Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:11:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkq_23903/12_2022/7mkq_23903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkq_23903/12_2022/7mkq_23903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkq_23903/12_2022/7mkq_23903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkq_23903/12_2022/7mkq_23903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkq_23903/12_2022/7mkq_23903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkq_23903/12_2022/7mkq_23903.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ASP 942": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32822 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10368 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 55, 'TRANS': 1282} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "L" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7696 Classifications: {'peptide': 967} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 931} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14615 SG CYS D 70 55.495 105.983 75.387 1.00133.55 S ATOM 14629 SG CYS D 72 55.698 108.938 73.205 1.00147.04 S ATOM 14737 SG CYS D 85 53.216 106.612 72.497 1.00124.31 S ATOM 14761 SG CYS D 88 56.783 105.846 71.863 1.00128.42 S ATOM 20449 SG CYS D 814 74.737 38.808 78.742 1.00 91.90 S ATOM 21014 SG CYS D 888 76.589 41.984 78.242 1.00 86.28 S ATOM 21065 SG CYS D 895 75.374 40.834 81.327 1.00 88.80 S ATOM 21086 SG CYS D 898 77.975 39.223 80.142 1.00 95.20 S Time building chain proxies: 18.45, per 1000 atoms: 0.56 Number of scatterers: 32822 At special positions: 0 Unit cell: (163.08, 167.4, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 133 16.00 Mg 1 11.99 O 6308 8.00 N 5816 7.00 C 20562 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: 13.41 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " Number of angles added : 12 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7760 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 51 sheets defined 42.9% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 4.247A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.944A 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 159 removed outlier: 3.548A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.075A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.775A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.527A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.988A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.816A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.556A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.595A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.889A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.651A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.815A 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 390 removed outlier: 3.710A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.593A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.538A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.677A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.952A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 668 removed outlier: 3.724A pdb=" N ILE C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 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 864 removed outlier: 3.722A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.669A pdb=" N GLN C 955 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.665A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.108A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.642A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.670A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.588A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1166 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: 3.575A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.745A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.651A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.510A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.978A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.788A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 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 485 through 489 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 573 through 581 Processing helix chain 'D' and resid 588 through 594 removed outlier: 4.327A pdb=" N GLN D 594 " --> pdb=" O ILE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.508A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.815A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.159A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.644A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.655A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.952A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.629A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.505A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.878A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.824A 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 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.596A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.631A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 18 Processing helix chain 'L' and resid 100 through 102 No H-bonds generated for 'chain 'L' and resid 100 through 102' Processing helix chain 'L' and resid 110 through 117 removed outlier: 4.672A pdb=" N LEU L 115 " --> pdb=" O GLN L 112 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE L 116 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 141 removed outlier: 3.748A pdb=" N ARG L 141 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 167 removed outlier: 3.805A pdb=" N ARG L 167 " --> pdb=" O HIS L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 Processing helix chain 'L' and resid 208 through 224 removed outlier: 4.523A pdb=" N HIS L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLN L 214 " --> pdb=" O THR L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 242 removed outlier: 3.523A pdb=" N ASP L 241 " --> pdb=" O GLU L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 248 removed outlier: 3.557A pdb=" N THR L 248 " --> pdb=" O PRO L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 260 Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 281 through 285 Processing helix chain 'L' and resid 293 through 303 removed outlier: 3.826A pdb=" N ALA L 298 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE L 299 " --> pdb=" O GLU L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 323 Processing helix chain 'L' and resid 324 through 332 removed outlier: 4.138A pdb=" N LEU L 330 " --> pdb=" O ALA L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 362 removed outlier: 3.528A pdb=" N PHE L 342 " --> pdb=" O ASP L 338 " (cutoff:3.500A) Proline residue: L 351 - end of helix Processing helix chain 'L' and resid 366 through 377 removed outlier: 4.134A pdb=" N MET L 372 " --> pdb=" O ASP L 368 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU L 375 " --> pdb=" O ASN L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 392 removed outlier: 3.527A pdb=" N ALA L 389 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP L 392 " --> pdb=" O ALA L 388 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 411 Processing helix chain 'L' and resid 441 through 455 Processing helix chain 'L' and resid 459 through 469 removed outlier: 4.286A pdb=" N TYR L 469 " --> pdb=" O ARG L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 470 through 472 No H-bonds generated for 'chain 'L' and resid 470 through 472' Processing helix chain 'L' and resid 473 through 478 removed outlier: 3.655A pdb=" N PHE L 477 " --> pdb=" O ILE L 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 487 removed outlier: 3.684A pdb=" N PHE L 487 " --> pdb=" O TRP L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 501 removed outlier: 3.850A pdb=" N GLU L 492 " --> pdb=" O ASP L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 512 through 528 Processing helix chain 'L' and resid 539 through 552 Processing helix chain 'L' and resid 586 through 598 removed outlier: 3.517A pdb=" N LEU L 590 " --> pdb=" O ASN L 586 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU L 597 " --> pdb=" O ARG L 593 " (cutoff:3.500A) Processing helix chain 'L' and resid 616 through 628 Processing helix chain 'L' and resid 638 through 656 removed outlier: 5.490A pdb=" N ASN L 648 " --> pdb=" O ASP L 644 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP L 649 " --> pdb=" O SER L 645 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN L 652 " --> pdb=" O ASN L 648 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR L 653 " --> pdb=" O ASP L 649 " (cutoff:3.500A) Processing helix chain 'L' and resid 662 through 683 Processing helix chain 'L' and resid 686 through 694 Processing helix chain 'L' and resid 695 through 710 removed outlier: 3.745A pdb=" N ALA L 699 " --> pdb=" O GLY L 695 " (cutoff:3.500A) Processing helix chain 'L' and resid 712 through 727 removed outlier: 4.135A pdb=" N ILE L 716 " --> pdb=" O ASP L 712 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN L 721 " --> pdb=" O ALA L 717 " (cutoff:3.500A) Processing helix chain 'L' and resid 764 through 771 Processing helix chain 'L' and resid 781 through 794 Processing helix chain 'L' and resid 827 through 835 removed outlier: 6.215A pdb=" N LEU L 832 " --> pdb=" O GLN L 829 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASN L 833 " --> pdb=" O LEU L 830 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG L 834 " --> pdb=" O GLN L 831 " (cutoff:3.500A) Processing helix chain 'L' and resid 857 through 864 removed outlier: 3.857A pdb=" N GLN L 864 " --> pdb=" O THR L 860 " (cutoff:3.500A) Processing helix chain 'L' and resid 869 through 879 removed outlier: 3.731A pdb=" N LYS L 875 " --> pdb=" O HIS L 871 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN L 878 " --> pdb=" O SER L 874 " (cutoff:3.500A) Processing helix chain 'L' and resid 880 through 926 removed outlier: 3.769A pdb=" N HIS L 885 " --> pdb=" O GLN L 881 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA L 886 " --> pdb=" O GLN L 882 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN L 889 " --> pdb=" O HIS L 885 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU L 890 " --> pdb=" O ALA L 886 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY L 891 " --> pdb=" O ILE L 887 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA L 893 " --> pdb=" O GLN L 889 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN L 894 " --> pdb=" O LEU L 890 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU L 896 " --> pdb=" O GLU L 892 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS L 897 " --> pdb=" O ALA L 893 " (cutoff:3.500A) Processing helix chain 'L' and resid 932 through 951 removed outlier: 3.609A pdb=" N LEU L 936 " --> pdb=" O ARG L 932 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 8.672A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.892A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (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 removed outlier: 3.690A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 17 removed outlier: 6.784A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 6.067A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.573A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.144A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.129A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.129A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.503A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.514A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.173A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.593A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 749 through 752 removed outlier: 7.020A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.854A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.828A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.812A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.823A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 888 removed outlier: 4.163A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.734A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.386A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 144 through 147 removed outlier: 4.215A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.210A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.700A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 997 removed outlier: 4.325A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AE5, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 4.136A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1186 through 1190 removed outlier: 4.359A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY D1161 " --> pdb=" O VAL D1204 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AE9, first strand: chain 'L' and resid 40 through 44 removed outlier: 6.818A pdb=" N THR L 29 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL L 25 " --> pdb=" O THR L 29 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR L 31 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 60 through 62 removed outlier: 7.296A pdb=" N ILE L 84 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL L 74 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR L 82 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU L 76 " --> pdb=" O LEU L 80 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU L 81 " --> pdb=" O ARG L 98 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG L 98 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR L 83 " --> pdb=" O ALA L 96 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA L 96 " --> pdb=" O TYR L 83 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY L 85 " --> pdb=" O GLY L 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 228 through 229 removed outlier: 3.584A pdb=" N ILE L 253 " --> pdb=" O ALA L 228 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL L 203 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N CYS L 254 " --> pdb=" O VAL L 203 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE L 205 " --> pdb=" O CYS L 254 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU L 277 " --> pdb=" O LEU L 310 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU L 312 " --> pdb=" O LEU L 277 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL L 279 " --> pdb=" O LEU L 312 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N PHE L 418 " --> pdb=" O ARG L 172 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU L 174 " --> pdb=" O PHE L 418 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 431 through 438 removed outlier: 6.796A pdb=" N GLU L 432 " --> pdb=" O ILE L 608 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL L 610 " --> pdb=" O GLU L 432 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS L 434 " --> pdb=" O VAL L 610 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TYR L 612 " --> pdb=" O HIS L 434 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE L 436 " --> pdb=" O TYR L 612 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 531 through 532 removed outlier: 3.635A pdb=" N ALA L 532 " --> pdb=" O VAL L 559 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 729 through 732 removed outlier: 7.093A pdb=" N THR L 760 " --> pdb=" O GLN L 775 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 799 through 804 removed outlier: 3.523A pdb=" N THR L 800 " --> pdb=" O LEU L 960 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE L 819 " --> pdb=" O ASP L 958 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU L 960 " --> pdb=" O GLU L 817 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU L 817 " --> pdb=" O LEU L 960 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU L 962 " --> pdb=" O LEU L 815 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU L 815 " --> pdb=" O LEU L 962 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.85 Time building geometry restraints manager: 14.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7000 1.33 - 1.45: 6896 1.45 - 1.57: 19205 1.57 - 1.69: 1 1.69 - 1.81: 233 Bond restraints: 33335 Sorted by residual: bond pdb=" N GLU B 29 " pdb=" CA GLU B 29 " ideal model delta sigma weight residual 1.461 1.494 -0.032 9.20e-03 1.18e+04 1.25e+01 bond pdb=" N VAL C1159 " pdb=" CA VAL C1159 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N THR B 27 " pdb=" CA THR B 27 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.21e-02 6.83e+03 9.88e+00 bond pdb=" N VAL C 939 " pdb=" CA VAL C 939 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.48e+00 bond pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.06e+00 ... (remaining 33330 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.16: 276 103.16 - 110.90: 11354 110.90 - 118.63: 15395 118.63 - 126.37: 17671 126.37 - 134.10: 361 Bond angle restraints: 45057 Sorted by residual: angle pdb=" CA PRO D 758 " pdb=" N PRO D 758 " pdb=" CD PRO D 758 " ideal model delta sigma weight residual 112.00 101.22 10.78 1.40e+00 5.10e-01 5.93e+01 angle pdb=" CA GLN C 46 " pdb=" CB GLN C 46 " pdb=" CG GLN C 46 " ideal model delta sigma weight residual 114.10 125.29 -11.19 2.00e+00 2.50e-01 3.13e+01 angle pdb=" N GLU L 912 " pdb=" CA GLU L 912 " pdb=" CB GLU L 912 " ideal model delta sigma weight residual 109.98 118.07 -8.09 1.45e+00 4.76e-01 3.11e+01 angle pdb=" CB ARG D 77 " pdb=" CG ARG D 77 " pdb=" CD ARG D 77 " ideal model delta sigma weight residual 111.30 98.84 12.46 2.30e+00 1.89e-01 2.93e+01 angle pdb=" CA VAL C1159 " pdb=" C VAL C1159 " pdb=" O VAL C1159 " ideal model delta sigma weight residual 121.63 116.73 4.90 9.90e-01 1.02e+00 2.45e+01 ... (remaining 45052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18381 17.98 - 35.95: 1655 35.95 - 53.93: 329 53.93 - 71.91: 82 71.91 - 89.89: 46 Dihedral angle restraints: 20493 sinusoidal: 8455 harmonic: 12038 Sorted by residual: dihedral pdb=" CA LEU L 560 " pdb=" C LEU L 560 " pdb=" N LEU L 561 " pdb=" CA LEU L 561 " ideal model delta harmonic sigma weight residual 180.00 124.47 55.53 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA GLU L 564 " pdb=" C GLU L 564 " pdb=" N ILE L 565 " pdb=" CA ILE L 565 " ideal model delta harmonic sigma weight residual -180.00 -126.08 -53.92 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA LYS C 236 " pdb=" C LYS C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 138.92 41.08 0 5.00e+00 4.00e-02 6.75e+01 ... (remaining 20490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4318 0.069 - 0.138: 732 0.138 - 0.207: 52 0.207 - 0.275: 6 0.275 - 0.344: 1 Chirality restraints: 5109 Sorted by residual: chirality pdb=" CA GLU L 912 " pdb=" N GLU L 912 " pdb=" C GLU L 912 " pdb=" CB GLU L 912 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE C1076 " pdb=" CA ILE C1076 " pdb=" CG1 ILE C1076 " pdb=" CG2 ILE C1076 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ASP C1160 " pdb=" N ASP C1160 " pdb=" C ASP C1160 " pdb=" CB ASP C1160 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 5106 not shown) Planarity restraints: 5943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 757 " -0.141 5.00e-02 4.00e+02 2.06e-01 6.77e+01 pdb=" N PRO D 758 " 0.355 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.120 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.095 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 938 " 0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLY C 938 " -0.074 2.00e-02 2.50e+03 pdb=" O GLY C 938 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL C 939 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 908 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ASN L 908 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN L 908 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU L 909 " -0.025 2.00e-02 2.50e+03 ... (remaining 5940 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 373 2.59 - 3.17: 29183 3.17 - 3.74: 49979 3.74 - 4.32: 67311 4.32 - 4.90: 109909 Nonbonded interactions: 256755 Sorted by model distance: nonbonded pdb=" OG1 THR D 816 " pdb=" OE1 GLU D 818 " model vdw 2.010 2.440 nonbonded pdb=" OD2 ASP D 464 " pdb="MG MG D2001 " model vdw 2.029 2.170 nonbonded pdb=" O LEU D1344 " pdb=" N GLY D1346 " model vdw 2.082 2.520 nonbonded pdb=" O PHE D 773 " pdb=" OG1 THR D 776 " model vdw 2.106 2.440 nonbonded pdb=" OH TYR C 301 " pdb=" OE1 GLU C 334 " model vdw 2.106 2.440 ... (remaining 256750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 235) selection = (chain 'B' and resid 7 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 133 5.16 5 C 20562 2.51 5 N 5816 2.21 5 O 6308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 12.890 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.280 Process input model: 93.130 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.004 0.086 33335 Z= 0.256 Angle : 0.908 18.956 45057 Z= 0.493 Chirality : 0.050 0.344 5109 Planarity : 0.006 0.206 5943 Dihedral : 15.073 89.886 12733 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.99 % Favored : 92.58 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.15 % 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: -2.42 (0.11), residues: 4166 helix: -0.92 (0.11), residues: 1544 sheet: -0.79 (0.21), residues: 507 loop : -2.38 (0.11), residues: 2115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 746 time to evaluate : 4.021 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 outliers start: 41 outliers final: 9 residues processed: 782 average time/residue: 0.5126 time to fit residues: 623.8009 Evaluate side-chains 349 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 340 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3511 time to fit residues: 10.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 3.9990 chunk 315 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 326 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 377 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 160 HIS ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1023 HIS ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 667 GLN D1218 HIS D1227 HIS D1279 GLN ** D1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 GLN L 397 GLN L 401 GLN L 786 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 33335 Z= 0.311 Angle : 0.765 12.098 45057 Z= 0.392 Chirality : 0.045 0.333 5109 Planarity : 0.006 0.094 5943 Dihedral : 5.420 43.537 4581 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.17 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.10 % 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: -1.14 (0.12), residues: 4166 helix: 0.35 (0.13), residues: 1628 sheet: -0.39 (0.21), residues: 551 loop : -1.84 (0.13), residues: 1987 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 372 time to evaluate : 4.006 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 outliers start: 8 outliers final: 3 residues processed: 380 average time/residue: 0.4591 time to fit residues: 279.9748 Evaluate side-chains 244 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 3.992 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2916 time to fit residues: 7.0402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 314 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 378 optimal weight: 8.9990 chunk 408 optimal weight: 5.9990 chunk 337 optimal weight: 20.0000 chunk 375 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1023 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN C1313 HIS D 448 GLN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 GLN L 736 ASN L 786 ASN L 945 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.123 33335 Z= 0.333 Angle : 0.745 12.838 45057 Z= 0.384 Chirality : 0.045 0.274 5109 Planarity : 0.005 0.069 5943 Dihedral : 5.479 38.448 4581 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.17 % Favored : 93.71 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.93 (0.12), residues: 4166 helix: 0.44 (0.13), residues: 1627 sheet: -0.19 (0.22), residues: 536 loop : -1.65 (0.13), residues: 2003 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 333 time to evaluate : 3.962 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 outliers start: 3 outliers final: 1 residues processed: 336 average time/residue: 0.4564 time to fit residues: 250.1536 Evaluate side-chains 219 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 4.071 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3349 time to fit residues: 6.0895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 254 optimal weight: 0.0870 chunk 379 optimal weight: 10.0000 chunk 402 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 359 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN C 46 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1023 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN D1367 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 558 GLN L 602 GLN L 786 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 33335 Z= 0.233 Angle : 0.658 11.601 45057 Z= 0.337 Chirality : 0.044 0.363 5109 Planarity : 0.004 0.055 5943 Dihedral : 5.166 33.377 4581 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.66 (0.13), residues: 4166 helix: 0.74 (0.13), residues: 1629 sheet: -0.16 (0.21), residues: 546 loop : -1.54 (0.13), residues: 1991 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.960 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 outliers start: 1 outliers final: 1 residues processed: 331 average time/residue: 0.4512 time to fit residues: 244.4446 Evaluate side-chains 212 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 3.856 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3386 time to fit residues: 6.1606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.0770 chunk 228 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 343 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 360 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 2.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1023 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 521 GLN L 786 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 33335 Z= 0.201 Angle : 0.642 12.413 45057 Z= 0.328 Chirality : 0.043 0.291 5109 Planarity : 0.004 0.056 5943 Dihedral : 5.028 29.327 4581 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.98 % Favored : 93.90 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.52 (0.13), residues: 4166 helix: 0.83 (0.13), residues: 1624 sheet: -0.08 (0.22), residues: 533 loop : -1.42 (0.13), residues: 2009 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 3.967 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 outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.4434 time to fit residues: 227.5135 Evaluate side-chains 218 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 3.992 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 0.2980 chunk 362 optimal weight: 20.0000 chunk 79 optimal weight: 50.0000 chunk 236 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 402 optimal weight: 4.9990 chunk 334 optimal weight: 0.0050 chunk 186 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 overall best weight: 3.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN C 83 GLN C 235 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1023 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 341 GLN L 786 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 33335 Z= 0.239 Angle : 0.659 11.516 45057 Z= 0.337 Chirality : 0.043 0.273 5109 Planarity : 0.004 0.059 5943 Dihedral : 5.032 28.829 4581 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.50 (0.13), residues: 4166 helix: 0.81 (0.13), residues: 1623 sheet: -0.06 (0.22), residues: 552 loop : -1.39 (0.14), residues: 1991 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 4.112 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 outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.4463 time to fit residues: 224.1405 Evaluate side-chains 212 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 4.045 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 chunk 293 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 338 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 400 optimal weight: 30.0000 chunk 250 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 60 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN C1023 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 504 GLN D1279 GLN D1367 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 341 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.122 33335 Z= 0.297 Angle : 0.701 11.971 45057 Z= 0.361 Chirality : 0.044 0.277 5109 Planarity : 0.005 0.060 5943 Dihedral : 5.269 29.592 4581 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.11 % Favored : 92.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.66 (0.13), residues: 4166 helix: 0.57 (0.13), residues: 1626 sheet: 0.04 (0.23), residues: 531 loop : -1.43 (0.13), residues: 2009 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 4.225 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 outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.4460 time to fit residues: 212.6788 Evaluate side-chains 200 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 239 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 273 optimal weight: 40.0000 chunk 198 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 33335 Z= 0.194 Angle : 0.641 11.659 45057 Z= 0.329 Chirality : 0.044 0.250 5109 Planarity : 0.004 0.055 5943 Dihedral : 5.034 29.426 4581 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.51 (0.13), residues: 4166 helix: 0.76 (0.13), residues: 1629 sheet: 0.03 (0.22), residues: 543 loop : -1.39 (0.14), residues: 1994 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.962 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 outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.4506 time to fit residues: 223.8982 Evaluate side-chains 209 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 4.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 3.9990 chunk 384 optimal weight: 20.0000 chunk 350 optimal weight: 1.9990 chunk 373 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 337 optimal weight: 6.9990 chunk 353 optimal weight: 8.9990 chunk 372 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 33335 Z= 0.196 Angle : 0.656 12.639 45057 Z= 0.334 Chirality : 0.044 0.456 5109 Planarity : 0.004 0.057 5943 Dihedral : 4.972 29.980 4581 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.53 (0.13), residues: 4166 helix: 0.75 (0.13), residues: 1629 sheet: -0.10 (0.22), residues: 554 loop : -1.38 (0.14), residues: 1983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 4.003 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: 290 average time/residue: 0.4416 time to fit residues: 214.7362 Evaluate side-chains 211 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 3.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 20.0000 chunk 395 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 414 optimal weight: 10.0000 chunk 381 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 254 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C 808 ASN C 932 GLN C1023 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 341 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 33335 Z= 0.258 Angle : 0.695 13.086 45057 Z= 0.353 Chirality : 0.045 0.320 5109 Planarity : 0.005 0.057 5943 Dihedral : 5.142 29.765 4581 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.13 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.63 (0.13), residues: 4166 helix: 0.66 (0.13), residues: 1635 sheet: -0.20 (0.22), residues: 547 loop : -1.41 (0.14), residues: 1984 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 3.994 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 outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.4328 time to fit residues: 195.9489 Evaluate side-chains 201 residues out of total 3564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 4.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 304 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 330 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 339 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D1279 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 341 GLN ** L 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 609 HIS ** 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 = 0.3216 r_free = 0.3216 target = 0.056901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.041660 restraints weight = 228940.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.042813 restraints weight = 138321.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.043623 restraints weight = 96703.376| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 33335 Z= 0.353 Angle : 0.779 13.499 45057 Z= 0.400 Chirality : 0.046 0.277 5109 Planarity : 0.005 0.060 5943 Dihedral : 5.601 29.896 4581 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 25.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.59 % Favored : 92.34 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -1.01 (0.13), residues: 4166 helix: 0.31 (0.13), residues: 1632 sheet: -0.42 (0.22), residues: 541 loop : -1.57 (0.13), residues: 1993 =============================================================================== Job complete usr+sys time: 6017.34 seconds wall clock time: 110 minutes 3.90 seconds (6603.90 seconds total)