Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 12 11:06:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fix_29212/07_2023/8fix_29212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fix_29212/07_2023/8fix_29212.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/8fix_29212/07_2023/8fix_29212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fix_29212/07_2023/8fix_29212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fix_29212/07_2023/8fix_29212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fix_29212/07_2023/8fix_29212.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 sd= 0.018 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 49 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16099 2.51 5 N 4589 2.21 5 O 5097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 76": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 950": "OE1" <-> "OE2" Residue "C GLU 1274": "OE1" <-> "OE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "C GLU 1338": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D GLU 925": "OE1" <-> "OE2" Residue "D GLU 1276": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 25943 Number of models: 1 Model: "" Number of chains: 9 Chain: "N" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "T" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 478 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} 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: {'PTRANS': 9, '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: {'PTRANS': 55, 'TRANS': 1263} Chain breaks: 1 Chain: "D" Number of atoms: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10397 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "R" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 232 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna3p': 10} 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: "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 15192 SG CYS D 72 102.008 116.349 90.749 1.00152.51 S ATOM 15300 SG CYS D 85 105.244 114.694 91.817 1.00144.54 S ATOM 15324 SG CYS D 88 102.262 113.409 92.321 1.00142.40 S ATOM 21012 SG CYS D 814 98.399 46.905 89.581 1.00 89.14 S ATOM 21577 SG CYS D 888 96.216 50.059 89.744 1.00 79.14 S ATOM 21628 SG CYS D 895 97.576 48.839 86.450 1.00 64.64 S ATOM 21649 SG CYS D 898 94.844 46.847 88.193 1.00 65.60 S Time building chain proxies: 12.34, per 1000 atoms: 0.48 Number of scatterers: 25943 At special positions: 0 Unit cell: (136.018, 147.594, 167.852, 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 106 16.00 P 49 15.00 Mg 1 11.99 O 5097 8.00 N 4589 7.00 C 16099 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: 11.20 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 6 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 45 sheets defined 38.8% alpha, 12.2% beta 9 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 7.83 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 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: 3.826A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.590A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.540A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.610A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.583A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (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 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 318 through 328 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: 4.135A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.404A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.883A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.792A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' 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: 4.189A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.199A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.067A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.751A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 4.354A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) 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 1311 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.756A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) 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 194 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 263 through 283 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 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 406 through 418 removed outlier: 4.031A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.702A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.672A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.604A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.258A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.576A pdb=" N CYS D 898 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.595A pdb=" N GLY D1071 " --> pdb=" O THR D1068 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1068 through 1072' Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.639A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1296 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 3.817A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 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 32 removed outlier: 3.730A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.550A pdb=" N GLY E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 74 removed outlier: 3.615A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 7.621A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 200 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 188 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.849A pdb=" N ILE A 144 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.424A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 15 removed outlier: 3.619A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 188 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 206 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 54 through 56 removed outlier: 3.728A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.520A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.691A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.567A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.572A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 75 removed outlier: 3.726A pdb=" N ARG C 101 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.790A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453 removed outlier: 5.891A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.581A pdb=" N ASP C 189 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.568A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.082A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 4.167A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.713A pdb=" N MET C 653 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 717 through 718 removed outlier: 3.847A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 7.439A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 775 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 817 through 818 removed outlier: 8.677A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 832 Processing sheet with id=AC9, first strand: chain 'C' and resid 835 through 841 removed outlier: 7.075A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 932 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C1053 " --> pdb=" O ASP C 930 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.023A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 888 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 Processing sheet with id=AD5, first strand: chain 'C' and resid 1336 through 1339 removed outlier: 3.983A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 104 through 111 removed outlier: 9.840A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.106A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 368 through 369 removed outlier: 5.879A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.106A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 707 through 708 removed outlier: 3.716A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.882A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 822 " --> pdb=" O VAL D 880 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 849 through 850 removed outlier: 4.372A pdb=" N ASP D 855 " --> pdb=" O LYS D 850 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 994 removed outlier: 6.265A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D1009 " --> pdb=" O ILE D 958 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.572A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1026 through 1027 Processing sheet with id=AE7, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE8, first strand: chain 'D' and resid 1188 through 1191 removed outlier: 3.528A pdb=" N ILE D1190 " --> pdb=" O ARG D1173 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 7.012A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2826 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 10.46 Time building geometry restraints manager: 11.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8775 1.35 - 1.47: 5707 1.47 - 1.60: 11716 1.60 - 1.73: 47 1.73 - 1.86: 184 Bond restraints: 26429 Sorted by residual: bond pdb=" N PHE C 812 " pdb=" CA PHE C 812 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.61e+00 bond pdb=" N PHE D1325 " pdb=" CA PHE D1325 " ideal model delta sigma weight residual 1.454 1.484 -0.029 1.17e-02 7.31e+03 6.30e+00 bond pdb=" N GLN D1326 " pdb=" CA GLN D1326 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.94e+00 bond pdb=" N MET C 741 " pdb=" CA MET C 741 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.17e-02 7.31e+03 5.94e+00 bond pdb=" N CYS D 70 " pdb=" CA CYS D 70 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 5.82e+00 ... (remaining 26424 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.69: 569 104.69 - 112.06: 13110 112.06 - 119.44: 9397 119.44 - 126.81: 12467 126.81 - 134.19: 363 Bond angle restraints: 35906 Sorted by residual: angle pdb=" N ASN D 458 " pdb=" CA ASN D 458 " pdb=" C ASN D 458 " ideal model delta sigma weight residual 111.39 103.84 7.55 1.38e+00 5.25e-01 2.99e+01 angle pdb=" CB MET C 239 " pdb=" CG MET C 239 " pdb=" SD MET C 239 " ideal model delta sigma weight residual 112.70 126.10 -13.40 3.00e+00 1.11e-01 2.00e+01 angle pdb=" CA ARG E 67 " pdb=" CB ARG E 67 " pdb=" CG ARG E 67 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.85e+01 angle pdb=" C GLN D1326 " pdb=" N GLU D1327 " pdb=" CA GLU D1327 " ideal model delta sigma weight residual 120.94 127.53 -6.59 1.57e+00 4.06e-01 1.76e+01 angle pdb=" C PHE B 35 " pdb=" CA PHE B 35 " pdb=" CB PHE B 35 " ideal model delta sigma weight residual 110.84 104.42 6.42 1.66e+00 3.63e-01 1.50e+01 ... (remaining 35901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 15773 35.42 - 70.83: 300 70.83 - 106.25: 32 106.25 - 141.67: 1 141.67 - 177.09: 1 Dihedral angle restraints: 16107 sinusoidal: 6965 harmonic: 9142 Sorted by residual: dihedral pdb=" CA PRO C1185 " pdb=" C PRO C1185 " pdb=" N VAL C1186 " pdb=" CA VAL C1186 " ideal model delta harmonic sigma weight residual -180.00 -152.26 -27.74 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" O4' U R 11 " pdb=" C1' U R 11 " pdb=" N1 U R 11 " pdb=" C2 U R 11 " ideal model delta sinusoidal sigma weight residual -160.00 -89.13 -70.87 1 1.50e+01 4.44e-03 2.87e+01 dihedral pdb=" CA ALA C 746 " pdb=" C ALA C 746 " pdb=" N GLY C 747 " pdb=" CA GLY C 747 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 16104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3367 0.056 - 0.112: 621 0.112 - 0.167: 99 0.167 - 0.223: 14 0.223 - 0.279: 4 Chirality restraints: 4105 Sorted by residual: chirality pdb=" CA PHE B 35 " pdb=" N PHE B 35 " pdb=" C PHE B 35 " pdb=" CB PHE B 35 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA GLU C1274 " pdb=" N GLU C1274 " pdb=" C GLU C1274 " pdb=" CB GLU C1274 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG E 67 " pdb=" N ARG E 67 " pdb=" C ARG E 67 " pdb=" CB ARG E 67 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 4102 not shown) Planarity restraints: 4535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 775 " 0.058 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO C 776 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 776 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 776 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 127 " -0.055 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO C 128 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 94 " 0.049 5.00e-02 4.00e+02 7.56e-02 9.13e+00 pdb=" N PRO C 95 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.041 5.00e-02 4.00e+02 ... (remaining 4532 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 175 2.53 - 3.12: 18993 3.12 - 3.71: 40404 3.71 - 4.31: 52890 4.31 - 4.90: 87957 Nonbonded interactions: 200419 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb=" OD2 ASP D 464 " model vdw 1.933 3.040 nonbonded pdb=" CE2 PHE C 812 " pdb=" CB PRO D 451 " model vdw 2.042 3.740 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.103 2.170 nonbonded pdb=" O PHE B 35 " pdb=" OG1 THR B 38 " model vdw 2.111 2.440 nonbonded pdb=" OG SER C 759 " pdb=" OG1 THR C 763 " model vdw 2.127 2.440 ... (remaining 200414 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) } 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.280 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 75.380 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 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 : 0.003 0.064 26429 Z= 0.180 Angle : 0.695 13.404 35906 Z= 0.367 Chirality : 0.045 0.279 4105 Planarity : 0.005 0.089 4535 Dihedral : 14.205 177.085 10227 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.78 % Favored : 87.06 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.13), residues: 3169 helix: -0.22 (0.14), residues: 1173 sheet: -1.94 (0.27), residues: 326 loop : -3.22 (0.12), residues: 1670 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 374 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 375 average time/residue: 0.3848 time to fit residues: 226.9712 Evaluate side-chains 252 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 1.9990 chunk 241 optimal weight: 0.0370 chunk 134 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 163 optimal weight: 0.0030 chunk 129 optimal weight: 0.0060 chunk 250 optimal weight: 4.9990 chunk 96 optimal weight: 0.1980 chunk 152 optimal weight: 0.4980 chunk 186 optimal weight: 8.9990 chunk 289 optimal weight: 0.7980 overall best weight: 0.1484 ------------------------------------------------------------------------------- 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 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN B 37 HIS C 686 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN C1288 GLN D1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 26429 Z= 0.154 Angle : 0.580 12.098 35906 Z= 0.289 Chirality : 0.042 0.241 4105 Planarity : 0.004 0.054 4535 Dihedral : 10.462 172.520 3993 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3169 helix: 0.55 (0.15), residues: 1187 sheet: -1.49 (0.28), residues: 331 loop : -2.83 (0.13), residues: 1651 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 294 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 304 average time/residue: 0.3712 time to fit residues: 183.6646 Evaluate side-chains 264 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 251 time to evaluate : 2.973 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2505 time to fit residues: 10.3910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 241 optimal weight: 0.0970 chunk 197 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 313 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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** B 41 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1236 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 26429 Z= 0.224 Angle : 0.602 11.664 35906 Z= 0.303 Chirality : 0.042 0.206 4105 Planarity : 0.005 0.054 4535 Dihedral : 10.445 168.489 3993 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.25 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3169 helix: 0.87 (0.15), residues: 1182 sheet: -1.29 (0.28), residues: 338 loop : -2.51 (0.14), residues: 1649 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 262 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 26 residues processed: 289 average time/residue: 0.3485 time to fit residues: 166.0165 Evaluate side-chains 264 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 238 time to evaluate : 3.098 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2378 time to fit residues: 15.8415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 308 optimal weight: 0.0050 chunk 152 optimal weight: 1.9990 chunk 276 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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 75 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 406 ASN C 580 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN C1236 ASN D 276 ASN D 861 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 26429 Z= 0.342 Angle : 0.708 11.416 35906 Z= 0.363 Chirality : 0.045 0.203 4105 Planarity : 0.005 0.057 4535 Dihedral : 10.725 165.127 3993 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.12 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3169 helix: 0.61 (0.15), residues: 1168 sheet: -1.25 (0.28), residues: 325 loop : -2.42 (0.14), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 254 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 43 residues processed: 312 average time/residue: 0.3502 time to fit residues: 179.8689 Evaluate side-chains 272 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 3.206 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2409 time to fit residues: 23.7588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 213 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 276 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** C 276 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 26429 Z= 0.175 Angle : 0.592 13.393 35906 Z= 0.295 Chirality : 0.042 0.343 4105 Planarity : 0.004 0.051 4535 Dihedral : 10.501 163.813 3993 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3169 helix: 0.98 (0.15), residues: 1175 sheet: -1.06 (0.29), residues: 315 loop : -2.22 (0.14), residues: 1679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 258 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 275 average time/residue: 0.3594 time to fit residues: 160.8186 Evaluate side-chains 240 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 2.839 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2278 time to fit residues: 8.7600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 2.9990 chunk 277 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 308 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1236 ASN C1288 GLN D 875 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 26429 Z= 0.180 Angle : 0.580 12.160 35906 Z= 0.288 Chirality : 0.042 0.326 4105 Planarity : 0.004 0.053 4535 Dihedral : 10.417 162.347 3993 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3169 helix: 1.11 (0.15), residues: 1173 sheet: -0.88 (0.29), residues: 329 loop : -2.14 (0.14), residues: 1667 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 240 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 259 average time/residue: 0.3702 time to fit residues: 157.0254 Evaluate side-chains 237 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 3.074 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2418 time to fit residues: 9.9752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 225 optimal weight: 0.5980 chunk 174 optimal weight: 2.9990 chunk 259 optimal weight: 0.0770 chunk 172 optimal weight: 0.1980 chunk 307 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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** B 132 HIS C 580 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 26429 Z= 0.147 Angle : 0.569 13.073 35906 Z= 0.280 Chirality : 0.042 0.355 4105 Planarity : 0.004 0.049 4535 Dihedral : 10.330 161.363 3993 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3169 helix: 1.23 (0.15), residues: 1180 sheet: -0.76 (0.29), residues: 331 loop : -2.03 (0.14), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 263 average time/residue: 0.3616 time to fit residues: 156.3460 Evaluate side-chains 240 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 233 time to evaluate : 3.105 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2413 time to fit residues: 7.3139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 195 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 26429 Z= 0.175 Angle : 0.589 17.161 35906 Z= 0.288 Chirality : 0.042 0.372 4105 Planarity : 0.004 0.048 4535 Dihedral : 10.325 160.135 3993 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3169 helix: 1.25 (0.15), residues: 1180 sheet: -0.79 (0.29), residues: 338 loop : -1.98 (0.14), residues: 1651 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 243 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 257 average time/residue: 0.3932 time to fit residues: 164.2039 Evaluate side-chains 235 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 3.085 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2582 time to fit residues: 7.4877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 0.8980 chunk 294 optimal weight: 0.6980 chunk 268 optimal weight: 0.9990 chunk 286 optimal weight: 0.0870 chunk 172 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 270 optimal weight: 0.7980 chunk 285 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1236 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 26429 Z= 0.155 Angle : 0.583 12.912 35906 Z= 0.286 Chirality : 0.042 0.386 4105 Planarity : 0.004 0.052 4535 Dihedral : 10.289 159.400 3993 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.60 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3169 helix: 1.26 (0.16), residues: 1181 sheet: -0.76 (0.29), residues: 341 loop : -1.92 (0.15), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 249 average time/residue: 0.3721 time to fit residues: 153.0877 Evaluate side-chains 238 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 231 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2696 time to fit residues: 8.0527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 3.9990 chunk 302 optimal weight: 0.5980 chunk 184 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 317 optimal weight: 0.6980 chunk 292 optimal weight: 0.0670 chunk 253 optimal weight: 0.0570 chunk 26 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 26429 Z= 0.147 Angle : 0.584 13.285 35906 Z= 0.283 Chirality : 0.042 0.391 4105 Planarity : 0.004 0.047 4535 Dihedral : 10.224 158.323 3993 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3169 helix: 1.34 (0.16), residues: 1181 sheet: -0.72 (0.29), residues: 344 loop : -1.89 (0.15), residues: 1644 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 239 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 242 average time/residue: 0.3719 time to fit residues: 148.1868 Evaluate side-chains 229 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 2.960 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2345 time to fit residues: 5.3730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 0.0060 chunk 269 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 253 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS C 65 ASN C 387 ASN C 686 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.114083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.083892 restraints weight = 75290.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.086341 restraints weight = 42978.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.087547 restraints weight = 27842.208| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 26429 Z= 0.181 Angle : 0.596 12.712 35906 Z= 0.291 Chirality : 0.042 0.417 4105 Planarity : 0.004 0.045 4535 Dihedral : 10.253 157.581 3993 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3169 helix: 1.34 (0.16), residues: 1180 sheet: -0.75 (0.29), residues: 341 loop : -1.89 (0.15), residues: 1648 =============================================================================== Job complete usr+sys time: 4474.43 seconds wall clock time: 82 minutes 54.38 seconds (4974.38 seconds total)