Starting phenix.real_space_refine on Sun Jun 22 13:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aby_15327/06_2025/8aby_15327.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aby_15327/06_2025/8aby_15327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aby_15327/06_2025/8aby_15327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aby_15327/06_2025/8aby_15327.map" model { file = "/net/cci-nas-00/data/ceres_data/8aby_15327/06_2025/8aby_15327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aby_15327/06_2025/8aby_15327.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 46 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 15974 2.51 5 N 4550 2.21 5 O 5040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.55s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25719 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1706 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "C" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "N" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "R" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 481 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} 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 14259 SG CYS D 72 109.773 102.792 86.932 1.00 74.52 S ATOM 14367 SG CYS D 85 110.968 102.437 88.537 1.00 78.84 S ATOM 14391 SG CYS D 88 107.679 101.230 89.334 1.00 69.26 S ATOM 20079 SG CYS D 814 84.994 37.015 89.023 1.00 31.53 S ATOM 20644 SG CYS D 888 84.182 40.637 89.043 1.00 17.04 S ATOM 20695 SG CYS D 895 85.304 38.534 85.665 1.00 20.01 S ATOM 20716 SG CYS D 898 81.907 38.327 87.362 1.00 22.29 S Time building chain proxies: 14.99, per 1000 atoms: 0.58 Number of scatterers: 25719 At special positions: 0 Unit cell: (128.7, 161.7, 163.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 46 15.00 Mg 1 11.99 O 5040 8.00 N 4550 7.00 C 15974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.71 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 47 sheets defined 39.4% alpha, 17.0% beta 22 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 9.73 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.687A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.957A 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: 3.635A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 159' Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.443A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 removed outlier: 3.667A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.787A 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 212 through 227 removed outlier: 3.745A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.885A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.714A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.683A 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: 4.091A 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 289 through 295 removed outlier: 4.106A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 295 " --> pdb=" O ILE C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 359 through 371 Processing helix chain 'C' and resid 377 through 390 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 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 481 removed outlier: 3.562A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (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: 3.865A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.557A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 819 through 825 removed outlier: 4.161A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 864 removed outlier: 4.312A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 985 through 992 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.610A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.597A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.667A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.584A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.515A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.570A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 4.137A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.951A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C1325 " --> pdb=" O GLU C1321 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.815A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.623A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.918A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.697A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 176 removed outlier: 4.002A pdb=" N PHE D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.511A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 3.901A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.510A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) 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 285 removed outlier: 3.530A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.552A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.563A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 removed outlier: 3.852A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.558A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.652A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.619A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.897A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.627A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.578A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.504A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.966A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.996A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 4.322A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.756A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.935A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 3.521A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.505A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.624A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.096A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 4.164A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.638A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.610A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1347 through 1353 removed outlier: 3.847A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.370A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.878A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.592A pdb=" N GLU E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 73 removed outlier: 3.536A pdb=" N ARG E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 3.858A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.667A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.768A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.546A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 8.051A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (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 removed outlier: 4.028A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.052A 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: 6.693A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.208A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 159 removed outlier: 5.218A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.946A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.608A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) 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 616 through 617 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.753A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.787A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 755 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 817 through 818 removed outlier: 3.633A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 817 through 818 removed outlier: 3.633A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.351A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.984A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.508A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.508A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.754A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.642A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 148 removed outlier: 5.405A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.599A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 removed outlier: 3.674A pdb=" N THR D 810 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.566A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.201A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 959 through 961 removed outlier: 4.003A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE7, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id=AE8, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 3.718A pdb=" N VAL D1081 " --> pdb=" O PHE D1034 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE D1115 " --> pdb=" O GLY D1033 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1046 through 1048 Processing sheet with id=AF1, first strand: chain 'D' and resid 1189 through 1190 removed outlier: 3.501A pdb=" N ILE D1190 " --> pdb=" O ARG D1173 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.908A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2784 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 12.60 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8496 1.34 - 1.46: 3457 1.46 - 1.58: 13967 1.58 - 1.69: 89 1.69 - 1.81: 184 Bond restraints: 26193 Sorted by residual: bond pdb=" CA ARG D 339 " pdb=" C ARG D 339 " ideal model delta sigma weight residual 1.522 1.494 0.028 1.38e-02 5.25e+03 4.26e+00 bond pdb=" C GLY D 358 " pdb=" N PRO D 359 " ideal model delta sigma weight residual 1.337 1.318 0.019 1.24e-02 6.50e+03 2.44e+00 bond pdb=" CB CYS D 895 " pdb=" SG CYS D 895 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB VAL C1225 " pdb=" CG2 VAL C1225 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" CB ASP D 413 " pdb=" CG ASP D 413 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 ... (remaining 26188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 35012 2.06 - 4.12: 508 4.12 - 6.18: 42 6.18 - 8.24: 3 8.24 - 10.30: 4 Bond angle restraints: 35569 Sorted by residual: angle pdb=" N VAL B 5 " pdb=" CA VAL B 5 " pdb=" C VAL B 5 " ideal model delta sigma weight residual 113.71 109.85 3.86 9.50e-01 1.11e+00 1.65e+01 angle pdb=" N ILE C 292 " pdb=" CA ILE C 292 " pdb=" C ILE C 292 " ideal model delta sigma weight residual 112.80 108.40 4.40 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N VAL D1267 " pdb=" CA VAL D1267 " pdb=" C VAL D1267 " ideal model delta sigma weight residual 111.48 108.12 3.36 9.40e-01 1.13e+00 1.28e+01 angle pdb=" N TYR C1018 " pdb=" CA TYR C1018 " pdb=" C TYR C1018 " ideal model delta sigma weight residual 111.07 107.29 3.78 1.07e+00 8.73e-01 1.25e+01 angle pdb=" N GLY C1282 " pdb=" CA GLY C1282 " pdb=" C GLY C1282 " ideal model delta sigma weight residual 115.73 110.48 5.25 1.59e+00 3.96e-01 1.09e+01 ... (remaining 35564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 15253 27.97 - 55.94: 737 55.94 - 83.92: 73 83.92 - 111.89: 5 111.89 - 139.86: 1 Dihedral angle restraints: 16069 sinusoidal: 6984 harmonic: 9085 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DG T 18 " pdb=" C3' DG T 18 " pdb=" O3' DG T 18 " pdb=" P DC T 19 " ideal model delta sinusoidal sigma weight residual 220.00 80.14 139.86 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA GLN C1017 " pdb=" C GLN C1017 " pdb=" N TYR C1018 " pdb=" CA TYR C1018 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 16066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2522 0.032 - 0.064: 998 0.064 - 0.096: 355 0.096 - 0.127: 183 0.127 - 0.159: 12 Chirality restraints: 4070 Sorted by residual: chirality pdb=" CB VAL C 353 " pdb=" CA VAL C 353 " pdb=" CG1 VAL C 353 " pdb=" CG2 VAL C 353 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA THR C1292 " pdb=" N THR C1292 " pdb=" C THR C1292 " pdb=" CB THR C1292 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 4067 not shown) Planarity restraints: 4498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO C 567 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 358 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO D 359 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 359 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 359 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " -0.019 2.00e-02 2.50e+03 1.27e-02 4.04e+00 pdb=" CG TRP C1276 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " 0.002 2.00e-02 2.50e+03 ... (remaining 4495 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 570 2.68 - 3.24: 25569 3.24 - 3.79: 39327 3.79 - 4.35: 50468 4.35 - 4.90: 82198 Nonbonded interactions: 198132 Sorted by model distance: nonbonded pdb=" OG SER C 4 " pdb=" OE1 GLU C 7 " model vdw 2.131 3.040 nonbonded pdb=" NH2 ARG C 528 " pdb=" O SER C 576 " model vdw 2.147 3.120 nonbonded pdb=" OG SER C 391 " pdb=" OD1 ASP C 393 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR C 91 " pdb=" O ILE C 138 " model vdw 2.160 3.040 nonbonded pdb=" O TYR C 262 " pdb=" NE2 GLN C 276 " model vdw 2.171 3.120 ... (remaining 198127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 158 or resid 170 through 232)) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 72.820 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 : 0.006 0.541 26200 Z= 0.223 Angle : 0.629 15.037 35575 Z= 0.342 Chirality : 0.042 0.159 4070 Planarity : 0.004 0.078 4498 Dihedral : 15.029 139.861 10225 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: -0.33 (0.15), residues: 3146 helix: 0.45 (0.16), residues: 1040 sheet: 0.19 (0.27), residues: 382 loop : -0.70 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C1276 HIS 0.006 0.001 HIS C 673 PHE 0.018 0.002 PHE D1145 TYR 0.014 0.001 TYR D 144 ARG 0.010 0.001 ARG D 417 Details of bonding type rmsd hydrogen bonds : bond 0.20842 ( 1038) hydrogen bonds : angle 6.88885 ( 2892) metal coordination : bond 0.20537 ( 7) metal coordination : angle 7.03284 ( 6) covalent geometry : bond 0.00442 (26193) covalent geometry : angle 0.62286 (35569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 2.975 Fit side-chains revert: symmetry clash REVERT: C 559 CYS cc_start: 0.8925 (t) cc_final: 0.8693 (t) REVERT: D 205 LEU cc_start: 0.8512 (mm) cc_final: 0.8177 (mm) REVERT: D 301 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7571 (mp0) REVERT: D 513 MET cc_start: 0.7848 (tpp) cc_final: 0.7552 (ttm) REVERT: D 724 MET cc_start: 0.8288 (mtp) cc_final: 0.7891 (mtm) REVERT: D 743 MET cc_start: 0.8026 (ptp) cc_final: 0.7788 (mtm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.3617 time to fit residues: 180.2127 Evaluate side-chains 231 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 288 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C1257 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 341 ASN D 365 GLN E 72 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094331 restraints weight = 46250.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091811 restraints weight = 41056.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.093085 restraints weight = 51370.929| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26200 Z= 0.133 Angle : 0.566 14.294 35575 Z= 0.292 Chirality : 0.042 0.172 4070 Planarity : 0.004 0.056 4498 Dihedral : 12.306 140.377 4032 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.63 % Allowed : 7.42 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: -0.04 (0.15), residues: 3146 helix: 0.90 (0.16), residues: 1086 sheet: 0.15 (0.25), residues: 426 loop : -0.68 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 997 HIS 0.004 0.001 HIS C 673 PHE 0.015 0.001 PHE D1145 TYR 0.020 0.001 TYR A 185 ARG 0.006 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 1038) hydrogen bonds : angle 4.80405 ( 2892) metal coordination : bond 0.01018 ( 7) metal coordination : angle 6.66353 ( 6) covalent geometry : bond 0.00304 (26193) covalent geometry : angle 0.55986 (35569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 265 time to evaluate : 2.927 Fit side-chains revert: symmetry clash REVERT: B 17 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7334 (tm-30) REVERT: C 207 THR cc_start: 0.8397 (m) cc_final: 0.8033 (p) REVERT: C 214 ASN cc_start: 0.8246 (m-40) cc_final: 0.8009 (p0) REVERT: C 403 MET cc_start: 0.8576 (tmm) cc_final: 0.8335 (tmm) REVERT: C 559 CYS cc_start: 0.9024 (t) cc_final: 0.8758 (t) REVERT: C 741 MET cc_start: 0.7678 (ptt) cc_final: 0.7290 (ptm) REVERT: D 205 LEU cc_start: 0.8675 (mm) cc_final: 0.8120 (mm) REVERT: D 724 MET cc_start: 0.8475 (mtp) cc_final: 0.8006 (mtm) outliers start: 17 outliers final: 12 residues processed: 274 average time/residue: 0.4311 time to fit residues: 194.2843 Evaluate side-chains 229 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 4.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 110 optimal weight: 3.9990 chunk 156 optimal weight: 0.4980 chunk 247 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 606 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088287 restraints weight = 46572.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.086891 restraints weight = 42376.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.087197 restraints weight = 45255.380| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 26200 Z= 0.251 Angle : 0.646 15.419 35575 Z= 0.329 Chirality : 0.045 0.264 4070 Planarity : 0.004 0.060 4498 Dihedral : 12.418 141.204 4032 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.48 % Allowed : 10.83 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: -0.14 (0.15), residues: 3146 helix: 0.91 (0.16), residues: 1085 sheet: -0.02 (0.24), residues: 434 loop : -0.77 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 997 HIS 0.007 0.001 HIS D 545 PHE 0.023 0.002 PHE D1145 TYR 0.016 0.002 TYR C1281 ARG 0.005 0.001 ARG D 799 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 1038) hydrogen bonds : angle 4.69339 ( 2892) metal coordination : bond 0.00831 ( 7) metal coordination : angle 7.14471 ( 6) covalent geometry : bond 0.00605 (26193) covalent geometry : angle 0.63916 (35569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 3.029 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9105 (tt) REVERT: C 207 THR cc_start: 0.8207 (m) cc_final: 0.7848 (p) REVERT: C 517 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: C 741 MET cc_start: 0.7792 (ptt) cc_final: 0.7490 (ptm) REVERT: D 46 TYR cc_start: 0.6630 (t80) cc_final: 0.6103 (t80) REVERT: D 205 LEU cc_start: 0.8854 (mm) cc_final: 0.8265 (mm) REVERT: D 298 MET cc_start: 0.7917 (ppp) cc_final: 0.7649 (tmm) REVERT: D 724 MET cc_start: 0.8636 (mtp) cc_final: 0.8176 (mtm) REVERT: D 1169 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7452 (p) REVERT: E 42 GLU cc_start: 0.8184 (mp0) cc_final: 0.7957 (mp0) REVERT: E 68 GLU cc_start: 0.8914 (pp20) cc_final: 0.8711 (pp20) outliers start: 40 outliers final: 32 residues processed: 263 average time/residue: 0.3343 time to fit residues: 145.3383 Evaluate side-chains 248 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 91 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 306 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C1116 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 365 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.130220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093422 restraints weight = 46266.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090249 restraints weight = 53238.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.091837 restraints weight = 48321.448| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26200 Z= 0.142 Angle : 0.552 14.443 35575 Z= 0.281 Chirality : 0.042 0.170 4070 Planarity : 0.004 0.052 4498 Dihedral : 12.337 140.519 4032 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.56 % Allowed : 13.01 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.06 (0.15), residues: 3146 helix: 1.12 (0.16), residues: 1082 sheet: 0.09 (0.25), residues: 430 loop : -0.69 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 997 HIS 0.004 0.001 HIS D 545 PHE 0.016 0.001 PHE D1145 TYR 0.019 0.001 TYR A 185 ARG 0.004 0.000 ARG D 417 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 1038) hydrogen bonds : angle 4.34132 ( 2892) metal coordination : bond 0.00777 ( 7) metal coordination : angle 6.83275 ( 6) covalent geometry : bond 0.00340 (26193) covalent geometry : angle 0.54478 (35569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 3.145 Fit side-chains revert: symmetry clash REVERT: C 207 THR cc_start: 0.8067 (m) cc_final: 0.7700 (p) REVERT: C 1240 ASP cc_start: 0.8169 (p0) cc_final: 0.7938 (p0) REVERT: D 46 TYR cc_start: 0.6438 (t80) cc_final: 0.6003 (t80) REVERT: D 205 LEU cc_start: 0.8868 (mm) cc_final: 0.8337 (mm) REVERT: D 298 MET cc_start: 0.7757 (ppp) cc_final: 0.7431 (ppp) REVERT: D 625 MET cc_start: 0.8810 (ttp) cc_final: 0.8289 (ttp) REVERT: D 724 MET cc_start: 0.8608 (mtp) cc_final: 0.8123 (mtm) REVERT: D 1169 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7275 (p) REVERT: D 1208 ASP cc_start: 0.8014 (t0) cc_final: 0.7543 (m-30) REVERT: E 68 GLU cc_start: 0.8924 (pp20) cc_final: 0.8686 (pp20) outliers start: 42 outliers final: 29 residues processed: 268 average time/residue: 0.4289 time to fit residues: 192.9206 Evaluate side-chains 246 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 127 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 308 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 265 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091330 restraints weight = 46102.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.087545 restraints weight = 45736.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.088918 restraints weight = 46866.804| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 26200 Z= 0.189 Angle : 0.581 14.547 35575 Z= 0.295 Chirality : 0.043 0.170 4070 Planarity : 0.004 0.057 4498 Dihedral : 12.359 141.129 4032 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.93 % Allowed : 14.05 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.05 (0.15), residues: 3146 helix: 1.13 (0.16), residues: 1083 sheet: 0.09 (0.25), residues: 440 loop : -0.72 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 997 HIS 0.004 0.001 HIS C 673 PHE 0.018 0.001 PHE D1145 TYR 0.015 0.001 TYR A 185 ARG 0.004 0.000 ARG C1301 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 1038) hydrogen bonds : angle 4.33166 ( 2892) metal coordination : bond 0.00775 ( 7) metal coordination : angle 6.93407 ( 6) covalent geometry : bond 0.00457 (26193) covalent geometry : angle 0.57402 (35569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 3.140 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9119 (tt) REVERT: C 207 THR cc_start: 0.8225 (m) cc_final: 0.7846 (p) REVERT: C 517 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8374 (pt0) REVERT: C 1240 ASP cc_start: 0.8221 (p0) cc_final: 0.7997 (p0) REVERT: D 205 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8357 (mm) REVERT: D 298 MET cc_start: 0.7905 (ppp) cc_final: 0.7584 (ppp) REVERT: D 724 MET cc_start: 0.8626 (mtp) cc_final: 0.8175 (mtm) REVERT: D 1025 MET cc_start: 0.8105 (tmm) cc_final: 0.7286 (mtt) REVERT: D 1169 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7416 (p) REVERT: D 1208 ASP cc_start: 0.8205 (t0) cc_final: 0.7587 (m-30) REVERT: E 68 GLU cc_start: 0.8948 (pp20) cc_final: 0.8618 (pp20) outliers start: 52 outliers final: 40 residues processed: 271 average time/residue: 0.3530 time to fit residues: 160.0088 Evaluate side-chains 260 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 252 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 227 optimal weight: 0.5980 chunk 209 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 278 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 317 optimal weight: 7.9990 chunk 288 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS C1209 GLN C1268 GLN D 777 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095177 restraints weight = 45611.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091975 restraints weight = 47429.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093445 restraints weight = 45954.257| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 26200 Z= 0.100 Angle : 0.521 15.870 35575 Z= 0.263 Chirality : 0.041 0.170 4070 Planarity : 0.004 0.056 4498 Dihedral : 12.180 140.766 4032 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.45 % Allowed : 15.09 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.29 (0.15), residues: 3146 helix: 1.36 (0.16), residues: 1082 sheet: 0.31 (0.25), residues: 417 loop : -0.61 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 997 HIS 0.005 0.001 HIS C 165 PHE 0.013 0.001 PHE C 934 TYR 0.021 0.001 TYR A 185 ARG 0.004 0.000 ARG C1177 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 1038) hydrogen bonds : angle 4.04959 ( 2892) metal coordination : bond 0.00983 ( 7) metal coordination : angle 7.71993 ( 6) covalent geometry : bond 0.00228 (26193) covalent geometry : angle 0.51162 (35569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 207 THR cc_start: 0.7984 (m) cc_final: 0.7624 (p) REVERT: C 741 MET cc_start: 0.8177 (ptm) cc_final: 0.7827 (ptt) REVERT: C 1240 ASP cc_start: 0.8203 (p0) cc_final: 0.7829 (p0) REVERT: D 205 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 298 MET cc_start: 0.7742 (ppp) cc_final: 0.7518 (tmm) REVERT: D 1025 MET cc_start: 0.8050 (tmm) cc_final: 0.7342 (mtt) REVERT: D 1208 ASP cc_start: 0.8021 (t0) cc_final: 0.7564 (m-30) REVERT: D 1305 ASP cc_start: 0.8275 (t70) cc_final: 0.8010 (t0) REVERT: E 68 GLU cc_start: 0.8893 (pp20) cc_final: 0.8572 (pp20) outliers start: 39 outliers final: 22 residues processed: 284 average time/residue: 0.3568 time to fit residues: 167.3056 Evaluate side-chains 249 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 253 optimal weight: 0.6980 chunk 278 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 0.0870 chunk 241 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 104 optimal weight: 0.0570 chunk 177 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C1313 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094991 restraints weight = 46253.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.092081 restraints weight = 47776.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.093398 restraints weight = 47940.321| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26200 Z= 0.112 Angle : 0.525 14.385 35575 Z= 0.266 Chirality : 0.041 0.178 4070 Planarity : 0.004 0.059 4498 Dihedral : 12.125 141.301 4032 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.56 % Allowed : 15.87 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.38 (0.15), residues: 3146 helix: 1.45 (0.16), residues: 1084 sheet: 0.42 (0.26), residues: 412 loop : -0.58 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 997 HIS 0.005 0.001 HIS C 165 PHE 0.037 0.001 PHE C1025 TYR 0.017 0.001 TYR A 185 ARG 0.004 0.000 ARG D 764 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 1038) hydrogen bonds : angle 3.98397 ( 2892) metal coordination : bond 0.00794 ( 7) metal coordination : angle 6.81645 ( 6) covalent geometry : bond 0.00265 (26193) covalent geometry : angle 0.51797 (35569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 3.226 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9105 (tt) REVERT: C 207 THR cc_start: 0.8083 (m) cc_final: 0.7722 (p) REVERT: C 517 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8145 (pt0) REVERT: C 636 CYS cc_start: 0.7756 (m) cc_final: 0.7444 (m) REVERT: C 741 MET cc_start: 0.8123 (ptm) cc_final: 0.7848 (ptt) REVERT: D 205 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8419 (mm) REVERT: D 298 MET cc_start: 0.7764 (ppp) cc_final: 0.7532 (tmm) REVERT: D 513 MET cc_start: 0.8270 (mmm) cc_final: 0.8024 (mtt) REVERT: D 1025 MET cc_start: 0.7969 (tmm) cc_final: 0.7350 (mtt) REVERT: D 1208 ASP cc_start: 0.7986 (t0) cc_final: 0.7585 (m-30) REVERT: D 1305 ASP cc_start: 0.8276 (t70) cc_final: 0.8024 (t0) REVERT: E 68 GLU cc_start: 0.8927 (pp20) cc_final: 0.8584 (pp20) outliers start: 42 outliers final: 29 residues processed: 271 average time/residue: 0.3851 time to fit residues: 174.0297 Evaluate side-chains 252 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 108 optimal weight: 0.3980 chunk 184 optimal weight: 0.9980 chunk 198 optimal weight: 0.2980 chunk 182 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094312 restraints weight = 45916.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091212 restraints weight = 42980.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093382 restraints weight = 45084.153| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26200 Z= 0.111 Angle : 0.531 14.781 35575 Z= 0.268 Chirality : 0.041 0.171 4070 Planarity : 0.004 0.061 4498 Dihedral : 12.096 141.430 4032 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.74 % Allowed : 16.54 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.44 (0.15), residues: 3146 helix: 1.49 (0.16), residues: 1084 sheet: 0.47 (0.26), residues: 402 loop : -0.54 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 997 HIS 0.005 0.001 HIS C 165 PHE 0.021 0.001 PHE C1025 TYR 0.018 0.001 TYR A 185 ARG 0.005 0.000 ARG D 764 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 1038) hydrogen bonds : angle 3.94546 ( 2892) metal coordination : bond 0.00787 ( 7) metal coordination : angle 6.87699 ( 6) covalent geometry : bond 0.00262 (26193) covalent geometry : angle 0.52395 (35569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 3.072 Fit side-chains revert: symmetry clash REVERT: B 127 GLN cc_start: 0.8704 (pm20) cc_final: 0.8455 (pm20) REVERT: C 207 THR cc_start: 0.8116 (m) cc_final: 0.7740 (p) REVERT: C 741 MET cc_start: 0.8151 (ptm) cc_final: 0.7862 (ptt) REVERT: D 205 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8449 (mm) REVERT: D 298 MET cc_start: 0.7745 (ppp) cc_final: 0.7342 (tmm) REVERT: D 513 MET cc_start: 0.8176 (mmm) cc_final: 0.7860 (mtt) REVERT: D 1025 MET cc_start: 0.7945 (tmm) cc_final: 0.7338 (mtt) REVERT: D 1208 ASP cc_start: 0.8091 (t0) cc_final: 0.7580 (m-30) REVERT: D 1305 ASP cc_start: 0.8298 (t70) cc_final: 0.8025 (t0) REVERT: E 68 GLU cc_start: 0.8975 (pp20) cc_final: 0.8633 (pp20) outliers start: 47 outliers final: 35 residues processed: 262 average time/residue: 0.3302 time to fit residues: 145.6149 Evaluate side-chains 257 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 77 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 317 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 305 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.093574 restraints weight = 46292.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.090618 restraints weight = 48261.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.091884 restraints weight = 49324.130| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26200 Z= 0.148 Angle : 0.564 14.938 35575 Z= 0.283 Chirality : 0.042 0.173 4070 Planarity : 0.004 0.062 4498 Dihedral : 12.144 141.587 4032 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.63 % Allowed : 16.72 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.39 (0.15), residues: 3146 helix: 1.46 (0.16), residues: 1084 sheet: 0.44 (0.26), residues: 397 loop : -0.57 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 997 HIS 0.006 0.001 HIS C 165 PHE 0.022 0.001 PHE C1025 TYR 0.017 0.001 TYR D 631 ARG 0.006 0.000 ARG D 764 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1038) hydrogen bonds : angle 4.02040 ( 2892) metal coordination : bond 0.00765 ( 7) metal coordination : angle 7.01364 ( 6) covalent geometry : bond 0.00358 (26193) covalent geometry : angle 0.55707 (35569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 3.218 Fit side-chains revert: symmetry clash REVERT: C 207 THR cc_start: 0.8247 (m) cc_final: 0.7889 (p) REVERT: C 741 MET cc_start: 0.8156 (ptm) cc_final: 0.7943 (ptt) REVERT: D 205 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8437 (mm) REVERT: D 298 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7511 (ppp) REVERT: D 513 MET cc_start: 0.8181 (mmm) cc_final: 0.7960 (mtt) REVERT: D 1025 MET cc_start: 0.7957 (tmm) cc_final: 0.7345 (mtt) REVERT: D 1305 ASP cc_start: 0.8276 (t70) cc_final: 0.8039 (t0) REVERT: E 68 GLU cc_start: 0.8937 (pp20) cc_final: 0.8612 (pp20) outliers start: 44 outliers final: 41 residues processed: 260 average time/residue: 0.3499 time to fit residues: 152.0676 Evaluate side-chains 264 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 953 LYS Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 176 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 285 optimal weight: 0.2980 chunk 198 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.131184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094595 restraints weight = 46029.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091410 restraints weight = 50550.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.092913 restraints weight = 47437.885| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26200 Z= 0.118 Angle : 0.554 15.042 35575 Z= 0.278 Chirality : 0.041 0.168 4070 Planarity : 0.004 0.062 4498 Dihedral : 12.113 141.696 4032 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.41 % Allowed : 17.24 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.42 (0.15), residues: 3146 helix: 1.47 (0.16), residues: 1082 sheet: 0.46 (0.27), residues: 391 loop : -0.55 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 997 HIS 0.006 0.001 HIS C 165 PHE 0.018 0.001 PHE C1025 TYR 0.018 0.001 TYR A 185 ARG 0.018 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 1038) hydrogen bonds : angle 3.95994 ( 2892) metal coordination : bond 0.00794 ( 7) metal coordination : angle 7.01601 ( 6) covalent geometry : bond 0.00281 (26193) covalent geometry : angle 0.54630 (35569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 GLN cc_start: 0.8641 (pm20) cc_final: 0.8377 (pm20) REVERT: C 207 THR cc_start: 0.8169 (m) cc_final: 0.7842 (p) REVERT: C 741 MET cc_start: 0.8099 (ptm) cc_final: 0.7847 (ptt) REVERT: D 205 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8425 (mm) REVERT: D 513 MET cc_start: 0.8147 (mmm) cc_final: 0.7933 (mtt) REVERT: D 1025 MET cc_start: 0.7846 (tmm) cc_final: 0.7303 (mtt) REVERT: D 1305 ASP cc_start: 0.8241 (t70) cc_final: 0.8005 (t0) REVERT: E 68 GLU cc_start: 0.8901 (pp20) cc_final: 0.8582 (pp20) outliers start: 38 outliers final: 36 residues processed: 253 average time/residue: 0.3507 time to fit residues: 147.1916 Evaluate side-chains 255 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 284 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.129045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.092559 restraints weight = 46202.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.089781 restraints weight = 47488.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.091873 restraints weight = 48418.541| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26200 Z= 0.175 Angle : 0.590 15.339 35575 Z= 0.297 Chirality : 0.042 0.171 4070 Planarity : 0.004 0.061 4498 Dihedral : 12.116 141.671 4032 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.71 % Allowed : 16.98 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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: 0.34 (0.15), residues: 3146 helix: 1.43 (0.16), residues: 1081 sheet: 0.36 (0.27), residues: 393 loop : -0.60 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 997 HIS 0.006 0.001 HIS C 165 PHE 0.018 0.001 PHE C1025 TYR 0.018 0.001 TYR A 185 ARG 0.005 0.000 ARG D 275 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 1038) hydrogen bonds : angle 4.06215 ( 2892) metal coordination : bond 0.00771 ( 7) metal coordination : angle 7.22397 ( 6) covalent geometry : bond 0.00421 (26193) covalent geometry : angle 0.58242 (35569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7519.26 seconds wall clock time: 133 minutes 34.40 seconds (8014.40 seconds total)