Starting phenix.real_space_refine on Sun Sep 13 21:33:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aby_15327/09_2026/8aby_15327.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aby_15327/09_2026/8aby_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 { model { file = "/net/cci-nas-00/data/ceres_data/8aby_15327/09_2026/8aby_15327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aby_15327/09_2026/8aby_15327.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8aby_15327/09_2026/8aby_15327.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aby_15327/09_2026/8aby_15327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aby_15327/09_2026/8aby_15327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aby_15327/09_2026/8aby_15327.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: 5.63, per 1000 atoms: 0.22 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 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: 3.27 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: 6.26 Time building geometry restraints manager: 3.34 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=" C3' DT N 28 " pdb=" C2' DT N 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT N 31 " pdb=" C2' DT N 31 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC T 19 " pdb=" O3' DC T 19 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 8.92e+00 bond pdb=" C3' DG T 10 " pdb=" C2' DG T 10 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.96e+00 bond pdb=" C3' DC T 19 " pdb=" C2' DC T 19 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.81e+00 ... (remaining 26188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 34955 2.06 - 4.12: 564 4.12 - 6.18: 43 6.18 - 8.24: 3 8.24 - 10.30: 4 Bond angle restraints: 35569 Sorted by residual: angle pdb=" O4' DG T 18 " pdb=" C4' DG T 18 " pdb=" C3' DG T 18 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.41e+01 angle pdb=" O4' DA T 25 " pdb=" C4' DA T 25 " pdb=" C3' DA T 25 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT N 29 " pdb=" C4 DT N 29 " pdb=" O4 DT N 29 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT N 31 " pdb=" C4 DT N 31 " pdb=" O4 DT N 31 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 ... (remaining 35564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 15227 27.97 - 55.94: 730 55.94 - 83.92: 61 83.92 - 111.89: 4 111.89 - 139.86: 1 Dihedral angle restraints: 16023 sinusoidal: 6938 harmonic: 9085 Sorted by residual: dihedral pdb=" C4' G R 84 " pdb=" C3' G R 84 " pdb=" C2' G R 84 " pdb=" C1' G R 84 " ideal model delta sinusoidal sigma weight residual 36.34 -36.10 72.44 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" O4' G R 84 " pdb=" C4' G R 84 " pdb=" C3' G R 84 " pdb=" C2' G R 84 " ideal model delta sinusoidal sigma weight residual -35.15 24.15 -59.30 1 4.00e+00 6.25e-02 2.94e+02 dihedral pdb=" O4' G R 84 " pdb=" C2' G R 84 " pdb=" C1' G R 84 " pdb=" C3' G R 84 " ideal model delta sinusoidal sigma weight residual -94.41 -36.62 -57.79 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 16020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3336 0.057 - 0.114: 672 0.114 - 0.171: 50 0.171 - 0.228: 4 0.228 - 0.285: 8 Chirality restraints: 4070 Sorted by residual: chirality pdb=" C2' G R 84 " pdb=" C3' G R 84 " pdb=" O2' G R 84 " pdb=" C1' G R 84 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" P G R 85 " pdb=" OP1 G R 85 " pdb=" OP2 G R 85 " pdb=" O5' G R 85 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C3' G R 84 " pdb=" C4' G R 84 " pdb=" O3' G R 84 " pdb=" C2' G R 84 " both_signs ideal model delta sigma weight residual False -2.50 -2.75 0.25 2.00e-01 2.50e+01 1.59e+00 ... (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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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= 0.254 Angle : 0.646 15.037 35575 Z= 0.372 Chirality : 0.045 0.285 4070 Planarity : 0.004 0.078 4498 Dihedral : 14.866 139.861 10179 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG D 417 TYR 0.014 0.001 TYR D 144 PHE 0.018 0.002 PHE D1145 TRP 0.033 0.002 TRP C1276 HIS 0.006 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (26193) covalent geometry : angle 0.63968 / 0.37 (35569) hydrogen bonds : bond 0.20842 / 14.30 ( 1038) hydrogen bonds : angle 6.88885 / 4.81 ( 2892) metal coordination : bond 0.20537 / 10.80 ( 7) metal coordination : angle 7.03284 / 3.25 ( 6) *********************** 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 : 0.991 Fit side-chains revert: symmetry clash REVERT: C 559 CYS cc_start: 0.8925 (t) cc_final: 0.8692 (t) REVERT: D 205 LEU cc_start: 0.8512 (mm) cc_final: 0.8178 (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: 0.7553 (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: 0.1752 time to fit residues: 87.6221 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 : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.0270 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.0470 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN B 132 HIS ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3746 r_free = 0.3746 target = 0.132454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095148 restraints weight = 46229.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093506 restraints weight = 41224.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094192 restraints weight = 53671.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094763 restraints weight = 33933.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095933 restraints weight = 28939.777| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26200 Z= 0.138 Angle : 0.616 14.135 35575 Z= 0.318 Chirality : 0.045 0.757 4070 Planarity : 0.004 0.055 4498 Dihedral : 11.559 141.678 3986 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.59 % Allowed : 6.86 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3146 helix: 0.88 (0.16), residues: 1074 sheet: 0.21 (0.25), residues: 405 loop : -0.63 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 211 TYR 0.023 0.001 TYR A 185 PHE 0.014 0.001 PHE C 35 TRP 0.023 0.002 TRP C 997 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (26193) covalent geometry : angle 0.61029 / 0.32 (35569) hydrogen bonds : bond 0.05286 / 3.60 ( 1038) hydrogen bonds : angle 5.08243 / 3.53 ( 2892) metal coordination : bond 0.01256 / 0.60 ( 7) metal coordination : angle 6.67117 / 3.10 ( 6) *********************** 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: 16 poor density : 266 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 17 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 200 LYS cc_start: 0.8878 (tttt) cc_final: 0.8674 (ttpt) REVERT: C 207 THR cc_start: 0.8340 (m) cc_final: 0.7973 (p) REVERT: C 403 MET cc_start: 0.8514 (tmm) cc_final: 0.8309 (tmm) REVERT: C 542 ARG cc_start: 0.7756 (ttt180) cc_final: 0.7466 (ttt180) REVERT: C 559 CYS cc_start: 0.9063 (t) cc_final: 0.8814 (t) REVERT: C 741 MET cc_start: 0.7497 (ptt) cc_final: 0.7186 (ptm) REVERT: C 1188 ASP cc_start: 0.7591 (t0) cc_final: 0.7379 (t0) REVERT: D 205 LEU cc_start: 0.8676 (mm) cc_final: 0.8089 (mm) REVERT: D 330 MET cc_start: 0.7826 (ttm) cc_final: 0.7619 (ttm) REVERT: D 724 MET cc_start: 0.8511 (mtp) cc_final: 0.8027 (mtm) REVERT: E 68 GLU cc_start: 0.8895 (pp20) cc_final: 0.8645 (pp20) outliers start: 16 outliers final: 10 residues processed: 276 average time/residue: 0.1648 time to fit residues: 75.1813 Evaluate side-chains 233 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU 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 353 SER Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 884 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 227 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 281 optimal weight: 30.0000 chunk 250 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091695 restraints weight = 46761.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089141 restraints weight = 48049.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.090477 restraints weight = 53809.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090818 restraints weight = 34469.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091892 restraints weight = 30558.758| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 26200 Z= 0.259 Angle : 0.659 14.765 35575 Z= 0.338 Chirality : 0.046 0.344 4070 Planarity : 0.005 0.062 4498 Dihedral : 11.657 144.648 3986 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.26 % Allowed : 10.49 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3146 helix: 0.90 (0.16), residues: 1082 sheet: -0.11 (0.25), residues: 411 loop : -0.73 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 944 TYR 0.019 0.002 TYR D 631 PHE 0.019 0.002 PHE D 461 TRP 0.039 0.002 TRP C 997 HIS 0.007 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (26193) covalent geometry : angle 0.65245 / 0.34 (35569) hydrogen bonds : bond 0.05371 / 3.66 ( 1038) hydrogen bonds : angle 4.85139 / 3.34 ( 2892) metal coordination : bond 0.00889 / 0.42 ( 7) metal coordination : angle 7.14134 / 3.31 ( 6) *********************** 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 270 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7133 (tm-30) REVERT: C 207 THR cc_start: 0.8204 (m) cc_final: 0.7763 (p) REVERT: C 741 MET cc_start: 0.7627 (ptt) cc_final: 0.7327 (ptm) REVERT: D 46 TYR cc_start: 0.6201 (t80) cc_final: 0.5823 (t80) REVERT: D 205 LEU cc_start: 0.8831 (mm) cc_final: 0.8221 (mm) REVERT: D 466 MET cc_start: 0.8220 (mmt) cc_final: 0.7965 (mmt) REVERT: D 625 MET cc_start: 0.8870 (ttp) cc_final: 0.8365 (ttp) REVERT: D 724 MET cc_start: 0.8522 (mtp) cc_final: 0.8092 (mtm) REVERT: D 1169 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7384 (p) outliers start: 34 outliers final: 26 residues processed: 252 average time/residue: 0.1651 time to fit residues: 68.7326 Evaluate side-chains 237 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS 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 135 THR 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 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 1107 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 198 CYS 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 1169 THR Chi-restraints excluded: chain D residue 1267 VAL 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 278 optimal weight: 30.0000 chunk 119 optimal weight: 0.0010 chunk 211 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 117 optimal weight: 0.0770 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 365 GLN E 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094161 restraints weight = 46028.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091098 restraints weight = 48548.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.093279 restraints weight = 47421.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093031 restraints weight = 29681.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093821 restraints weight = 27463.254| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 26200 Z= 0.126 Angle : 0.559 14.278 35575 Z= 0.287 Chirality : 0.043 0.257 4070 Planarity : 0.004 0.057 4498 Dihedral : 11.588 144.229 3986 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.41 % Allowed : 11.79 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3146 helix: 1.08 (0.16), residues: 1077 sheet: 0.13 (0.25), residues: 431 loop : -0.70 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 220 TYR 0.020 0.001 TYR A 185 PHE 0.015 0.001 PHE D1145 TRP 0.032 0.002 TRP C 997 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (26193) covalent geometry : angle 0.55215 / 0.29 (35569) hydrogen bonds : bond 0.04275 / 2.89 ( 1038) hydrogen bonds : angle 4.50924 / 3.12 ( 2892) metal coordination : bond 0.00799 / 0.33 ( 7) metal coordination : angle 6.77550 / 3.14 ( 6) *********************** 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 274 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9092 (tt) REVERT: B 10 LYS cc_start: 0.8353 (mppt) cc_final: 0.8101 (mmtp) REVERT: B 17 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7199 (tm-30) REVERT: C 207 THR cc_start: 0.8027 (m) cc_final: 0.7667 (p) REVERT: C 517 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: C 741 MET cc_start: 0.7509 (ptt) cc_final: 0.7189 (ptm) REVERT: D 46 TYR cc_start: 0.6427 (t80) cc_final: 0.5986 (t80) REVERT: D 205 LEU cc_start: 0.8818 (mm) cc_final: 0.8233 (mm) REVERT: D 1169 THR cc_start: 0.7539 (OUTLIER) cc_final: 0.7327 (p) outliers start: 38 outliers final: 26 residues processed: 258 average time/residue: 0.1628 time to fit residues: 69.3869 Evaluate side-chains 245 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL 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 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1107 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 353 SER 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 1169 THR 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 233 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091603 restraints weight = 45977.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089822 restraints weight = 40819.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090465 restraints weight = 52461.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091001 restraints weight = 33898.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.091637 restraints weight = 28763.445| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1727 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= 0.197 Angle : 0.594 14.289 35575 Z= 0.304 Chirality : 0.044 0.170 4070 Planarity : 0.004 0.061 4498 Dihedral : 11.606 144.995 3986 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.82 % Allowed : 12.61 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3146 helix: 1.08 (0.16), residues: 1078 sheet: 0.05 (0.24), residues: 443 loop : -0.72 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 515 TYR 0.016 0.001 TYR A 185 PHE 0.019 0.001 PHE D1145 TRP 0.014 0.001 TRP C 997 HIS 0.006 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (26193) covalent geometry : angle 0.58701 / 0.30 (35569) hydrogen bonds : bond 0.04534 / 3.08 ( 1038) hydrogen bonds : angle 4.47526 / 3.09 ( 2892) metal coordination : bond 0.00775 / 0.32 ( 7) metal coordination : angle 6.85246 / 3.17 ( 6) *********************** 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 277 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9051 (tt) REVERT: C 207 THR cc_start: 0.8198 (m) cc_final: 0.7838 (p) REVERT: C 517 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: D 46 TYR cc_start: 0.6425 (t80) cc_final: 0.6031 (t80) REVERT: D 205 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8295 (mm) REVERT: D 1169 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7354 (p) outliers start: 49 outliers final: 35 residues processed: 260 average time/residue: 0.1601 time to fit residues: 69.5174 Evaluate side-chains 249 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 95 LYS Chi-restraints excluded: chain A residue 228 LEU 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 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 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1107 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 205 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 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 210 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 225 optimal weight: 0.6980 chunk 216 optimal weight: 0.0270 chunk 252 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 177 optimal weight: 0.0980 chunk 230 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 686 GLN C1268 GLN D 365 GLN ** 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 = 0.3734 r_free = 0.3734 target = 0.131798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095580 restraints weight = 45709.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092568 restraints weight = 50850.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.094590 restraints weight = 51032.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094492 restraints weight = 31868.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095698 restraints weight = 29156.943| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 26200 Z= 0.106 Angle : 0.545 13.956 35575 Z= 0.278 Chirality : 0.042 0.165 4070 Planarity : 0.004 0.060 4498 Dihedral : 11.541 144.394 3986 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.41 % Allowed : 13.83 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3146 helix: 1.23 (0.16), residues: 1082 sheet: 0.28 (0.25), residues: 424 loop : -0.61 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 417 TYR 0.021 0.001 TYR A 185 PHE 0.010 0.001 PHE D1145 TRP 0.012 0.001 TRP C1276 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (26193) covalent geometry : angle 0.53855 / 0.28 (35569) hydrogen bonds : bond 0.03794 / 2.56 ( 1038) hydrogen bonds : angle 4.27666 / 2.97 ( 2892) metal coordination : bond 0.00853 / 0.38 ( 7) metal coordination : angle 6.60157 / 3.06 ( 6) *********************** 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 275 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9019 (mt) REVERT: C 207 THR cc_start: 0.8043 (m) cc_final: 0.7688 (p) REVERT: C 517 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: C 741 MET cc_start: 0.7692 (ptt) cc_final: 0.7285 (ptm) REVERT: C 1319 MET cc_start: 0.8093 (tmm) cc_final: 0.7701 (ttm) REVERT: D 46 TYR cc_start: 0.6319 (t80) cc_final: 0.5937 (t80) REVERT: D 130 MET cc_start: 0.7721 (mmt) cc_final: 0.7476 (mmt) REVERT: D 205 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8293 (mm) REVERT: D 1025 MET cc_start: 0.7872 (tmm) cc_final: 0.6924 (mtt) outliers start: 38 outliers final: 27 residues processed: 260 average time/residue: 0.1612 time to fit residues: 69.9445 Evaluate side-chains 244 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 135 THR 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 523 GLU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1107 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 205 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 770 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 894 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 64 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 317 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3684 r_free = 0.3684 target = 0.127994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089469 restraints weight = 46048.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088074 restraints weight = 42605.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.088342 restraints weight = 46637.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.088896 restraints weight = 35558.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090204 restraints weight = 29710.912| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26200 Z= 0.224 Angle : 0.617 14.248 35575 Z= 0.314 Chirality : 0.044 0.185 4070 Planarity : 0.004 0.062 4498 Dihedral : 11.609 145.331 3986 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.08 % Allowed : 14.05 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3146 helix: 1.14 (0.16), residues: 1077 sheet: 0.13 (0.25), residues: 438 loop : -0.68 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1301 TYR 0.017 0.001 TYR C1281 PHE 0.022 0.002 PHE D1145 TRP 0.026 0.002 TRP C 997 HIS 0.007 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (26193) covalent geometry : angle 0.61087 / 0.31 (35569) hydrogen bonds : bond 0.04562 / 3.10 ( 1038) hydrogen bonds : angle 4.39640 / 3.04 ( 2892) metal coordination : bond 0.00806 / 0.35 ( 7) metal coordination : angle 6.88781 / 3.19 ( 6) *********************** 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 277 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9049 (tt) REVERT: C 207 THR cc_start: 0.8281 (m) cc_final: 0.7892 (p) REVERT: C 517 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8464 (pt0) REVERT: D 144 TYR cc_start: 0.7142 (m-80) cc_final: 0.6887 (m-80) REVERT: D 205 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8294 (mm) REVERT: D 298 MET cc_start: 0.7903 (ppp) cc_final: 0.7524 (tmm) REVERT: D 1025 MET cc_start: 0.7868 (tmm) cc_final: 0.7137 (mtt) REVERT: D 1332 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8879 (mt) outliers start: 56 outliers final: 41 residues processed: 259 average time/residue: 0.1600 time to fit residues: 70.0572 Evaluate side-chains 255 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 95 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 74 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 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 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 1083 GLU Chi-restraints excluded: chain C residue 1107 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 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 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 1003 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1332 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 32 optimal weight: 1.9990 chunk 255 optimal weight: 0.0040 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 249 optimal weight: 0.6980 chunk 226 optimal weight: 0.7980 chunk 301 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.0970 chunk 49 optimal weight: 7.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094000 restraints weight = 45724.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090444 restraints weight = 45330.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.092003 restraints weight = 43666.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092696 restraints weight = 29786.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.092842 restraints weight = 26967.159| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 26200 Z= 0.106 Angle : 0.559 15.085 35575 Z= 0.283 Chirality : 0.042 0.167 4070 Planarity : 0.004 0.061 4498 Dihedral : 11.545 148.776 3986 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.41 % Allowed : 15.09 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3146 helix: 1.31 (0.16), residues: 1077 sheet: 0.30 (0.25), residues: 424 loop : -0.58 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 944 TYR 0.023 0.001 TYR A 185 PHE 0.011 0.001 PHE D1165 TRP 0.045 0.002 TRP C 997 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (26193) covalent geometry : angle 0.55092 / 0.28 (35569) hydrogen bonds : bond 0.03667 / 2.48 ( 1038) hydrogen bonds : angle 4.18002 / 2.90 ( 2892) metal coordination : bond 0.01032 / 0.46 ( 7) metal coordination : angle 7.19119 / 3.35 ( 6) *********************** 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 274 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9059 (mt) REVERT: C 207 THR cc_start: 0.8089 (m) cc_final: 0.7720 (p) REVERT: C 517 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.7750 (pt0) REVERT: C 1240 ASP cc_start: 0.7920 (p0) cc_final: 0.7683 (p0) REVERT: D 46 TYR cc_start: 0.6514 (t80) cc_final: 0.5938 (t80) REVERT: D 205 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8331 (mm) REVERT: D 298 MET cc_start: 0.7785 (ppp) cc_final: 0.7386 (tmm) REVERT: D 983 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7746 (mmtm) REVERT: D 1025 MET cc_start: 0.7973 (tmm) cc_final: 0.7065 (mtt) outliers start: 38 outliers final: 26 residues processed: 259 average time/residue: 0.1601 time to fit residues: 69.3844 Evaluate side-chains 251 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 459 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 877 VAL 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 1107 MET Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 205 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 770 LEU 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 983 LYS 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 43 ASN 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 225 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 316 optimal weight: 50.0000 chunk 166 optimal weight: 0.6980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C1209 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089475 restraints weight = 46382.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088173 restraints weight = 44064.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088363 restraints weight = 47435.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.088999 restraints weight = 36037.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090609 restraints weight = 29638.648| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26200 Z= 0.234 Angle : 0.638 15.122 35575 Z= 0.322 Chirality : 0.044 0.192 4070 Planarity : 0.004 0.062 4498 Dihedral : 11.569 150.864 3986 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.41 % Allowed : 15.50 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3146 helix: 1.16 (0.16), residues: 1084 sheet: 0.18 (0.25), residues: 422 loop : -0.72 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1301 TYR 0.017 0.001 TYR C1281 PHE 0.025 0.002 PHE C 230 TRP 0.028 0.002 TRP C 997 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (26193) covalent geometry : angle 0.63093 / 0.32 (35569) hydrogen bonds : bond 0.04424 / 3.01 ( 1038) hydrogen bonds : angle 4.33755 / 2.99 ( 2892) metal coordination : bond 0.00825 / 0.35 ( 7) metal coordination : angle 7.31801 / 3.39 ( 6) *********************** 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 257 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9082 (tt) REVERT: C 207 THR cc_start: 0.8296 (m) cc_final: 0.7909 (p) REVERT: C 517 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: C 741 MET cc_start: 0.8092 (ptm) cc_final: 0.7724 (ptt) REVERT: D 205 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8306 (mm) REVERT: D 298 MET cc_start: 0.7975 (ppp) cc_final: 0.7602 (tmm) REVERT: D 1025 MET cc_start: 0.7960 (tmm) cc_final: 0.7199 (mtt) outliers start: 38 outliers final: 31 residues processed: 245 average time/residue: 0.1586 time to fit residues: 65.3421 Evaluate side-chains 244 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 360 LEU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU 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 1107 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 205 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 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 43 ASN 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 155 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 179 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.089300 restraints weight = 45682.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.087158 restraints weight = 47323.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.088063 restraints weight = 39666.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088470 restraints weight = 33426.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089208 restraints weight = 27521.479| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26200 Z= 0.188 Angle : 0.608 15.367 35575 Z= 0.307 Chirality : 0.043 0.174 4070 Planarity : 0.004 0.059 4498 Dihedral : 11.551 151.326 3986 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.30 % Allowed : 15.54 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3146 helix: 1.20 (0.16), residues: 1075 sheet: 0.11 (0.25), residues: 418 loop : -0.70 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1058 TYR 0.021 0.001 TYR D 46 PHE 0.025 0.001 PHE C 230 TRP 0.029 0.001 TRP C 997 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (26193) covalent geometry : angle 0.60072 / 0.31 (35569) hydrogen bonds : bond 0.04225 / 2.88 ( 1038) hydrogen bonds : angle 4.27818 / 2.95 ( 2892) metal coordination : bond 0.00796 / 0.31 ( 7) metal coordination : angle 7.29535 / 3.35 ( 6) ********************** 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 248 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: C 207 THR cc_start: 0.8336 (m) cc_final: 0.7930 (p) REVERT: C 517 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: C 741 MET cc_start: 0.8105 (ptm) cc_final: 0.7770 (ptt) REVERT: D 205 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8295 (mm) REVERT: D 298 MET cc_start: 0.7971 (ppp) cc_final: 0.7603 (tmm) REVERT: D 1025 MET cc_start: 0.8095 (tmm) cc_final: 0.7247 (mtt) outliers start: 35 outliers final: 32 residues processed: 235 average time/residue: 0.1567 time to fit residues: 61.7708 Evaluate side-chains 245 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 360 LEU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU 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 1107 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 205 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 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 43 ASN 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 295 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 298 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089702 restraints weight = 45421.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.087864 restraints weight = 48129.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.088681 restraints weight = 38290.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089056 restraints weight = 33604.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090209 restraints weight = 27421.258| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26200 Z= 0.146 Angle : 0.586 15.406 35575 Z= 0.295 Chirality : 0.043 0.176 4070 Planarity : 0.004 0.060 4498 Dihedral : 11.503 152.315 3986 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.37 % Allowed : 15.42 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3146 helix: 1.30 (0.16), residues: 1073 sheet: 0.25 (0.26), residues: 411 loop : -0.67 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.019 0.001 TYR A 185 PHE 0.021 0.001 PHE C 230 TRP 0.025 0.001 TRP C 997 HIS 0.004 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (26193) covalent geometry : angle 0.57886 / 0.30 (35569) hydrogen bonds : bond 0.03997 / 2.72 ( 1038) hydrogen bonds : angle 4.20267 / 2.91 ( 2892) metal coordination : bond 0.00812 / 0.32 ( 7) metal coordination : angle 7.28623 / 3.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3721.23 seconds wall clock time: 65 minutes 33.84 seconds (3933.84 seconds total)