LEU 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 44 ASP Chi-restraints excluded: chain E residue 61 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 35 optimal weight: 0.0030 chunk 153 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 341 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 305 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 HIS ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29014 Z= 0.223 Angle : 0.625 14.952 39493 Z= 0.324 Chirality : 0.043 0.236 4519 Planarity : 0.005 0.093 4965 Dihedral : 14.067 139.822 4602 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.72 % Allowed : 13.44 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3503 helix: 0.92 (0.15), residues: 1286 sheet: -1.48 (0.24), residues: 438 loop : -2.17 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 35 HIS 0.006 0.001 HIS C1070 PHE 0.020 0.002 PHE A 35 TYR 0.019 0.001 TYR C1229 ARG 0.007 0.000 ARG D 250 *********************** 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 366 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 288 time to evaluate : 3.544 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: 0.9150 (tt0) cc_final: 0.8950 (pt0) REVERT: F 72 LEU cc_start: 0.8974 (mm) cc_final: 0.8570 (mm) REVERT: A 177 TYR cc_start: 0.7953 (m-80) cc_final: 0.7313 (m-80) REVERT: B 18 GLN cc_start: 0.8451 (mp10) cc_final: 0.8171 (pp30) REVERT: B 186 ASN cc_start: 0.8432 (m-40) cc_final: 0.8124 (m-40) REVERT: B 205 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7741 (tmm) REVERT: C 14 ASP cc_start: 0.6955 (t70) cc_final: 0.6744 (t0) REVERT: C 47 TYR cc_start: 0.7965 (p90) cc_final: 0.7254 (m-80) REVERT: C 200 ARG cc_start: 0.5075 (OUTLIER) cc_final: 0.3770 (mtt180) REVERT: C 221 LEU cc_start: 0.9204 (mt) cc_final: 0.8902 (tp) REVERT: C 233 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7263 (ptm160) REVERT: C 237 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7141 (pp) REVERT: C 241 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8949 (mm) REVERT: C 285 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7119 (mp) REVERT: C 454 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8281 (mtt180) REVERT: C 488 MET cc_start: 0.8697 (mmt) cc_final: 0.8224 (mmm) REVERT: C 492 MET cc_start: 0.8178 (ttm) cc_final: 0.7968 (ttm) REVERT: C 517 GLN cc_start: 0.7454 (tm-30) cc_final: 0.6994 (tm-30) REVERT: C 696 ASP cc_start: 0.7464 (t0) cc_final: 0.6943 (t70) REVERT: C 844 LYS cc_start: 0.5120 (mttt) cc_final: 0.4846 (mttt) REVERT: C 865 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8677 (tp) REVERT: C 922 ASN cc_start: 0.7698 (t0) cc_final: 0.7112 (p0) REVERT: C 992 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6607 (mp) REVERT: C 994 ARG cc_start: 0.8599 (mtp180) cc_final: 0.8312 (mtt-85) REVERT: C 1170 MET cc_start: 0.8904 (tpp) cc_final: 0.8668 (tpp) REVERT: D 46 TYR cc_start: 0.7186 (t80) cc_final: 0.6869 (t80) REVERT: D 298 MET cc_start: 0.8236 (tpp) cc_final: 0.7892 (tpp) REVERT: D 349 TYR cc_start: 0.8573 (m-80) cc_final: 0.8345 (m-80) REVERT: D 610 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8350 (ptt-90) REVERT: D 895 CYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7957 (p) REVERT: D 913 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7607 (mt-10) REVERT: D 1059 LEU cc_start: 0.8360 (mp) cc_final: 0.7879 (tt) REVERT: D 1095 MET cc_start: 0.7495 (ttp) cc_final: 0.7046 (ppp) REVERT: D 1239 ASP cc_start: 0.7921 (t0) cc_final: 0.7352 (t0) REVERT: E 43 ASN cc_start: 0.8311 (t0) cc_final: 0.7823 (t0) outliers start: 78 outliers final: 32 residues processed: 344 average time/residue: 0.4014 time to fit residues: 223.5814 Evaluate side-chains 286 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 245 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 484 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 677 ASN Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 610 ARG Chi-restraints excluded: chain D residue 753 SER 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 E residue 8 ASP Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 0.2980 chunk 193 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 306 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN A 137 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN E 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29014 Z= 0.271 Angle : 0.629 13.874 39493 Z= 0.327 Chirality : 0.043 0.219 4519 Planarity : 0.004 0.094 4965 Dihedral : 14.025 141.566 4602 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.76 % Allowed : 14.45 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3503 helix: 1.04 (0.15), residues: 1287 sheet: -1.40 (0.24), residues: 451 loop : -2.04 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 35 HIS 0.005 0.001 HIS C 150 PHE 0.021 0.002 PHE C 156 TYR 0.015 0.001 TYR C1229 ARG 0.011 0.000 ARG D 481 *********************** 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 329 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 250 time to evaluate : 3.315 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 34 THR cc_start: 0.9068 (m) cc_final: 0.8599 (p) REVERT: F 72 LEU cc_start: 0.8961 (mm) cc_final: 0.8563 (mm) REVERT: F 112 PHE cc_start: 0.6099 (m-80) cc_final: 0.5801 (m-80) REVERT: A 177 TYR cc_start: 0.8016 (m-80) cc_final: 0.7172 (m-10) REVERT: B 18 GLN cc_start: 0.8453 (mp10) cc_final: 0.8176 (pp30) REVERT: B 186 ASN cc_start: 0.8574 (m-40) cc_final: 0.8276 (m-40) REVERT: C 14 ASP cc_start: 0.7101 (t70) cc_final: 0.6887 (t0) REVERT: C 47 TYR cc_start: 0.7942 (p90) cc_final: 0.7225 (m-80) REVERT: C 200 ARG cc_start: 0.5271 (OUTLIER) cc_final: 0.3904 (mtt180) REVERT: C 221 LEU cc_start: 0.9235 (mt) cc_final: 0.8969 (tp) REVERT: C 233 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7294 (ptm160) REVERT: C 237 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7077 (pp) REVERT: C 241 LEU cc_start: 0.9423 (tt) cc_final: 0.8934 (mm) REVERT: C 281 ASP cc_start: 0.7380 (t0) cc_final: 0.7087 (m-30) REVERT: C 324 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7829 (ptpp) REVERT: C 488 MET cc_start: 0.8734 (mmt) cc_final: 0.8261 (mmm) REVERT: C 517 GLN cc_start: 0.7532 (tm-30) cc_final: 0.7284 (tm-30) REVERT: C 696 ASP cc_start: 0.7430 (t0) cc_final: 0.6817 (t70) REVERT: C 865 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8582 (tp) REVERT: C 922 ASN cc_start: 0.7807 (t0) cc_final: 0.7311 (p0) REVERT: C 992 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6615 (mp) REVERT: C 994 ARG cc_start: 0.8558 (mtp180) cc_final: 0.8279 (mtt-85) REVERT: C 1088 ASP cc_start: 0.8329 (p0) cc_final: 0.8012 (p0) REVERT: C 1170 MET cc_start: 0.8910 (tpp) cc_final: 0.8695 (tpp) REVERT: C 1180 MET cc_start: 0.9159 (tpp) cc_final: 0.8916 (tpp) REVERT: D 298 MET cc_start: 0.8285 (tpp) cc_final: 0.7919 (tpp) REVERT: D 458 ASN cc_start: 0.8659 (t0) cc_final: 0.8429 (t0) REVERT: D 895 CYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8038 (p) REVERT: D 913 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7621 (mt-10) REVERT: D 1059 LEU cc_start: 0.8261 (mp) cc_final: 0.7835 (tt) REVERT: D 1095 MET cc_start: 0.7419 (ttp) cc_final: 0.6984 (ppp) REVERT: D 1146 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8557 (mm-30) REVERT: D 1239 ASP cc_start: 0.7948 (t0) cc_final: 0.7377 (t0) REVERT: E 43 ASN cc_start: 0.8460 (t0) cc_final: 0.7847 (t0) outliers start: 79 outliers final: 48 residues processed: 307 average time/residue: 0.3892 time to fit residues: 195.9386 Evaluate side-chains 292 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 3.535 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1098 LEU 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 71 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 93 THR 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 290 ILE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 356 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 1146 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 61 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 341 optimal weight: 20.0000 chunk 283 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29014 Z= 0.225 Angle : 0.609 15.354 39493 Z= 0.315 Chirality : 0.042 0.219 4519 Planarity : 0.004 0.092 4965 Dihedral : 13.975 142.164 4602 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.32 % Allowed : 14.38 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3503 helix: 1.14 (0.15), residues: 1286 sheet: -1.32 (0.24), residues: 466 loop : -1.93 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 35 HIS 0.013 0.001 HIS D 817 PHE 0.020 0.001 PHE C1025 TYR 0.013 0.001 TYR D 679 ARG 0.009 0.000 ARG D 860 *********************** 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 352 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 257 time to evaluate : 3.684 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 34 THR cc_start: 0.9062 (m) cc_final: 0.8587 (p) REVERT: F 72 LEU cc_start: 0.8683 (mm) cc_final: 0.8390 (mm) REVERT: F 112 PHE cc_start: 0.6199 (m-80) cc_final: 0.5969 (m-80) REVERT: B 18 GLN cc_start: 0.8458 (mp10) cc_final: 0.8211 (pp30) REVERT: B 186 ASN cc_start: 0.8563 (m-40) cc_final: 0.8345 (m-40) REVERT: C 14 ASP cc_start: 0.7180 (t70) cc_final: 0.6965 (t0) REVERT: C 47 TYR cc_start: 0.7991 (p90) cc_final: 0.7278 (m-80) REVERT: C 121 GLU cc_start: 0.7789 (pm20) cc_final: 0.7499 (pm20) REVERT: C 200 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.3846 (mtt180) REVERT: C 233 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7299 (ptm160) REVERT: C 237 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7024 (pp) REVERT: C 241 LEU cc_start: 0.9407 (tt) cc_final: 0.8975 (mm) REVERT: C 281 ASP cc_start: 0.7397 (t0) cc_final: 0.7143 (m-30) REVERT: C 285 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7451 (mp) REVERT: C 488 MET cc_start: 0.8735 (mmt) cc_final: 0.8257 (mmm) REVERT: C 492 MET cc_start: 0.8471 (ttm) cc_final: 0.8193 (tpp) REVERT: C 517 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7339 (tm-30) REVERT: C 696 ASP cc_start: 0.7372 (t0) cc_final: 0.6832 (t70) REVERT: C 800 MET cc_start: 0.8114 (mmm) cc_final: 0.7904 (mmp) REVERT: C 922 ASN cc_start: 0.7892 (t0) cc_final: 0.7405 (p0) REVERT: C 992 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6633 (mp) REVERT: C 994 ARG cc_start: 0.8545 (mtp180) cc_final: 0.8263 (mtp180) REVERT: C 1088 ASP cc_start: 0.8286 (p0) cc_final: 0.7961 (p0) REVERT: C 1105 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8915 (m) REVERT: C 1180 MET cc_start: 0.9159 (tpp) cc_final: 0.8907 (tpp) REVERT: D 298 MET cc_start: 0.8310 (tpp) cc_final: 0.7945 (tpp) REVERT: D 895 CYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8001 (p) REVERT: D 913 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7651 (mt-10) REVERT: D 1059 LEU cc_start: 0.8266 (mp) cc_final: 0.7814 (tt) REVERT: D 1095 MET cc_start: 0.7516 (ttp) cc_final: 0.7086 (ppp) REVERT: D 1146 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8556 (mm-30) REVERT: D 1239 ASP cc_start: 0.7922 (t0) cc_final: 0.7331 (t0) REVERT: E 43 ASN cc_start: 0.8611 (t0) cc_final: 0.7979 (t0) outliers start: 95 outliers final: 60 residues processed: 328 average time/residue: 0.3829 time to fit residues: 209.6304 Evaluate side-chains 305 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 238 time to evaluate : 3.320 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 121 VAL 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 123 TYR Chi-restraints excluded: chain C residue 155 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 285 ILE 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 630 VAL Chi-restraints excluded: chain C residue 677 ASN 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 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1024 GLU 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 93 THR 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 356 THR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 801 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 1133 ASP Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 61 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 249 optimal weight: 0.5980 chunk 193 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 190 optimal weight: 0.7980 chunk 340 optimal weight: 40.0000 chunk 212 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 147 GLN C 41 GLN C 165 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29014 Z= 0.183 Angle : 0.605 15.661 39493 Z= 0.309 Chirality : 0.042 0.179 4519 Planarity : 0.004 0.090 4965 Dihedral : 13.881 140.487 4602 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.72 % Allowed : 15.32 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3503 helix: 1.26 (0.15), residues: 1277 sheet: -1.11 (0.24), residues: 456 loop : -1.82 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 35 HIS 0.012 0.001 HIS B 23 PHE 0.018 0.001 PHE C1025 TYR 0.012 0.001 TYR C 123 ARG 0.004 0.000 ARG E 28 *********************** 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 358 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 280 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 34 THR cc_start: 0.9030 (m) cc_final: 0.8540 (p) REVERT: F 112 PHE cc_start: 0.6009 (m-80) cc_final: 0.5790 (m-80) REVERT: F 124 MET cc_start: 0.8595 (mmm) cc_final: 0.8318 (tpp) REVERT: A 51 MET cc_start: 0.8354 (mmm) cc_final: 0.8101 (mmm) REVERT: B 18 GLN cc_start: 0.8454 (mp10) cc_final: 0.8206 (pp30) REVERT: C 47 TYR cc_start: 0.7914 (p90) cc_final: 0.7299 (m-80) REVERT: C 200 ARG cc_start: 0.5459 (OUTLIER) cc_final: 0.3752 (mtt180) REVERT: C 233 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7403 (ptm160) REVERT: C 241 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8982 (mm) REVERT: C 281 ASP cc_start: 0.7382 (t0) cc_final: 0.7097 (m-30) REVERT: C 488 MET cc_start: 0.8790 (mmt) cc_final: 0.8287 (mmm) REVERT: C 492 MET cc_start: 0.8429 (ttm) cc_final: 0.8212 (tpp) REVERT: C 517 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7008 (tm-30) REVERT: C 668 ILE cc_start: 0.9366 (mm) cc_final: 0.8971 (tp) REVERT: C 672 GLU cc_start: 0.8853 (pm20) cc_final: 0.8312 (pm20) REVERT: C 696 ASP cc_start: 0.7276 (t0) cc_final: 0.6776 (t70) REVERT: C 922 ASN cc_start: 0.7870 (t0) cc_final: 0.7402 (p0) REVERT: C 992 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6612 (mp) REVERT: C 994 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8271 (mtp180) REVERT: C 1088 ASP cc_start: 0.8231 (p0) cc_final: 0.7962 (p0) REVERT: C 1180 MET cc_start: 0.9161 (tpp) cc_final: 0.8925 (tpp) REVERT: D 298 MET cc_start: 0.8326 (tpp) cc_final: 0.7995 (tpp) REVERT: D 330 MET cc_start: 0.8369 (ttm) cc_final: 0.8033 (mtp) REVERT: D 484 MET cc_start: 0.9070 (mmm) cc_final: 0.8667 (mmt) REVERT: D 697 MET cc_start: 0.8698 (ttp) cc_final: 0.8190 (tmm) REVERT: D 913 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7655 (mt-10) REVERT: D 1059 LEU cc_start: 0.8225 (mp) cc_final: 0.7851 (tt) REVERT: D 1095 MET cc_start: 0.7439 (ttp) cc_final: 0.7085 (ppp) REVERT: D 1146 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8502 (mm-30) REVERT: D 1239 ASP cc_start: 0.7902 (t0) cc_final: 0.7339 (t0) REVERT: E 43 ASN cc_start: 0.8697 (t0) cc_final: 0.8239 (t0) outliers start: 78 outliers final: 47 residues processed: 335 average time/residue: 0.3725 time to fit residues: 207.9912 Evaluate side-chains 296 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 245 time to evaluate : 3.339 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain A residue 95 LYS 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 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 572 ILE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 677 ASN 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 826 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1225 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 307 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 61 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 102 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 31 optimal weight: 0.0270 chunk 267 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN B 194 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1049 GLN ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29014 Z= 0.162 Angle : 0.603 12.787 39493 Z= 0.307 Chirality : 0.041 0.234 4519 Planarity : 0.004 0.088 4965 Dihedral : 13.777 138.866 4602 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.30 % Allowed : 16.37 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3503 helix: 1.28 (0.15), residues: 1282 sheet: -1.01 (0.24), residues: 459 loop : -1.77 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 35 HIS 0.006 0.001 HIS C 165 PHE 0.024 0.001 PHE B 8 TYR 0.012 0.001 TYR C 123 ARG 0.004 0.000 ARG D 905 *********************** 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 345 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 279 time to evaluate : 3.395 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 34 THR cc_start: 0.8980 (m) cc_final: 0.8500 (p) REVERT: F 72 LEU cc_start: 0.8566 (mm) cc_final: 0.8103 (mm) REVERT: F 112 PHE cc_start: 0.5887 (m-80) cc_final: 0.5633 (m-80) REVERT: F 128 LEU cc_start: 0.9225 (tp) cc_final: 0.8978 (tt) REVERT: B 18 GLN cc_start: 0.8388 (mp10) cc_final: 0.7936 (pp30) REVERT: C 47 TYR cc_start: 0.7914 (p90) cc_final: 0.7348 (m-80) REVERT: C 163 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8319 (ptpp) REVERT: C 200 ARG cc_start: 0.5398 (OUTLIER) cc_final: 0.3673 (mtt180) REVERT: C 241 LEU cc_start: 0.9392 (tt) cc_final: 0.9005 (mm) REVERT: C 281 ASP cc_start: 0.7473 (t0) cc_final: 0.7192 (m-30) REVERT: C 429 MET cc_start: 0.9019 (mmt) cc_final: 0.8569 (mmt) REVERT: C 492 MET cc_start: 0.8426 (ttm) cc_final: 0.8226 (tpp) REVERT: C 668 ILE cc_start: 0.9342 (mm) cc_final: 0.8970 (tp) REVERT: C 696 ASP cc_start: 0.7170 (t0) cc_final: 0.6915 (t70) REVERT: C 800 MET cc_start: 0.8095 (mmm) cc_final: 0.7737 (mmp) REVERT: C 922 ASN cc_start: 0.7884 (t0) cc_final: 0.7436 (p0) REVERT: C 992 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6575 (mp) REVERT: C 994 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8282 (mmm160) REVERT: C 1088 ASP cc_start: 0.8149 (p0) cc_final: 0.7925 (p0) REVERT: C 1180 MET cc_start: 0.9176 (tpp) cc_final: 0.8905 (tpp) REVERT: D 298 MET cc_start: 0.8340 (tpp) cc_final: 0.7991 (tpp) REVERT: D 330 MET cc_start: 0.8320 (ttm) cc_final: 0.8008 (mtp) REVERT: D 895 CYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7832 (p) REVERT: D 913 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7652 (mt-10) REVERT: D 1049 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7974 (pp30) REVERT: D 1059 LEU cc_start: 0.8302 (mp) cc_final: 0.7920 (tt) REVERT: D 1095 MET cc_start: 0.7308 (ttp) cc_final: 0.7067 (ppp) REVERT: D 1146 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8478 (mm-30) REVERT: D 1239 ASP cc_start: 0.7868 (t0) cc_final: 0.7302 (t0) REVERT: E 43 ASN cc_start: 0.8699 (t0) cc_final: 0.8087 (t0) outliers start: 66 outliers final: 40 residues processed: 324 average time/residue: 0.3989 time to fit residues: 211.3910 Evaluate side-chains 291 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 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 630 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 639 VAL 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 1040 MET Chi-restraints excluded: chain D residue 1049 GLN Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 61 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 0.8980 chunk 325 optimal weight: 3.9990 chunk 297 optimal weight: 20.0000 chunk 317 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 286 optimal weight: 0.3980 chunk 299 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1307 ASN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 HIS ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29014 Z= 0.167 Angle : 0.601 15.026 39493 Z= 0.308 Chirality : 0.041 0.281 4519 Planarity : 0.004 0.087 4965 Dihedral : 13.713 138.431 4602 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.99 % Allowed : 16.72 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3503 helix: 1.28 (0.15), residues: 1292 sheet: -0.86 (0.25), residues: 448 loop : -1.72 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 35 HIS 0.018 0.001 HIS C 165 PHE 0.023 0.001 PHE C 514 TYR 0.018 0.001 TYR F 108 ARG 0.008 0.000 ARG D 933 *********************** 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 fitting. rotamer outliers: 57 poor density : 259 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 34 THR cc_start: 0.8973 (m) cc_final: 0.8490 (p) REVERT: F 72 LEU cc_start: 0.8528 (mm) cc_final: 0.8096 (mm) REVERT: F 112 PHE cc_start: 0.5847 (m-80) cc_final: 0.5587 (m-80) REVERT: F 128 LEU cc_start: 0.9230 (tp) cc_final: 0.8992 (tt) REVERT: B 18 GLN cc_start: 0.8385 (mp10) cc_final: 0.7939 (pp30) REVERT: C 47 TYR cc_start: 0.7929 (p90) cc_final: 0.7326 (m-80) REVERT: C 200 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.3681 (mtt180) REVERT: C 241 LEU cc_start: 0.9375 (tt) cc_final: 0.9016 (mm) REVERT: C 281 ASP cc_start: 0.7434 (t0) cc_final: 0.7170 (m-30) REVERT: C 429 MET cc_start: 0.9054 (mmt) cc_final: 0.8740 (mmt) REVERT: C 671 LEU cc_start: 0.9258 (tt) cc_final: 0.8968 (tp) REVERT: C 696 ASP cc_start: 0.7157 (t0) cc_final: 0.6842 (t70) REVERT: C 922 ASN cc_start: 0.7943 (t0) cc_final: 0.7505 (p0) REVERT: C 994 ARG cc_start: 0.8484 (mtp180) cc_final: 0.8238 (mmm160) REVERT: C 1088 ASP cc_start: 0.8169 (p0) cc_final: 0.7937 (p0) REVERT: C 1180 MET cc_start: 0.9177 (tpp) cc_final: 0.8900 (tpp) REVERT: C 1232 MET cc_start: 0.8228 (mtp) cc_final: 0.7928 (mtt) REVERT: D 298 MET cc_start: 0.8352 (tpp) cc_final: 0.8010 (tpp) REVERT: D 330 MET cc_start: 0.8295 (ttm) cc_final: 0.8007 (mtp) REVERT: D 697 MET cc_start: 0.8524 (ttp) cc_final: 0.7746 (tmm) REVERT: D 895 CYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7814 (p) REVERT: D 913 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7620 (mt-10) REVERT: D 1059 LEU cc_start: 0.8235 (mp) cc_final: 0.7826 (tt) REVERT: D 1095 MET cc_start: 0.7261 (ttp) cc_final: 0.7061 (ppp) REVERT: D 1146 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8492 (mm-30) REVERT: D 1239 ASP cc_start: 0.7888 (t0) cc_final: 0.7309 (t0) outliers start: 57 outliers final: 41 residues processed: 296 average time/residue: 0.3758 time to fit residues: 184.5966 Evaluate side-chains 286 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 3.114 ------------------------------------------------------------------------------- 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 95 LYS Chi-restraints excluded: chain A residue 137 ASN 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 123 TYR Chi-restraints excluded: chain C residue 200 ARG 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 630 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1254 VAL 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 428 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 639 VAL 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 1040 MET Chi-restraints excluded: chain D residue 1133 ASP Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 61 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 3.9990 chunk 335 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 351 optimal weight: 50.0000 chunk 323 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 HIS ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.224 29014 Z= 0.286 Angle : 0.736 59.199 39493 Z= 0.396 Chirality : 0.044 0.456 4519 Planarity : 0.004 0.103 4965 Dihedral : 13.721 138.410 4602 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.85 % Allowed : 17.14 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3503 helix: 1.26 (0.15), residues: 1292 sheet: -0.87 (0.24), residues: 459 loop : -1.71 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1276 HIS 0.017 0.001 HIS C 165 PHE 0.022 0.001 PHE C 514 TYR 0.024 0.001 TYR C1281 ARG 0.020 0.000 ARG C 478 ********************** 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 297 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 3.627 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 34 THR cc_start: 0.8971 (m) cc_final: 0.8493 (p) REVERT: F 72 LEU cc_start: 0.8517 (mm) cc_final: 0.8084 (mm) REVERT: F 112 PHE cc_start: 0.5849 (m-80) cc_final: 0.5591 (m-80) REVERT: A 137 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8143 (p0) REVERT: B 18 GLN cc_start: 0.8384 (mp10) cc_final: 0.7939 (pp30) REVERT: C 47 TYR cc_start: 0.7933 (p90) cc_final: 0.7327 (m-80) REVERT: C 200 ARG cc_start: 0.5416 (OUTLIER) cc_final: 0.3686 (mtt180) REVERT: C 241 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9012 (mm) REVERT: C 281 ASP cc_start: 0.7433 (t0) cc_final: 0.7171 (m-30) REVERT: C 429 MET cc_start: 0.9057 (mmt) cc_final: 0.8686 (mmt) REVERT: C 696 ASP cc_start: 0.7144 (t0) cc_final: 0.6848 (t70) REVERT: C 922 ASN cc_start: 0.7948 (t0) cc_final: 0.7506 (p0) REVERT: C 994 ARG cc_start: 0.8511 (mtp180) cc_final: 0.8227 (mmm160) REVERT: C 1088 ASP cc_start: 0.8190 (p0) cc_final: 0.7938 (p0) REVERT: C 1180 MET cc_start: 0.9209 (tpp) cc_final: 0.8920 (tpp) REVERT: C 1232 MET cc_start: 0.8312 (mtp) cc_final: 0.7919 (mtt) REVERT: D 298 MET cc_start: 0.8354 (tpp) cc_final: 0.8012 (tpp) REVERT: D 330 MET cc_start: 0.8288 (ttm) cc_final: 0.8042 (mtp) REVERT: D 484 MET cc_start: 0.9050 (mmm) cc_final: 0.8798 (mmm) REVERT: D 697 MET cc_start: 0.8528 (ttp) cc_final: 0.7720 (tmm) REVERT: D 895 CYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7825 (p) REVERT: D 913 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 1059 LEU cc_start: 0.8236 (mp) cc_final: 0.7828 (tt) REVERT: D 1146 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: D 1239 ASP cc_start: 0.7890 (t0) cc_final: 0.7314 (t0) outliers start: 53 outliers final: 43 residues processed: 277 average time/residue: 0.3778 time to fit residues: 174.6132 Evaluate side-chains 289 residues out of total 3002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 241 time to evaluate : 3.311 ------------------------------------------------------------------------------- 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 95 LYS Chi-restraints excluded: chain A residue 137 ASN 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 123 TYR 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 351 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1254 VAL 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 428 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 639 VAL 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 1040 MET Chi-restraints excluded: chain D residue 1133 ASP Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 61 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 3.9990 chunk 298 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 280 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 288 optimal weight: 7.9990 chunk 35 optimal weight: 0.0870 chunk 51 optimal weight: 0.0070 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 HIS ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.082806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.060634 restraints weight = 95683.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.062472 restraints weight = 50869.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063697 restraints weight = 33382.902| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.224 29014 Z= 0.285 Angle : 0.732 55.258 39493 Z= 0.397 Chirality : 0.044 0.456 4519 Planarity : 0.004 0.103 4965 Dihedral : 13.721 138.410 4602 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.71 % Allowed : 17.21 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3503 helix: 1.26 (0.15), residues: 1292 sheet: -0.87 (0.24), residues: 459 loop : -1.71 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1276 HIS 0.017 0.001 HIS C 165 PHE 0.022 0.001 PHE C 514 TYR 0.024 0.001 TYR C1281 ARG 0.020 0.000 ARG C 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5714.98 seconds wall clock time: 105 minutes 17.16 seconds (6317.16 seconds total)