Starting phenix.real_space_refine on Sat Dec 16 04:06:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bef_12156/12_2023/7bef_12156.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bef_12156/12_2023/7bef_12156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bef_12156/12_2023/7bef_12156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bef_12156/12_2023/7bef_12156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bef_12156/12_2023/7bef_12156.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bef_12156/12_2023/7bef_12156.pdb" } resolution = 4.5 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= 0.001 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 146 5.49 5 S 132 5.16 5 C 20770 2.51 5 N 6015 2.21 5 O 6804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 944": "NH1" <-> "NH2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "F ARG 468": "NH1" <-> "NH2" Residue "G ARG 30": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33867 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2376 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "C" Number of atoms: 10556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10556 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10568 Classifications: {'peptide': 1362} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1306} Chain: "E" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 708 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4014 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 1 Chain: "G" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 881 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1501 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "N" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1496 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Time building chain proxies: 16.63, per 1000 atoms: 0.49 Number of scatterers: 33867 At special positions: 0 Unit cell: (161.516, 200.54, 191.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 146 15.00 O 6804 8.00 N 6015 7.00 C 20770 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: 13.93 Conformation dependent library (CDL) restraints added in 5.7 seconds 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7292 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 45 sheets defined 44.5% alpha, 11.4% beta 44 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 11.03 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.991A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.970A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.595A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.709A pdb=" N CYS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 removed outlier: 3.669A pdb=" N GLU A 273 " --> pdb=" O LEU A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.580A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.004A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.653A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.654A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.738A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 4.015A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.916A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.515A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.009A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (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 389 removed outlier: 3.964A 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 423 through 438 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.665A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.617A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.661A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.934A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 569 " --> pdb=" O GLY C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.544A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 944 through 956 removed outlier: 4.070A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 983 Processing helix chain 'C' and resid 993 through 997 removed outlier: 3.679A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1039 removed outlier: 3.716A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1107 removed outlier: 3.566A pdb=" N ARG C1106 " --> pdb=" O VAL C1103 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET C1107 " --> pdb=" O PRO C1104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1103 through 1107' Processing helix chain 'C' and resid 1110 through 1133 Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.510A 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 removed outlier: 3.592A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 removed outlier: 3.527A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.714A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.604A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG D 101 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.886A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.503A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 170 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.602A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.543A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 337 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 403 removed outlier: 3.566A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.718A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.741A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.937A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 671 removed outlier: 4.230A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.469A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.114A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.758A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 915 through 938 removed outlier: 3.589A pdb=" N ALA D 919 " --> pdb=" O ILE D 915 " (cutoff:3.500A) Proline residue: D 926 - end of helix removed outlier: 4.175A pdb=" N PHE D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1136 Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.535A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.514A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.591A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.276A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1296 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.523A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.825A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 91 Processing helix chain 'F' and resid 80 through 91 Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.874A pdb=" N THR F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 136 removed outlier: 3.843A pdb=" N ASP F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.147A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 4.670A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.910A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 296 removed outlier: 4.114A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 310 removed outlier: 3.667A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.833A pdb=" N GLU F 328 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 352 removed outlier: 4.350A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 394 removed outlier: 4.938A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 417 Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.108A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.512A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 Processing helix chain 'F' and resid 490 through 501 removed outlier: 3.721A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 551 Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.734A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 605 Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.632A pdb=" N VAL G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 30 removed outlier: 3.943A pdb=" N ARG G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 35 through 46 removed outlier: 3.689A pdb=" N ARG G 41 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU G 42 " --> pdb=" O HIS G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 67 removed outlier: 3.519A pdb=" N ARG G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.551A pdb=" N ILE G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N CYS G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 73 through 78' Processing helix chain 'G' and resid 85 through 97 removed outlier: 3.566A pdb=" N PHE G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 107 removed outlier: 3.971A pdb=" N GLU G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 31 removed outlier: 3.611A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 7.075A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 59 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.225A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 177 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 20 removed outlier: 7.407A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 19 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 20 removed outlier: 7.407A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 19 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 99 removed outlier: 3.726A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 3.726A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.953A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.670A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.448A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.927A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 removed outlier: 4.116A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 529 through 531 removed outlier: 4.358A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.854A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 598 through 599 Processing sheet with id=AC5, first strand: chain 'C' and resid 722 through 727 removed outlier: 6.856A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.219A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.970A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 832 through 834 Processing sheet with id=AC9, first strand: chain 'C' and resid 837 through 840 removed outlier: 3.805A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.817A 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 889 removed outlier: 3.792A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (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 1268 through 1270 removed outlier: 3.659A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1336 removed outlier: 3.534A pdb=" N ALA D 23 " --> pdb=" O ASN C1336 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.832A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.255A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 158 through 160 removed outlier: 4.268A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.946A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 366 through 369 Processing sheet with id=AE2, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.543A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.725A pdb=" N ILE D 820 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 959 removed outlier: 3.656A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 983 " --> pdb=" O LYS D 959 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.942A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.839A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 3.581A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AE9, first strand: chain 'D' and resid 1278 through 1281 removed outlier: 4.495A pdb=" N GLU D1278 " --> pdb=" O ILE D1266 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D1266 " --> pdb=" O GLU D1278 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA D1264 " --> pdb=" O VAL D1280 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 18.48 Time building geometry restraints manager: 14.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10597 1.34 - 1.45: 4745 1.45 - 1.57: 18823 1.57 - 1.69: 291 1.69 - 1.81: 231 Bond restraints: 34687 Sorted by residual: bond pdb=" CA ASP A 197 " pdb=" C ASP A 197 " ideal model delta sigma weight residual 1.524 1.576 -0.052 1.29e-02 6.01e+03 1.65e+01 bond pdb=" CA ASP A 199 " pdb=" C ASP A 199 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.24e-02 6.50e+03 1.56e+01 bond pdb=" N LEU A 198 " pdb=" CA LEU A 198 " ideal model delta sigma weight residual 1.454 1.501 -0.047 1.34e-02 5.57e+03 1.25e+01 bond pdb=" C1' DA N -41 " pdb=" N9 DA N -41 " ideal model delta sigma weight residual 1.460 1.523 -0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" N ARG G 30 " pdb=" CA ARG G 30 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.75e+00 ... (remaining 34682 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.86: 1728 106.86 - 113.64: 19145 113.64 - 120.41: 13291 120.41 - 127.19: 12758 127.19 - 133.96: 547 Bond angle restraints: 47469 Sorted by residual: angle pdb=" N LEU A 198 " pdb=" CA LEU A 198 " pdb=" C LEU A 198 " ideal model delta sigma weight residual 110.53 124.06 -13.53 1.32e+00 5.74e-01 1.05e+02 angle pdb=" N ASP A 199 " pdb=" CA ASP A 199 " pdb=" C ASP A 199 " ideal model delta sigma weight residual 108.96 123.13 -14.17 1.49e+00 4.50e-01 9.05e+01 angle pdb=" N ILE G 28 " pdb=" CA ILE G 28 " pdb=" C ILE G 28 " ideal model delta sigma weight residual 110.72 120.28 -9.56 1.01e+00 9.80e-01 8.96e+01 angle pdb=" C LEU D 368 " pdb=" N PRO D 369 " pdb=" CA PRO D 369 " ideal model delta sigma weight residual 120.03 128.34 -8.31 9.90e-01 1.02e+00 7.05e+01 angle pdb=" C2' DG T 47 " pdb=" C1' DG T 47 " pdb=" N9 DG T 47 " ideal model delta sigma weight residual 113.50 103.54 9.96 1.50e+00 4.44e-01 4.41e+01 ... (remaining 47464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 20382 35.82 - 71.64: 606 71.64 - 107.46: 3 107.46 - 143.28: 0 143.28 - 179.09: 2 Dihedral angle restraints: 20993 sinusoidal: 9681 harmonic: 11312 Sorted by residual: dihedral pdb=" CA VAL C 146 " pdb=" C VAL C 146 " pdb=" N SER C 147 " pdb=" CA SER C 147 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL D 501 " pdb=" C VAL D 501 " pdb=" N PRO D 502 " pdb=" CA PRO D 502 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN D 504 " pdb=" C GLN D 504 " pdb=" N ASP D 505 " pdb=" CA ASP D 505 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 20990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5007 0.071 - 0.143: 377 0.143 - 0.214: 11 0.214 - 0.285: 1 0.285 - 0.357: 3 Chirality restraints: 5399 Sorted by residual: chirality pdb=" CA LEU A 198 " pdb=" N LEU A 198 " pdb=" C LEU A 198 " pdb=" CB LEU A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA ASP A 199 " pdb=" N ASP A 199 " pdb=" C ASP A 199 " pdb=" CB ASP A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C1' DG T 47 " pdb=" O4' DG T 47 " pdb=" C2' DG T 47 " pdb=" N9 DG T 47 " both_signs ideal model delta sigma weight residual False 2.42 2.71 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5396 not shown) Planarity restraints: 5694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 196 " 0.029 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C THR A 196 " -0.100 2.00e-02 2.50e+03 pdb=" O THR A 196 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP A 197 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 368 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C LEU D 368 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU D 368 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO D 369 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 27 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C ASP G 27 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP G 27 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE G 28 " -0.015 2.00e-02 2.50e+03 ... (remaining 5691 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 242 2.58 - 3.16: 26621 3.16 - 3.74: 51440 3.74 - 4.32: 67793 4.32 - 4.90: 111431 Nonbonded interactions: 257527 Sorted by model distance: nonbonded pdb=" C7 DT T 6 " pdb=" C5 DT T 7 " model vdw 2.003 3.680 nonbonded pdb=" O ARG B 45 " pdb=" OG SER B 49 " model vdw 2.228 2.440 nonbonded pdb=" NE1 TRP G 37 " pdb=" N7 DG N -48 " model vdw 2.249 2.600 nonbonded pdb=" C7 DT T 6 " pdb=" C6 DT T 7 " model vdw 2.256 3.760 nonbonded pdb=" OG1 THR C 657 " pdb=" O VAL C1186 " model vdw 2.264 2.440 ... (remaining 257522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.30 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.070 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 97.420 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.140 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.063 34687 Z= 0.154 Angle : 0.527 14.173 47469 Z= 0.342 Chirality : 0.039 0.357 5399 Planarity : 0.003 0.058 5694 Dihedral : 13.208 179.095 13701 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 1.70 % Allowed : 4.62 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -2.16 (0.12), residues: 3909 helix: -0.01 (0.12), residues: 1582 sheet: -1.55 (0.25), residues: 337 loop : -2.71 (0.11), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 321 HIS 0.002 0.000 HIS D 777 PHE 0.008 0.001 PHE F 522 TYR 0.008 0.001 TYR D 679 ARG 0.002 0.000 ARG D 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 402 time to evaluate : 4.379 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: 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 outliers start: 57 outliers final: 10 residues processed: 451 average time/residue: 0.5117 time to fit residues: 364.5657 Evaluate side-chains 226 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 3.568 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4308 time to fit residues: 12.2354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 147 GLN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 406 ASN C 568 ASN C 658 GLN C 760 ASN C 767 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN C1264 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN D 700 ASN D 951 GLN D 954 ASN F 129 GLN F 406 GLN F 409 ASN G 45 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 34687 Z= 0.398 Angle : 0.750 12.017 47469 Z= 0.388 Chirality : 0.043 0.246 5399 Planarity : 0.006 0.103 5694 Dihedral : 17.253 179.819 5939 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 0.18 % Allowed : 2.68 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.10 (0.13), residues: 3909 helix: 0.99 (0.13), residues: 1618 sheet: -1.21 (0.25), residues: 381 loop : -2.25 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 115 HIS 0.019 0.002 HIS C 150 PHE 0.020 0.002 PHE C 670 TYR 0.027 0.002 TYR C1305 ARG 0.026 0.001 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 229 time to evaluate : 3.741 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 outliers start: 6 outliers final: 4 residues processed: 232 average time/residue: 0.5060 time to fit residues: 187.7576 Evaluate side-chains 171 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 3.738 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3267 time to fit residues: 7.4486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 305 optimal weight: 40.0000 chunk 249 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 367 optimal weight: 0.3980 chunk 397 optimal weight: 20.0000 chunk 327 optimal weight: 20.0000 chunk 364 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 294 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN F 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34687 Z= 0.200 Angle : 0.527 8.850 47469 Z= 0.281 Chirality : 0.040 0.261 5399 Planarity : 0.003 0.054 5694 Dihedral : 17.291 176.631 5939 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 0.12 % Allowed : 2.27 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.62 (0.13), residues: 3909 helix: 1.42 (0.13), residues: 1644 sheet: -1.00 (0.26), residues: 360 loop : -2.03 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 315 HIS 0.015 0.001 HIS C 150 PHE 0.021 0.001 PHE D 57 TYR 0.021 0.001 TYR F 143 ARG 0.005 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.4964 time to fit residues: 174.3247 Evaluate side-chains 174 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 3.841 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3508 time to fit residues: 5.7481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 368 optimal weight: 20.0000 chunk 390 optimal weight: 11.9990 chunk 192 optimal weight: 9.9990 chunk 349 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 462 ASN C 554 HIS C 658 GLN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1289 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 455 HIS ** F 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 34687 Z= 0.487 Angle : 0.840 14.263 47469 Z= 0.437 Chirality : 0.045 0.285 5399 Planarity : 0.006 0.073 5694 Dihedral : 17.664 176.897 5939 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 26.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 0.12 % Allowed : 3.94 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.02 (0.13), residues: 3909 helix: 0.80 (0.13), residues: 1630 sheet: -1.18 (0.25), residues: 374 loop : -1.95 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 433 HIS 0.017 0.003 HIS C 150 PHE 0.022 0.003 PHE C 186 TYR 0.029 0.003 TYR C 872 ARG 0.014 0.001 ARG D 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 3.775 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 outliers start: 4 outliers final: 0 residues processed: 190 average time/residue: 0.4797 time to fit residues: 150.1588 Evaluate side-chains 152 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 30.0000 chunk 221 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 290 optimal weight: 50.0000 chunk 161 optimal weight: 5.9990 chunk 333 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 350 optimal weight: 50.0000 chunk 98 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS C 462 ASN C 554 HIS C 658 GLN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 GLN ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 489 ASN ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1289 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 34687 Z= 0.314 Angle : 0.631 12.027 47469 Z= 0.335 Chirality : 0.041 0.199 5399 Planarity : 0.004 0.051 5694 Dihedral : 17.831 177.432 5939 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.67 (0.13), residues: 3909 helix: 1.20 (0.13), residues: 1626 sheet: -1.11 (0.26), residues: 378 loop : -1.83 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 409 HIS 0.021 0.002 HIS C 150 PHE 0.031 0.002 PHE C 230 TYR 0.017 0.002 TYR D 631 ARG 0.007 0.001 ARG D 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 3.701 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 outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.5007 time to fit residues: 147.3654 Evaluate side-chains 154 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 4.017 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 9.9990 chunk 351 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 229 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 390 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 129 optimal weight: 0.0070 chunk 205 optimal weight: 20.0000 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 761 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34687 Z= 0.234 Angle : 0.576 10.677 47469 Z= 0.306 Chirality : 0.041 0.205 5399 Planarity : 0.004 0.050 5694 Dihedral : 17.728 177.800 5939 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.41 (0.14), residues: 3909 helix: 1.43 (0.13), residues: 1635 sheet: -0.95 (0.25), residues: 402 loop : -1.73 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 115 HIS 0.018 0.002 HIS C 150 PHE 0.028 0.001 PHE D 461 TYR 0.017 0.001 TYR A 68 ARG 0.007 0.000 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 3.712 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 outliers start: 2 outliers final: 0 residues processed: 186 average time/residue: 0.5009 time to fit residues: 153.6668 Evaluate side-chains 157 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 4.071 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 222 optimal weight: 1.9990 chunk 285 optimal weight: 30.0000 chunk 221 optimal weight: 2.9990 chunk 329 optimal weight: 7.9990 chunk 218 optimal weight: 0.9980 chunk 389 optimal weight: 0.0170 chunk 243 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 179 optimal weight: 0.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 658 GLN C1268 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34687 Z= 0.154 Angle : 0.543 11.855 47469 Z= 0.287 Chirality : 0.041 0.199 5399 Planarity : 0.003 0.049 5694 Dihedral : 17.590 176.990 5939 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.13 (0.14), residues: 3909 helix: 1.63 (0.13), residues: 1638 sheet: -0.72 (0.25), residues: 398 loop : -1.57 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 115 HIS 0.012 0.001 HIS C 150 PHE 0.017 0.001 PHE D 461 TYR 0.028 0.001 TYR C1229 ARG 0.007 0.000 ARG C 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.767 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 outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.5060 time to fit residues: 160.1896 Evaluate side-chains 152 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.210 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 232 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 0.0670 chunk 75 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 36 optimal weight: 0.2980 chunk 306 optimal weight: 0.7980 overall best weight: 2.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 832 HIS C1134 GLN ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34687 Z= 0.181 Angle : 0.548 10.636 47469 Z= 0.289 Chirality : 0.040 0.190 5399 Planarity : 0.003 0.050 5694 Dihedral : 17.509 176.550 5939 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.03 (0.14), residues: 3909 helix: 1.70 (0.13), residues: 1637 sheet: -0.66 (0.26), residues: 393 loop : -1.50 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 115 HIS 0.013 0.001 HIS C 150 PHE 0.012 0.001 PHE C 186 TYR 0.027 0.001 TYR C1229 ARG 0.006 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.555 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 outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.5019 time to fit residues: 146.9743 Evaluate side-chains 146 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 4.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 340 optimal weight: 3.9990 chunk 362 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 327 optimal weight: 30.0000 chunk 343 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN C 658 GLN C1134 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34687 Z= 0.233 Angle : 0.578 10.051 47469 Z= 0.305 Chirality : 0.040 0.199 5399 Planarity : 0.004 0.049 5694 Dihedral : 17.569 176.787 5939 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.04 (0.14), residues: 3909 helix: 1.67 (0.13), residues: 1643 sheet: -0.69 (0.26), residues: 393 loop : -1.49 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.014 0.001 HIS C 150 PHE 0.019 0.001 PHE C 464 TYR 0.025 0.001 TYR C1229 ARG 0.010 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.695 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 outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.4691 time to fit residues: 132.0164 Evaluate side-chains 142 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 0.0010 chunk 238 optimal weight: 10.0000 chunk 383 optimal weight: 30.0000 chunk 234 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 266 optimal weight: 40.0000 chunk 402 optimal weight: 10.0000 chunk 370 optimal weight: 20.0000 chunk 320 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 overall best weight: 2.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS C 658 GLN ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34687 Z= 0.183 Angle : 0.556 10.062 47469 Z= 0.293 Chirality : 0.040 0.197 5399 Planarity : 0.003 0.049 5694 Dihedral : 17.578 176.381 5939 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.55 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.02 (0.14), residues: 3909 helix: 1.72 (0.13), residues: 1645 sheet: -0.74 (0.25), residues: 407 loop : -1.44 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1276 HIS 0.013 0.001 HIS C 150 PHE 0.026 0.001 PHE C 464 TYR 0.027 0.001 TYR C1229 ARG 0.008 0.000 ARG D 738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 4.101 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 outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.4870 time to fit residues: 142.2785 Evaluate side-chains 146 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 4.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 341 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 295 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 103 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 406 ASN C 462 ASN C 658 GLN ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.048881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033790 restraints weight = 390266.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.034201 restraints weight = 282785.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.034456 restraints weight = 227489.028| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 34687 Z= 0.428 Angle : 0.772 13.462 47469 Z= 0.405 Chirality : 0.044 0.233 5399 Planarity : 0.005 0.057 5694 Dihedral : 17.944 178.137 5939 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 26.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.03 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.57 (0.13), residues: 3909 helix: 1.08 (0.13), residues: 1650 sheet: -0.97 (0.25), residues: 391 loop : -1.63 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C1276 HIS 0.018 0.002 HIS C 150 PHE 0.047 0.002 PHE C 464 TYR 0.035 0.002 TYR C1229 ARG 0.034 0.001 ARG C 996 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5634.36 seconds wall clock time: 105 minutes 20.71 seconds (6320.71 seconds total)