Starting phenix.real_space_refine on Mon Aug 25 06:45:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aby_15327/08_2025/8aby_15327.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aby_15327/08_2025/8aby_15327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8aby_15327/08_2025/8aby_15327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aby_15327/08_2025/8aby_15327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aby_15327/08_2025/8aby_15327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aby_15327/08_2025/8aby_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 481 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14259 SG CYS D 72 109.773 102.792 86.932 1.00 74.52 S ATOM 14367 SG CYS D 85 110.968 102.437 88.537 1.00 78.84 S ATOM 14391 SG CYS D 88 107.679 101.230 89.334 1.00 69.26 S ATOM 20079 SG CYS D 814 84.994 37.015 89.023 1.00 31.53 S ATOM 20644 SG CYS D 888 84.182 40.637 89.043 1.00 17.04 S ATOM 20695 SG CYS D 895 85.304 38.534 85.665 1.00 20.01 S ATOM 20716 SG CYS D 898 81.907 38.327 87.362 1.00 22.29 S Time building chain proxies: 5.16, per 1000 atoms: 0.20 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: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.56 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: 6.46 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8496 1.34 - 1.46: 3457 1.46 - 1.58: 13967 1.58 - 1.69: 89 1.69 - 1.81: 184 Bond restraints: 26193 Sorted by residual: bond pdb=" CA ARG D 339 " pdb=" C ARG D 339 " ideal model delta sigma weight residual 1.522 1.494 0.028 1.38e-02 5.25e+03 4.26e+00 bond pdb=" C GLY D 358 " pdb=" N PRO D 359 " ideal model delta sigma weight residual 1.337 1.318 0.019 1.24e-02 6.50e+03 2.44e+00 bond pdb=" CB CYS D 895 " pdb=" SG CYS D 895 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB VAL C1225 " pdb=" CG2 VAL C1225 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" CB ASP D 413 " pdb=" CG ASP D 413 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 ... (remaining 26188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 35012 2.06 - 4.12: 508 4.12 - 6.18: 42 6.18 - 8.24: 3 8.24 - 10.30: 4 Bond angle restraints: 35569 Sorted by residual: angle pdb=" N VAL B 5 " pdb=" CA VAL B 5 " pdb=" C VAL B 5 " ideal model delta sigma weight residual 113.71 109.85 3.86 9.50e-01 1.11e+00 1.65e+01 angle pdb=" N ILE C 292 " pdb=" CA ILE C 292 " pdb=" C ILE C 292 " ideal model delta sigma weight residual 112.80 108.40 4.40 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N VAL D1267 " pdb=" CA VAL D1267 " pdb=" C VAL D1267 " ideal model delta sigma weight residual 111.48 108.12 3.36 9.40e-01 1.13e+00 1.28e+01 angle pdb=" N TYR C1018 " pdb=" CA TYR C1018 " pdb=" C TYR C1018 " ideal model delta sigma weight residual 111.07 107.29 3.78 1.07e+00 8.73e-01 1.25e+01 angle pdb=" N GLY C1282 " pdb=" CA GLY C1282 " pdb=" C GLY C1282 " ideal model delta sigma weight residual 115.73 110.48 5.25 1.59e+00 3.96e-01 1.09e+01 ... (remaining 35564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 15253 27.97 - 55.94: 737 55.94 - 83.92: 73 83.92 - 111.89: 5 111.89 - 139.86: 1 Dihedral angle restraints: 16069 sinusoidal: 6984 harmonic: 9085 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DG T 18 " pdb=" C3' DG T 18 " pdb=" O3' DG T 18 " pdb=" P DC T 19 " ideal model delta sinusoidal sigma weight residual 220.00 80.14 139.86 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA GLN C1017 " pdb=" C GLN C1017 " pdb=" N TYR C1018 " pdb=" CA TYR C1018 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 16066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2522 0.032 - 0.064: 998 0.064 - 0.096: 355 0.096 - 0.127: 183 0.127 - 0.159: 12 Chirality restraints: 4070 Sorted by residual: chirality pdb=" CB VAL C 353 " pdb=" CA VAL C 353 " pdb=" CG1 VAL C 353 " pdb=" CG2 VAL C 353 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA THR C1292 " pdb=" N THR C1292 " pdb=" C THR C1292 " pdb=" CB THR C1292 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 4067 not shown) Planarity restraints: 4498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO C 567 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 358 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO D 359 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 359 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 359 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " -0.019 2.00e-02 2.50e+03 1.27e-02 4.04e+00 pdb=" CG TRP C1276 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " 0.002 2.00e-02 2.50e+03 ... (remaining 4495 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 570 2.68 - 3.24: 25569 3.24 - 3.79: 39327 3.79 - 4.35: 50468 4.35 - 4.90: 82198 Nonbonded interactions: 198132 Sorted by model distance: nonbonded pdb=" OG SER C 4 " pdb=" OE1 GLU C 7 " model vdw 2.131 3.040 nonbonded pdb=" NH2 ARG C 528 " pdb=" O SER C 576 " model vdw 2.147 3.120 nonbonded pdb=" OG SER C 391 " pdb=" OD1 ASP C 393 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR C 91 " pdb=" O ILE C 138 " model vdw 2.160 3.040 nonbonded pdb=" O TYR C 262 " pdb=" NE2 GLN C 276 " model vdw 2.171 3.120 ... (remaining 198127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 158 or resid 170 through 232)) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.541 26200 Z= 0.223 Angle : 0.629 15.037 35575 Z= 0.342 Chirality : 0.042 0.159 4070 Planarity : 0.004 0.078 4498 Dihedral : 15.029 139.861 10225 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.09 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 aren 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 covalent geometry : bond 0.00442 (26193) covalent geometry : angle 0.62286 (35569) hydrogen bonds : bond 0.20842 ( 1038) hydrogen bonds : angle 6.88885 ( 2892) metal coordination : bond 0.20537 ( 7) metal coordination : angle 7.03284 ( 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 : 1.168 Fit side-chains revert: symmetry clash REVERT: C 559 CYS cc_start: 0.8925 (t) cc_final: 0.8693 (t) REVERT: D 205 LEU cc_start: 0.8512 (mm) cc_final: 0.8177 (mm) REVERT: D 301 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7571 (mp0) REVERT: D 513 MET cc_start: 0.7848 (tpp) cc_final: 0.7552 (ttm) REVERT: D 724 MET cc_start: 0.8288 (mtp) cc_final: 0.7891 (mtm) REVERT: D 743 MET cc_start: 0.8026 (ptp) cc_final: 0.7788 (mtm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1551 time to fit residues: 77.6678 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 : 0.784 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 132 HIS ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C1257 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 341 ASN D 365 GLN E 72 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095957 restraints weight = 45736.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094332 restraints weight = 39887.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095296 restraints weight = 46393.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095645 restraints weight = 30936.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096113 restraints weight = 27419.627| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26200 Z= 0.117 Angle : 0.556 13.872 35575 Z= 0.287 Chirality : 0.042 0.171 4070 Planarity : 0.004 0.054 4498 Dihedral : 12.269 140.146 4032 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.63 % Allowed : 7.38 % Favored : 91.99 % 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 aren not related in a simple way. whole: 0.02 (0.15), residues: 3146 helix: 0.93 (0.16), residues: 1087 sheet: 0.21 (0.25), residues: 416 loop : -0.63 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 69 TYR 0.020 0.001 TYR A 185 PHE 0.013 0.001 PHE D1145 TRP 0.021 0.001 TRP C 997 HIS 0.003 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00256 (26193) covalent geometry : angle 0.54980 (35569) hydrogen bonds : bond 0.04368 ( 1038) hydrogen bonds : angle 4.71261 ( 2892) metal coordination : bond 0.00998 ( 7) metal coordination : angle 6.44880 ( 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 299 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7226 (tm-30) REVERT: C 207 THR cc_start: 0.8339 (m) cc_final: 0.7989 (p) REVERT: C 403 MET cc_start: 0.8559 (tmm) cc_final: 0.8314 (tmm) REVERT: C 559 CYS cc_start: 0.9056 (t) cc_final: 0.8771 (t) REVERT: C 741 MET cc_start: 0.7564 (ptt) cc_final: 0.7178 (ptm) REVERT: C 1188 ASP cc_start: 0.7611 (t0) cc_final: 0.7369 (t0) REVERT: C 1289 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7940 (mm-30) REVERT: D 205 LEU cc_start: 0.8831 (mm) cc_final: 0.8303 (mm) REVERT: D 724 MET cc_start: 0.8444 (mtp) cc_final: 0.7960 (mtm) outliers start: 17 outliers final: 11 residues processed: 291 average time/residue: 0.1447 time to fit residues: 68.4033 Evaluate side-chains 228 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 227 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 281 optimal weight: 30.0000 chunk 250 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C1116 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088319 restraints weight = 47173.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.086728 restraints weight = 42954.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.087181 restraints weight = 46213.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.087637 restraints weight = 35986.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.088996 restraints weight = 30292.111| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 26200 Z= 0.257 Angle : 0.648 14.805 35575 Z= 0.332 Chirality : 0.045 0.171 4070 Planarity : 0.004 0.059 4498 Dihedral : 12.410 141.171 4032 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.22 % Allowed : 11.09 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.15), residues: 3146 helix: 0.92 (0.16), residues: 1085 sheet: -0.06 (0.24), residues: 430 loop : -0.72 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 842 TYR 0.017 0.002 TYR C1281 PHE 0.022 0.002 PHE D1145 TRP 0.025 0.002 TRP C 997 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd covalent geometry : bond 0.00618 (26193) covalent geometry : angle 0.64118 (35569) hydrogen bonds : bond 0.05159 ( 1038) hydrogen bonds : angle 4.67483 ( 2892) metal coordination : bond 0.00856 ( 7) metal coordination : angle 7.12122 ( 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 269 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: C 207 THR cc_start: 0.8180 (m) cc_final: 0.7828 (p) REVERT: C 517 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8373 (pt0) REVERT: C 741 MET cc_start: 0.7645 (ptt) cc_final: 0.7355 (ptm) REVERT: D 46 TYR cc_start: 0.6506 (t80) cc_final: 0.5973 (t80) REVERT: D 205 LEU cc_start: 0.8870 (mm) cc_final: 0.8289 (mm) REVERT: D 724 MET cc_start: 0.8577 (mtp) cc_final: 0.8107 (mtm) REVERT: D 1169 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7405 (p) outliers start: 33 outliers final: 27 residues processed: 257 average time/residue: 0.1394 time to fit residues: 59.0688 Evaluate side-chains 241 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 THR 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 442 VAL 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 757 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 303 VAL 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 8 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 40.0000 chunk 119 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 309 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3704 r_free = 0.3704 target = 0.129553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090770 restraints weight = 46180.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089709 restraints weight = 43721.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.090081 restraints weight = 42641.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090416 restraints weight = 36141.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.092054 restraints weight = 29641.733| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 26200 Z= 0.160 Angle : 0.563 14.512 35575 Z= 0.288 Chirality : 0.042 0.170 4070 Planarity : 0.004 0.054 4498 Dihedral : 12.363 140.633 4032 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.71 % Allowed : 12.79 % Favored : 85.50 % 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 aren not related in a simple way. whole: 0.05 (0.15), residues: 3146 helix: 1.08 (0.16), residues: 1082 sheet: 0.09 (0.25), residues: 431 loop : -0.67 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 417 TYR 0.018 0.001 TYR A 185 PHE 0.016 0.001 PHE D1145 TRP 0.029 0.001 TRP C 997 HIS 0.005 0.001 HIS D 545 Details of bonding type rmsd covalent geometry : bond 0.00387 (26193) covalent geometry : angle 0.55553 (35569) hydrogen bonds : bond 0.04204 ( 1038) hydrogen bonds : angle 4.39017 ( 2892) metal coordination : bond 0.00760 ( 7) metal coordination : angle 6.88913 ( 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 284 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9007 (tt) REVERT: C 207 THR cc_start: 0.8113 (m) cc_final: 0.7758 (p) REVERT: C 403 MET cc_start: 0.8503 (tmm) cc_final: 0.8298 (tmm) REVERT: C 1240 ASP cc_start: 0.8113 (p0) cc_final: 0.7897 (p0) REVERT: D 46 TYR cc_start: 0.6457 (t80) cc_final: 0.5991 (t80) REVERT: D 205 LEU cc_start: 0.8878 (mm) cc_final: 0.8340 (mm) REVERT: D 298 MET cc_start: 0.7923 (ppp) cc_final: 0.7630 (ppp) REVERT: D 625 MET cc_start: 0.8839 (ttp) cc_final: 0.8344 (ttp) REVERT: D 724 MET cc_start: 0.8609 (mtp) cc_final: 0.8149 (mtm) REVERT: D 1169 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7375 (p) REVERT: D 1208 ASP cc_start: 0.8059 (t0) cc_final: 0.7552 (m-30) outliers start: 46 outliers final: 32 residues processed: 270 average time/residue: 0.1501 time to fit residues: 67.2440 Evaluate side-chains 243 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 207 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 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 249 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 884 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 233 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 194 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 213 optimal weight: 0.0970 chunk 126 optimal weight: 0.7980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092784 restraints weight = 45861.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089818 restraints weight = 46145.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091103 restraints weight = 47763.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.092017 restraints weight = 30757.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.092099 restraints weight = 28143.618| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26200 Z= 0.148 Angle : 0.550 15.764 35575 Z= 0.279 Chirality : 0.042 0.169 4070 Planarity : 0.004 0.053 4498 Dihedral : 12.307 140.953 4032 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.93 % Allowed : 13.94 % Favored : 84.13 % 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 aren not related in a simple way. whole: 0.13 (0.15), residues: 3146 helix: 1.18 (0.16), residues: 1086 sheet: 0.12 (0.25), residues: 440 loop : -0.65 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 417 TYR 0.017 0.001 TYR A 185 PHE 0.014 0.001 PHE D1145 TRP 0.028 0.001 TRP C 997 HIS 0.004 0.001 HIS D 545 Details of bonding type rmsd covalent geometry : bond 0.00356 (26193) covalent geometry : angle 0.54076 (35569) hydrogen bonds : bond 0.03988 ( 1038) hydrogen bonds : angle 4.25205 ( 2892) metal coordination : bond 0.00834 ( 7) metal coordination : angle 7.59027 ( 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 285 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 207 THR cc_start: 0.8092 (m) cc_final: 0.7737 (p) REVERT: C 403 MET cc_start: 0.8517 (tmm) cc_final: 0.8245 (tmm) REVERT: C 1240 ASP cc_start: 0.8142 (p0) cc_final: 0.7875 (p0) REVERT: D 205 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8371 (mm) REVERT: D 298 MET cc_start: 0.7979 (ppp) cc_final: 0.7438 (ppp) REVERT: D 724 MET cc_start: 0.8601 (mtp) cc_final: 0.8261 (mtm) REVERT: D 1169 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7405 (p) REVERT: D 1208 ASP cc_start: 0.8069 (t0) cc_final: 0.7587 (m-30) REVERT: D 1305 ASP cc_start: 0.8272 (t70) cc_final: 0.8038 (t0) outliers start: 52 outliers final: 35 residues processed: 267 average time/residue: 0.1498 time to fit residues: 66.3033 Evaluate side-chains 254 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 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 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: 2.9990 chunk 3 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 177 optimal weight: 0.0770 chunk 230 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN D 276 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092661 restraints weight = 45966.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.089434 restraints weight = 47244.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.090843 restraints weight = 47275.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.091781 restraints weight = 30212.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.092026 restraints weight = 27382.577| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26200 Z= 0.151 Angle : 0.549 14.967 35575 Z= 0.279 Chirality : 0.042 0.168 4070 Planarity : 0.004 0.056 4498 Dihedral : 12.279 141.039 4032 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.04 % Allowed : 14.53 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3146 helix: 1.25 (0.16), residues: 1086 sheet: 0.23 (0.25), residues: 438 loop : -0.66 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 764 TYR 0.017 0.001 TYR D 46 PHE 0.014 0.001 PHE D1145 TRP 0.022 0.001 TRP C 997 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00363 (26193) covalent geometry : angle 0.54160 (35569) hydrogen bonds : bond 0.03922 ( 1038) hydrogen bonds : angle 4.17882 ( 2892) metal coordination : bond 0.00775 ( 7) metal coordination : angle 7.14958 ( 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 289 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 207 THR cc_start: 0.8156 (m) cc_final: 0.7775 (p) REVERT: C 403 MET cc_start: 0.8470 (tmm) cc_final: 0.8162 (tmm) REVERT: C 517 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: C 741 MET cc_start: 0.8132 (ptm) cc_final: 0.7897 (ptt) REVERT: C 1240 ASP cc_start: 0.8125 (p0) cc_final: 0.7870 (p0) REVERT: C 1319 MET cc_start: 0.8115 (tmm) cc_final: 0.7795 (ttm) REVERT: D 205 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8395 (mm) REVERT: D 298 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7358 (ppp) REVERT: D 724 MET cc_start: 0.8571 (mtp) cc_final: 0.8247 (mtm) REVERT: D 1025 MET cc_start: 0.7944 (tmm) cc_final: 0.6896 (mpp) REVERT: D 1208 ASP cc_start: 0.8058 (t0) cc_final: 0.7619 (m-30) REVERT: D 1305 ASP cc_start: 0.8266 (t70) cc_final: 0.8044 (t0) outliers start: 55 outliers final: 42 residues processed: 271 average time/residue: 0.1530 time to fit residues: 68.5005 Evaluate side-chains 263 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 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 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain 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 298 MET 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 884 SER Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1003 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 64 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 317 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C1209 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093136 restraints weight = 45909.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.089624 restraints weight = 43808.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091833 restraints weight = 44443.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091667 restraints weight = 28972.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092739 restraints weight = 26741.823| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26200 Z= 0.124 Angle : 0.532 14.822 35575 Z= 0.269 Chirality : 0.041 0.185 4070 Planarity : 0.004 0.059 4498 Dihedral : 12.216 141.265 4032 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.71 % Allowed : 15.28 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3146 helix: 1.39 (0.16), residues: 1078 sheet: 0.32 (0.25), residues: 439 loop : -0.60 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 764 TYR 0.019 0.001 TYR A 185 PHE 0.011 0.001 PHE D1145 TRP 0.016 0.001 TRP C 997 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00297 (26193) covalent geometry : angle 0.52364 (35569) hydrogen bonds : bond 0.03637 ( 1038) hydrogen bonds : angle 4.07233 ( 2892) metal coordination : bond 0.00795 ( 7) metal coordination : angle 7.04290 ( 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 278 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9169 (tt) REVERT: C 207 THR cc_start: 0.8065 (m) cc_final: 0.7691 (p) REVERT: C 403 MET cc_start: 0.8408 (tmm) cc_final: 0.8124 (tmm) REVERT: C 517 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: C 741 MET cc_start: 0.8128 (ptm) cc_final: 0.7891 (ptt) REVERT: D 205 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8406 (mm) REVERT: D 298 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7352 (ppp) REVERT: D 724 MET cc_start: 0.8480 (mtp) cc_final: 0.8157 (mtm) REVERT: D 1025 MET cc_start: 0.7978 (tmm) cc_final: 0.6982 (mpp) REVERT: D 1208 ASP cc_start: 0.8041 (t0) cc_final: 0.7623 (m-30) REVERT: D 1305 ASP cc_start: 0.8214 (t70) cc_final: 0.8011 (t0) REVERT: E 68 GLU cc_start: 0.8710 (pp20) cc_final: 0.8477 (pp20) outliers start: 46 outliers final: 36 residues processed: 263 average time/residue: 0.1476 time to fit residues: 64.5633 Evaluate side-chains 255 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 32 optimal weight: 4.9990 chunk 255 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 301 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094498 restraints weight = 46025.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.091360 restraints weight = 49681.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.092778 restraints weight = 48226.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093680 restraints weight = 30432.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093967 restraints weight = 27968.160| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26200 Z= 0.112 Angle : 0.531 14.353 35575 Z= 0.268 Chirality : 0.041 0.174 4070 Planarity : 0.004 0.063 4498 Dihedral : 12.161 141.405 4032 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.78 % Allowed : 15.57 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.15), residues: 3146 helix: 1.45 (0.16), residues: 1079 sheet: 0.33 (0.25), residues: 422 loop : -0.53 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 764 TYR 0.019 0.001 TYR D 46 PHE 0.011 0.001 PHE C 934 TRP 0.047 0.001 TRP C 997 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00265 (26193) covalent geometry : angle 0.52398 (35569) hydrogen bonds : bond 0.03473 ( 1038) hydrogen bonds : angle 3.99721 ( 2892) metal coordination : bond 0.00782 ( 7) metal coordination : angle 6.76984 ( 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 275 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: C 207 THR cc_start: 0.8105 (m) cc_final: 0.7717 (p) REVERT: C 315 MET cc_start: 0.7463 (tpp) cc_final: 0.7016 (tpp) REVERT: C 403 MET cc_start: 0.8499 (tmm) cc_final: 0.8173 (tmm) REVERT: C 517 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8504 (pt0) REVERT: C 741 MET cc_start: 0.8164 (ptm) cc_final: 0.7894 (ptt) REVERT: D 205 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8395 (mm) REVERT: D 298 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7354 (ppp) REVERT: D 724 MET cc_start: 0.8505 (mtp) cc_final: 0.8058 (mtm) REVERT: D 1025 MET cc_start: 0.7852 (tmm) cc_final: 0.7012 (mpp) REVERT: D 1208 ASP cc_start: 0.8007 (t0) cc_final: 0.7621 (m-30) REVERT: D 1305 ASP cc_start: 0.8292 (t70) cc_final: 0.8054 (t0) REVERT: E 68 GLU cc_start: 0.8728 (pp20) cc_final: 0.8505 (pp20) outliers start: 48 outliers final: 36 residues processed: 261 average time/residue: 0.1376 time to fit residues: 60.5374 Evaluate side-chains 254 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 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 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 617 THR 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 997 VAL Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 225 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 279 optimal weight: 50.0000 chunk 270 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 316 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 554 HIS D 266 ASN 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 = 0.3642 r_free = 0.3642 target = 0.124967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088529 restraints weight = 46819.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085077 restraints weight = 48553.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.086497 restraints weight = 49461.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.087321 restraints weight = 31515.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.087491 restraints weight = 29127.838| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 26200 Z= 0.350 Angle : 0.742 15.741 35575 Z= 0.377 Chirality : 0.047 0.193 4070 Planarity : 0.005 0.067 4498 Dihedral : 12.479 141.395 4032 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.04 % Allowed : 15.87 % Favored : 82.09 % 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 aren not related in a simple way. whole: -0.10 (0.15), residues: 3146 helix: 1.04 (0.16), residues: 1071 sheet: -0.11 (0.25), residues: 405 loop : -0.78 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 764 TYR 0.018 0.002 TYR C 756 PHE 0.025 0.002 PHE D1145 TRP 0.042 0.002 TRP C 997 HIS 0.008 0.002 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00846 (26193) covalent geometry : angle 0.73518 (35569) hydrogen bonds : bond 0.05324 ( 1038) hydrogen bonds : angle 4.53951 ( 2892) metal coordination : bond 0.01165 ( 7) metal coordination : angle 7.79803 ( 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 278 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: C 207 THR cc_start: 0.8591 (m) cc_final: 0.8211 (p) REVERT: C 315 MET cc_start: 0.7543 (tpp) cc_final: 0.7104 (tpp) REVERT: C 517 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8459 (pt0) REVERT: C 741 MET cc_start: 0.8159 (ptm) cc_final: 0.7908 (ptt) REVERT: D 205 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8329 (mm) REVERT: D 298 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7294 (tmm) REVERT: D 413 ASP cc_start: 0.7995 (t0) cc_final: 0.7776 (t0) REVERT: D 625 MET cc_start: 0.8878 (ttp) cc_final: 0.8493 (ttp) REVERT: D 724 MET cc_start: 0.8596 (mtp) cc_final: 0.8237 (mtm) REVERT: D 1025 MET cc_start: 0.7847 (tmm) cc_final: 0.7019 (mpp) REVERT: D 1208 ASP cc_start: 0.8221 (t0) cc_final: 0.7730 (m-30) REVERT: D 1332 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9034 (mt) outliers start: 55 outliers final: 42 residues processed: 263 average time/residue: 0.1505 time to fit residues: 66.3269 Evaluate side-chains 261 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 A residue 232 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 757 THR 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 1180 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 997 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 155 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN D 365 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090721 restraints weight = 46037.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.088140 restraints weight = 45003.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.089676 restraints weight = 49043.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.089653 restraints weight = 31189.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090613 restraints weight = 27873.395| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26200 Z= 0.193 Angle : 0.621 15.508 35575 Z= 0.314 Chirality : 0.043 0.182 4070 Planarity : 0.004 0.058 4498 Dihedral : 12.390 141.369 4032 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.52 % Allowed : 16.83 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.15), residues: 3146 helix: 1.16 (0.16), residues: 1073 sheet: -0.11 (0.26), residues: 398 loop : -0.72 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 275 TYR 0.019 0.001 TYR D 46 PHE 0.020 0.001 PHE D 176 TRP 0.035 0.001 TRP C 997 HIS 0.006 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00463 (26193) covalent geometry : angle 0.61315 (35569) hydrogen bonds : bond 0.04375 ( 1038) hydrogen bonds : angle 4.31233 ( 2892) metal coordination : bond 0.00834 ( 7) metal coordination : angle 7.49680 ( 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 273 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7914 (tp30) cc_final: 0.7649 (tp30) REVERT: C 207 THR cc_start: 0.8439 (m) cc_final: 0.8067 (p) REVERT: C 315 MET cc_start: 0.7594 (tpp) cc_final: 0.7141 (tpp) REVERT: C 517 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: C 741 MET cc_start: 0.8139 (ptm) cc_final: 0.7889 (ptt) REVERT: C 1119 MET cc_start: 0.8657 (tpp) cc_final: 0.8352 (ttp) REVERT: D 205 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8389 (mm) REVERT: D 298 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7367 (tmm) REVERT: D 413 ASP cc_start: 0.8079 (t0) cc_final: 0.7853 (t0) REVERT: D 724 MET cc_start: 0.8641 (mtp) cc_final: 0.8304 (mtm) REVERT: D 1025 MET cc_start: 0.7859 (tmm) cc_final: 0.7056 (mpp) REVERT: D 1208 ASP cc_start: 0.8202 (t0) cc_final: 0.7710 (m-30) REVERT: D 1305 ASP cc_start: 0.8290 (t70) cc_final: 0.8053 (t0) outliers start: 41 outliers final: 35 residues processed: 263 average time/residue: 0.1456 time to fit residues: 64.8337 Evaluate side-chains 253 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 A residue 232 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 202 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 517 GLN Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 757 THR 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 1180 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET 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 849 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 295 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 197 optimal weight: 0.0570 chunk 308 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN D 777 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093699 restraints weight = 45722.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090860 restraints weight = 43733.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092158 restraints weight = 44227.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.092949 restraints weight = 29250.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.093091 restraints weight = 26897.755| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 26200 Z= 0.108 Angle : 0.562 15.246 35575 Z= 0.283 Chirality : 0.041 0.172 4070 Planarity : 0.004 0.063 4498 Dihedral : 12.128 141.409 4032 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.30 % Allowed : 17.09 % Favored : 81.61 % 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 aren not related in a simple way. whole: 0.26 (0.15), residues: 3146 helix: 1.41 (0.16), residues: 1077 sheet: 0.04 (0.25), residues: 416 loop : -0.59 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 275 TYR 0.022 0.001 TYR D 46 PHE 0.012 0.001 PHE C 934 TRP 0.028 0.001 TRP C 997 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00249 (26193) covalent geometry : angle 0.55450 (35569) hydrogen bonds : bond 0.03445 ( 1038) hydrogen bonds : angle 4.05702 ( 2892) metal coordination : bond 0.00892 ( 7) metal coordination : angle 7.21598 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3393.33 seconds wall clock time: 59 minutes 40.76 seconds (3580.76 seconds total)