Starting phenix.real_space_refine on Sat Jun 28 22:16:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvr_35047/06_2025/8hvr_35047_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvr_35047/06_2025/8hvr_35047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hvr_35047/06_2025/8hvr_35047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvr_35047/06_2025/8hvr_35047.map" model { file = "/net/cci-nas-00/data/ceres_data/8hvr_35047/06_2025/8hvr_35047_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvr_35047/06_2025/8hvr_35047_neut.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 122 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 20877 2.51 5 N 6065 2.21 5 O 6760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33932 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8675 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 58, 'TRANS': 1055} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2398 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "G" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 734 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain: "H" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1241 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 4, 'TRANS': 153} Chain: "I" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1934 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "J" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1934 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "K" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 545 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "O" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1233 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "P" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1258 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} 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 12656 SG CYS D 60 45.272 85.376 121.038 1.00 25.13 S ATOM 12674 SG CYS D 62 46.691 83.846 124.016 1.00 24.86 S ATOM 12783 SG CYS D 75 42.982 84.587 123.975 1.00 23.85 S ATOM 12809 SG CYS D 78 45.416 87.546 124.121 1.00 22.58 S ATOM 19208 SG CYS D 886 18.086 134.730 86.285 1.00 27.04 S ATOM 19772 SG CYS D 962 21.636 135.315 87.152 1.00 16.47 S ATOM 19820 SG CYS D 969 20.454 133.421 83.804 1.00 12.42 S ATOM 19839 SG CYS D 972 20.655 136.885 83.915 1.00 11.59 S Time building chain proxies: 20.56, per 1000 atoms: 0.61 Number of scatterers: 33932 At special positions: 0 Unit cell: (131.25, 184.8, 194.25, 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 105 16.00 P 122 15.00 Mg 1 11.99 O 6760 8.00 N 6065 7.00 C 20877 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: 8.79 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " Number of angles added : 12 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7450 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 44 sheets defined 47.1% alpha, 13.7% beta 32 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 12.30 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.575A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.644A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.628A pdb=" N ALA A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.502A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.622A pdb=" N GLN B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 220 Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.552A pdb=" N LEU B 225 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 4.170A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 73 through 81 removed outlier: 3.602A pdb=" N ILE C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 288 removed outlier: 3.795A pdb=" N TYR C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 320 through 337 Processing helix chain 'C' and resid 366 through 392 removed outlier: 3.596A pdb=" N THR C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 removed outlier: 4.293A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 455 through 460 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.857A pdb=" N TYR C 466 " --> pdb=" O PRO C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.963A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.901A pdb=" N GLU C 553 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 4.403A pdb=" N MET C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 580 Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 599 through 601 No H-bonds generated for 'chain 'C' and resid 599 through 601' Processing helix chain 'C' and resid 616 through 623 Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 765 through 770 removed outlier: 4.595A pdb=" N ASP C 769 " --> pdb=" O VAL C 766 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 770 " --> pdb=" O LEU C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.225A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 Processing helix chain 'C' and resid 1021 through 1026 Processing helix chain 'C' and resid 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1075 Processing helix chain 'C' and resid 1082 through 1094 Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.651A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.530A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.696A pdb=" N ASP D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 188 removed outlier: 3.639A pdb=" N GLY D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 3.586A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.616A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.596A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 304 removed outlier: 3.549A pdb=" N LYS D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.658A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.898A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 removed outlier: 3.692A pdb=" N MET D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 491 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 532 removed outlier: 3.503A pdb=" N VAL D 528 " --> pdb=" O HIS D 525 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N THR D 530 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.853A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 672 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 721 Processing helix chain 'D' and resid 735 through 756 removed outlier: 4.578A pdb=" N GLU D 739 " --> pdb=" O ASP D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 799 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 840 through 877 removed outlier: 3.769A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 970 through 974 Processing helix chain 'D' and resid 988 through 999 Processing helix chain 'D' and resid 1000 through 1002 No H-bonds generated for 'chain 'D' and resid 1000 through 1002' Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1109 Processing helix chain 'D' and resid 1109 through 1127 Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 4.023A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1179 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1209 Processing helix chain 'D' and resid 1213 through 1223 Processing helix chain 'D' and resid 1231 through 1238 removed outlier: 3.842A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1246 Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 Processing helix chain 'E' and resid 15 through 24 removed outlier: 3.703A pdb=" N LEU E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 45 Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'F' and resid 213 through 223 removed outlier: 3.789A pdb=" N ASP F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 292 removed outlier: 4.978A pdb=" N ARG F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.896A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.518A pdb=" N ASP F 420 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 421 " --> pdb=" O PHE F 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 421' Processing helix chain 'F' and resid 429 through 450 removed outlier: 3.711A pdb=" N HIS F 444 " --> pdb=" O GLN F 440 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 450 " --> pdb=" O VAL F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 471 through 476 Processing helix chain 'F' and resid 482 through 498 Processing helix chain 'F' and resid 499 through 503 removed outlier: 3.603A pdb=" N SER F 503 " --> pdb=" O PRO F 500 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 91 through 110 Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 64 through 76 removed outlier: 4.309A pdb=" N LEU H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP H 69 " --> pdb=" O GLN H 65 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG H 70 " --> pdb=" O ASP H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 100 removed outlier: 3.921A pdb=" N ARG H 89 " --> pdb=" O ASN H 85 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU H 95 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 119 Processing helix chain 'H' and resid 123 through 142 removed outlier: 4.092A pdb=" N ARG H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU H 142 " --> pdb=" O SER H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 155 removed outlier: 3.737A pdb=" N LEU H 155 " --> pdb=" O ALA H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'I' and resid 46 through 58 Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 82 through 97 removed outlier: 3.594A pdb=" N VAL I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 138 Processing helix chain 'I' and resid 139 through 152 removed outlier: 3.832A pdb=" N ALA I 143 " --> pdb=" O ASP I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 193 Processing helix chain 'I' and resid 195 through 209 Processing helix chain 'I' and resid 212 through 225 Processing helix chain 'I' and resid 229 through 247 Processing helix chain 'I' and resid 252 through 264 removed outlier: 3.631A pdb=" N GLN I 256 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 66 through 75 removed outlier: 3.517A pdb=" N GLY J 75 " --> pdb=" O ASP J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 97 Processing helix chain 'J' and resid 119 through 137 Processing helix chain 'J' and resid 139 through 152 Processing helix chain 'J' and resid 164 through 192 Processing helix chain 'J' and resid 194 through 209 removed outlier: 3.844A pdb=" N ALA J 198 " --> pdb=" O CYS J 194 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 227 removed outlier: 3.712A pdb=" N ARG J 216 " --> pdb=" O ARG J 212 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 247 Processing helix chain 'J' and resid 252 through 264 Processing helix chain 'K' and resid 240 through 249 Processing helix chain 'K' and resid 250 through 255 removed outlier: 3.565A pdb=" N GLU K 253 " --> pdb=" O PRO K 250 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU K 255 " --> pdb=" O GLU K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 267 removed outlier: 3.622A pdb=" N GLU K 267 " --> pdb=" O CYS K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 278 Processing helix chain 'K' and resid 279 through 285 removed outlier: 3.678A pdb=" N LEU K 283 " --> pdb=" O SER K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 305 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.829A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 6.216A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 13 removed outlier: 5.245A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL B 22 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 190 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR B 187 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG B 182 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE B 189 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA B 180 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 99 removed outlier: 3.837A pdb=" N SER B 53 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.507A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.470A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 100 removed outlier: 6.362A pdb=" N THR C 124 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS C 98 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE C 122 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE C 100 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA H 22 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS H 39 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE H 20 " --> pdb=" O LYS H 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 362 through 365 removed outlier: 6.463A pdb=" N SER C 165 " --> pdb=" O ASN C 442 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.636A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 7.058A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.941A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 653 through 657 removed outlier: 6.869A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.372A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 735 through 746 removed outlier: 5.803A pdb=" N SER C 735 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS C 862 " --> pdb=" O SER C 735 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS C 737 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA C 860 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU C 739 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR C 858 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS C 741 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG C 856 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 743 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU C 854 " --> pdb=" O VAL C 743 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA C 745 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASN C 852 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP C 840 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 854 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 838 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG C 856 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL C 836 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR C 858 " --> pdb=" O ILE C 834 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.523A pdb=" N GLU C 754 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 787 through 789 removed outlier: 7.164A pdb=" N LEU C 823 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 6.289A pdb=" N CYS D 441 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL D 431 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1052 through 1053 Processing sheet with id=AD1, first strand: chain 'C' and resid 1121 through 1123 Processing sheet with id=AD2, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.382A pdb=" N HIS D 94 " --> pdb=" O HIS D 25 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.520A pdb=" N GLU D 235 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.208A pdb=" N PHE D 335 " --> pdb=" O ILE F 404 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 603 through 604 removed outlier: 3.565A pdb=" N PHE D 657 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 881 through 883 Processing sheet with id=AD7, first strand: chain 'D' and resid 892 through 895 removed outlier: 4.154A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 924 through 925 removed outlier: 7.480A pdb=" N VAL D 924 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1070 through 1074 Processing sheet with id=AE1, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 4.587A pdb=" N ARG D1147 " --> pdb=" O GLN D1189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN D1189 " --> pdb=" O ARG D1147 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1253 through 1257 removed outlier: 3.632A pdb=" N GLU D1256 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 81 " --> pdb=" O GLU D1256 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 39 through 45 removed outlier: 4.012A pdb=" N TRP G 54 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 28 removed outlier: 4.699A pdb=" N ALA I 35 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 102 through 105 Processing sheet with id=AE7, first strand: chain 'J' and resid 25 through 28 Processing sheet with id=AE8, first strand: chain 'J' and resid 64 through 65 removed outlier: 3.698A pdb=" N ALA J 64 " --> pdb=" O TYR J 109 " (cutoff:3.500A) 1515 hydrogen bonds defined for protein. 4326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 17.74 Time building geometry restraints manager: 10.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9635 1.33 - 1.46: 6887 1.46 - 1.58: 17769 1.58 - 1.70: 242 1.70 - 1.83: 187 Bond restraints: 34720 Sorted by residual: bond pdb=" N ARG C 819 " pdb=" CA ARG C 819 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.68e+00 bond pdb=" CA GLU D 963 " pdb=" CB GLU D 963 " ideal model delta sigma weight residual 1.527 1.578 -0.051 1.75e-02 3.27e+03 8.57e+00 bond pdb=" N VAL G 105 " pdb=" CA VAL G 105 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.36e+00 bond pdb=" N ILE G 22 " pdb=" CA ILE G 22 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.23e+00 bond pdb=" N VAL C 395 " pdb=" CA VAL C 395 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.35e-02 5.49e+03 8.08e+00 ... (remaining 34715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 46092 1.90 - 3.80: 1184 3.80 - 5.70: 146 5.70 - 7.60: 53 7.60 - 9.50: 10 Bond angle restraints: 47485 Sorted by residual: angle pdb=" CA GLY C 812 " pdb=" C GLY C 812 " pdb=" O GLY C 812 " ideal model delta sigma weight residual 122.24 117.97 4.27 8.70e-01 1.32e+00 2.40e+01 angle pdb=" C LEU F 464 " pdb=" CA LEU F 464 " pdb=" CB LEU F 464 " ideal model delta sigma weight residual 116.63 111.02 5.61 1.16e+00 7.43e-01 2.34e+01 angle pdb=" N GLY C 812 " pdb=" CA GLY C 812 " pdb=" C GLY C 812 " ideal model delta sigma weight residual 112.48 107.30 5.18 1.21e+00 6.83e-01 1.83e+01 angle pdb=" CA THR C 801 " pdb=" C THR C 801 " pdb=" N PRO C 802 " ideal model delta sigma weight residual 117.60 122.54 -4.94 1.20e+00 6.94e-01 1.70e+01 angle pdb=" CA THR C 801 " pdb=" C THR C 801 " pdb=" O THR C 801 " ideal model delta sigma weight residual 120.64 116.53 4.11 1.03e+00 9.43e-01 1.59e+01 ... (remaining 47480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 20162 35.62 - 71.24: 777 71.24 - 106.86: 28 106.86 - 142.49: 2 142.49 - 178.11: 4 Dihedral angle restraints: 20973 sinusoidal: 9405 harmonic: 11568 Sorted by residual: dihedral pdb=" CA GLU B 24 " pdb=" C GLU B 24 " pdb=" N PRO B 25 " pdb=" CA PRO B 25 " ideal model delta harmonic sigma weight residual -180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASN D 824 " pdb=" C ASN D 824 " pdb=" N GLU D 825 " pdb=" CA GLU D 825 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG C 985 " pdb=" C ARG C 985 " pdb=" N MET C 986 " pdb=" CA MET C 986 " ideal model delta harmonic sigma weight residual 180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 20970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4256 0.052 - 0.103: 908 0.103 - 0.155: 206 0.155 - 0.206: 27 0.206 - 0.258: 7 Chirality restraints: 5404 Sorted by residual: chirality pdb=" CB VAL D 528 " pdb=" CA VAL D 528 " pdb=" CG1 VAL D 528 " pdb=" CG2 VAL D 528 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ASP J 187 " pdb=" N ASP J 187 " pdb=" C ASP J 187 " pdb=" CB ASP J 187 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE C 920 " pdb=" CA ILE C 920 " pdb=" CG1 ILE C 920 " pdb=" CG2 ILE C 920 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 5401 not shown) Planarity restraints: 5820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 13 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO E 14 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 810 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ILE C 810 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE C 810 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE C 811 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 91 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C THR G 91 " 0.063 2.00e-02 2.50e+03 pdb=" O THR G 91 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG G 92 " -0.021 2.00e-02 2.50e+03 ... (remaining 5817 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2478 2.74 - 3.28: 33223 3.28 - 3.82: 58219 3.82 - 4.36: 67630 4.36 - 4.90: 113446 Nonbonded interactions: 274996 Sorted by model distance: nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D1401 " model vdw 2.199 2.170 nonbonded pdb=" OH TYR C 502 " pdb=" OE2 GLU C 522 " model vdw 2.243 3.040 nonbonded pdb=" O LEU D 438 " pdb=" OG SER D 561 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP D 147 " pdb=" OH TYR D 251 " model vdw 2.274 3.040 nonbonded pdb=" O GLN D 287 " pdb=" OG1 THR D 290 " model vdw 2.275 3.040 ... (remaining 274991 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' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.460 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 97.570 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34728 Z= 0.199 Angle : 0.724 14.702 47497 Z= 0.392 Chirality : 0.046 0.258 5404 Planarity : 0.005 0.108 5820 Dihedral : 17.108 178.107 13523 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.12 % Allowed : 1.16 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4019 helix: 0.18 (0.12), residues: 1727 sheet: -0.76 (0.25), residues: 427 loop : -0.85 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP F 333 HIS 0.009 0.001 HIS G 82 PHE 0.023 0.002 PHE F 436 TYR 0.032 0.001 TYR I 236 ARG 0.011 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.15490 ( 1592) hydrogen bonds : angle 6.31914 ( 4484) metal coordination : bond 0.00840 ( 8) metal coordination : angle 7.10675 ( 12) covalent geometry : bond 0.00387 (34720) covalent geometry : angle 0.71526 (47485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 387 time to evaluate : 3.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 390 average time/residue: 0.4370 time to fit residues: 280.3543 Evaluate side-chains 302 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 704 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 347 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 322 optimal weight: 20.0000 chunk 124 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 373 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS B 129 ASN C 358 HIS C 916 GLN ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 ASN D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.192951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159770 restraints weight = 45822.981| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.69 r_work: 0.3544 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34728 Z= 0.184 Angle : 0.639 16.332 47497 Z= 0.324 Chirality : 0.043 0.289 5404 Planarity : 0.005 0.067 5820 Dihedral : 16.527 178.329 5747 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.28 % Allowed : 8.80 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4019 helix: 0.80 (0.12), residues: 1765 sheet: -0.62 (0.25), residues: 434 loop : -0.76 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 105 HIS 0.006 0.001 HIS G 82 PHE 0.028 0.002 PHE D1169 TYR 0.019 0.001 TYR C1064 ARG 0.007 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 1592) hydrogen bonds : angle 4.66839 ( 4484) metal coordination : bond 0.00971 ( 8) metal coordination : angle 7.07450 ( 12) covalent geometry : bond 0.00436 (34720) covalent geometry : angle 0.62935 (47485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 338 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8388 (ptpp) cc_final: 0.8087 (ptpp) REVERT: B 217 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7196 (pt0) REVERT: C 1014 TYR cc_start: 0.9034 (t80) cc_final: 0.8827 (t80) REVERT: D 690 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: F 333 TRP cc_start: 0.7270 (m100) cc_final: 0.6989 (m100) outliers start: 43 outliers final: 23 residues processed: 360 average time/residue: 0.5078 time to fit residues: 300.7432 Evaluate side-chains 313 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 288 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain J residue 188 MET Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 333 optimal weight: 1.9990 chunk 321 optimal weight: 20.0000 chunk 164 optimal weight: 1.9990 chunk 379 optimal weight: 50.0000 chunk 205 optimal weight: 0.4980 chunk 362 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 290 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 157 ASN C 648 ASN C 741 HIS ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN D 375 GLN ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.190552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157396 restraints weight = 45920.588| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.69 r_work: 0.3529 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34728 Z= 0.206 Angle : 0.642 21.278 47497 Z= 0.322 Chirality : 0.043 0.329 5404 Planarity : 0.004 0.051 5820 Dihedral : 16.649 178.903 5747 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.85 % Allowed : 11.61 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4019 helix: 1.06 (0.12), residues: 1749 sheet: -0.61 (0.24), residues: 439 loop : -0.78 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 154 HIS 0.007 0.001 HIS G 82 PHE 0.019 0.002 PHE D1169 TYR 0.018 0.002 TYR I 89 ARG 0.005 0.000 ARG C 808 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 1592) hydrogen bonds : angle 4.52398 ( 4484) metal coordination : bond 0.01165 ( 8) metal coordination : angle 7.48298 ( 12) covalent geometry : bond 0.00496 (34720) covalent geometry : angle 0.63055 (47485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8469 (t80) cc_final: 0.8240 (t80) REVERT: C 1014 TYR cc_start: 0.9128 (t80) cc_final: 0.8848 (t80) REVERT: D 124 ASP cc_start: 0.7602 (t70) cc_final: 0.7394 (t0) REVERT: E 72 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8216 (mt) REVERT: F 333 TRP cc_start: 0.7139 (m100) cc_final: 0.6841 (m100) REVERT: K 256 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5213 (pt) outliers start: 62 outliers final: 36 residues processed: 346 average time/residue: 0.5397 time to fit residues: 316.2529 Evaluate side-chains 321 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 849 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2608 > 50: distance: 39 - 152: 8.171 distance: 128 - 132: 12.075 distance: 132 - 133: 6.368 distance: 133 - 134: 6.141 distance: 134 - 135: 19.652 distance: 136 - 137: 3.423 distance: 137 - 138: 6.675 distance: 137 - 140: 8.926 distance: 138 - 139: 10.940 distance: 138 - 145: 11.272 distance: 140 - 141: 20.017 distance: 141 - 142: 12.562 distance: 142 - 143: 16.919 distance: 142 - 144: 11.388 distance: 146 - 147: 12.621 distance: 147 - 148: 11.950 distance: 147 - 152: 4.828 distance: 149 - 150: 11.847 distance: 149 - 151: 12.681 distance: 152 - 153: 9.376 distance: 153 - 154: 9.614 distance: 153 - 156: 7.932 distance: 154 - 155: 13.378 distance: 154 - 160: 17.602 distance: 156 - 157: 11.939 distance: 157 - 158: 10.323 distance: 157 - 159: 12.760 distance: 160 - 161: 12.289 distance: 161 - 162: 6.846 distance: 161 - 164: 19.461 distance: 162 - 163: 12.917 distance: 162 - 165: 9.469 distance: 165 - 166: 18.422 distance: 166 - 167: 18.943 distance: 166 - 169: 17.240 distance: 167 - 168: 25.229 distance: 167 - 173: 23.875 distance: 169 - 170: 13.491 distance: 170 - 171: 9.100 distance: 170 - 172: 7.001 distance: 173 - 174: 16.767 distance: 174 - 175: 25.780 distance: 175 - 176: 6.047 distance: 175 - 177: 37.854 distance: 177 - 178: 16.778 distance: 177 - 183: 11.374 distance: 178 - 179: 22.863 distance: 178 - 181: 8.482 distance: 179 - 180: 11.824 distance: 179 - 184: 11.735 distance: 181 - 182: 40.388 distance: 182 - 183: 28.030 distance: 184 - 185: 10.665 distance: 185 - 186: 8.058 distance: 185 - 188: 8.733 distance: 186 - 187: 19.292 distance: 186 - 189: 4.845 distance: 189 - 190: 3.896 distance: 190 - 191: 5.571 distance: 190 - 193: 12.148 distance: 191 - 192: 7.614 distance: 191 - 196: 6.492 distance: 193 - 194: 16.514 distance: 193 - 195: 24.083