Starting phenix.real_space_refine on Tue Aug 26 05:05:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvr_35047/08_2025/8hvr_35047_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvr_35047/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hvr_35047/08_2025/8hvr_35047_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvr_35047/08_2025/8hvr_35047_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hvr_35047/08_2025/8hvr_35047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvr_35047/08_2025/8hvr_35047.map" } resolution = 3.35 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= 0.002 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): 0.03s 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: 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: 7.60, per 1000 atoms: 0.22 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.55 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: 9.06 Time building geometry restraints manager: 3.94 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: 3.050 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 40.860 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.490 ------------------------------------------------------------------------------- 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 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: -0.66 (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 ARG 0.011 0.000 ARG D 146 TYR 0.032 0.001 TYR I 236 PHE 0.023 0.002 PHE F 436 TRP 0.050 0.003 TRP F 333 HIS 0.009 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00387 (34720) covalent geometry : angle 0.71526 (47485) hydrogen bonds : bond 0.15490 ( 1592) hydrogen bonds : angle 6.31914 ( 4484) metal coordination : bond 0.00840 ( 8) metal coordination : angle 7.10675 ( 12) *********************** 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 : 1.292 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: 0.2239 time to fit residues: 143.7192 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 : 1.385 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0060 overall best weight: 0.6876 ------------------------------------------------------------------------------- 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 C1020 HIS ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 ASN D 849 HIS D 949 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.194951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.162365 restraints weight = 46503.788| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.65 r_work: 0.3593 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34728 Z= 0.142 Angle : 0.603 14.585 47497 Z= 0.308 Chirality : 0.041 0.315 5404 Planarity : 0.004 0.070 5820 Dihedral : 16.411 178.178 5747 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.92 % Allowed : 8.77 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.13), residues: 4019 helix: 0.78 (0.12), residues: 1774 sheet: -0.53 (0.25), residues: 422 loop : -0.74 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 62 TYR 0.016 0.001 TYR C1014 PHE 0.025 0.001 PHE D1169 TRP 0.024 0.002 TRP C 199 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00322 (34720) covalent geometry : angle 0.59387 (47485) hydrogen bonds : bond 0.04456 ( 1592) hydrogen bonds : angle 4.70255 ( 4484) metal coordination : bond 0.00681 ( 8) metal coordination : angle 6.61384 ( 12) *********************** 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 374 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 343 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8356 (ptpp) cc_final: 0.8058 (ptpp) REVERT: C 1014 TYR cc_start: 0.8998 (t80) cc_final: 0.8771 (t80) REVERT: D 576 MET cc_start: 0.6628 (ppp) cc_final: 0.4022 (tpt) REVERT: D 690 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: D 809 MET cc_start: 0.7620 (mmm) cc_final: 0.7402 (mmm) REVERT: D 1254 ARG cc_start: 0.7790 (ttp-110) cc_final: 0.7527 (ttp80) outliers start: 31 outliers final: 14 residues processed: 358 average time/residue: 0.2235 time to fit residues: 132.6269 Evaluate side-chains 307 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 292 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain H residue 154 LEU 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 387 optimal weight: 50.0000 chunk 86 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 chunk 381 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 chunk 408 optimal weight: 7.9990 chunk 198 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 648 ASN C1020 HIS D 747 GLN D 849 HIS D 949 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.195056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.161795 restraints weight = 46121.839| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.71 r_work: 0.3589 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34728 Z= 0.124 Angle : 0.580 21.877 47497 Z= 0.292 Chirality : 0.041 0.351 5404 Planarity : 0.004 0.051 5820 Dihedral : 16.563 178.745 5747 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.43 % Allowed : 10.68 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.13), residues: 4019 helix: 1.15 (0.12), residues: 1767 sheet: -0.45 (0.25), residues: 422 loop : -0.64 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 113 TYR 0.016 0.001 TYR I 236 PHE 0.018 0.001 PHE D1169 TRP 0.023 0.002 TRP I 154 HIS 0.005 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00282 (34720) covalent geometry : angle 0.57061 (47485) hydrogen bonds : bond 0.03820 ( 1592) hydrogen bonds : angle 4.40920 ( 4484) metal coordination : bond 0.00635 ( 8) metal coordination : angle 6.44953 ( 12) *********************** 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 380 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 332 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: C 986 MET cc_start: 0.8630 (ttm) cc_final: 0.8257 (ttm) REVERT: C 1014 TYR cc_start: 0.9013 (t80) cc_final: 0.8744 (t80) REVERT: D 690 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: D 747 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5185 (tt0) REVERT: D 1175 ARG cc_start: 0.7055 (ttp-170) cc_final: 0.6788 (ttt180) REVERT: D 1254 ARG cc_start: 0.7766 (ttp-110) cc_final: 0.7518 (ttp80) REVERT: E 83 GLU cc_start: 0.7072 (pm20) cc_final: 0.6773 (pm20) REVERT: K 256 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5450 (pt) outliers start: 48 outliers final: 26 residues processed: 362 average time/residue: 0.2167 time to fit residues: 128.7724 Evaluate side-chains 322 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 B residue 217 GLU Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 741 HIS 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 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 504 LEU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 1021 GLN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain E residue 82 SER 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 G residue 82 HIS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 110 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 292 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 409 optimal weight: 10.0000 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN D 375 GLN D 494 HIS D 747 GLN D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.192952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.158491 restraints weight = 45781.483| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.72 r_work: 0.3538 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34728 Z= 0.168 Angle : 0.610 18.532 47497 Z= 0.305 Chirality : 0.042 0.286 5404 Planarity : 0.004 0.052 5820 Dihedral : 16.589 179.629 5747 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.91 % Allowed : 13.07 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.13), residues: 4019 helix: 1.21 (0.12), residues: 1775 sheet: -0.48 (0.25), residues: 436 loop : -0.67 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 146 TYR 0.016 0.001 TYR I 236 PHE 0.014 0.001 PHE D1169 TRP 0.021 0.002 TRP I 154 HIS 0.004 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00402 (34720) covalent geometry : angle 0.59964 (47485) hydrogen bonds : bond 0.03866 ( 1592) hydrogen bonds : angle 4.35091 ( 4484) metal coordination : bond 0.00906 ( 8) metal coordination : angle 7.00074 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 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 371 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: C 741 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7715 (p-80) REVERT: C 986 MET cc_start: 0.8666 (ttm) cc_final: 0.8375 (tpp) REVERT: C 1014 TYR cc_start: 0.9108 (t80) cc_final: 0.8894 (t80) REVERT: D 415 GLN cc_start: 0.7804 (tt0) cc_final: 0.7518 (tt0) REVERT: D 606 SER cc_start: 0.8927 (t) cc_final: 0.8615 (m) REVERT: D 1175 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6757 (ttt180) REVERT: E 83 GLU cc_start: 0.7243 (pm20) cc_final: 0.6799 (pm20) REVERT: I 220 MET cc_start: 0.5329 (mmp) cc_final: 0.5117 (mmp) REVERT: K 264 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.5190 (pp) outliers start: 64 outliers final: 38 residues processed: 349 average time/residue: 0.1883 time to fit residues: 108.8358 Evaluate side-chains 335 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 294 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 124 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 196 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 398 ILE 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 741 HIS 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 818 VAL 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 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 787 ASN Chi-restraints excluded: chain D residue 849 HIS Chi-restraints excluded: chain D residue 1021 GLN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 308 ASN 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 154 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 408 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 391 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 251 optimal weight: 0.1980 chunk 185 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 326 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 600 GLN C1020 HIS D 564 ASN D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.191514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155974 restraints weight = 46005.611| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.85 r_work: 0.3482 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 34728 Z= 0.194 Angle : 0.628 16.607 47497 Z= 0.313 Chirality : 0.043 0.320 5404 Planarity : 0.004 0.051 5820 Dihedral : 16.633 178.795 5747 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.30 % Allowed : 13.63 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.13), residues: 4019 helix: 1.29 (0.12), residues: 1755 sheet: -0.45 (0.25), residues: 436 loop : -0.70 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 819 TYR 0.019 0.001 TYR F 399 PHE 0.018 0.001 PHE D 138 TRP 0.023 0.002 TRP F 333 HIS 0.023 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00468 (34720) covalent geometry : angle 0.61752 (47485) hydrogen bonds : bond 0.04006 ( 1592) hydrogen bonds : angle 4.36186 ( 4484) metal coordination : bond 0.01068 ( 8) metal coordination : angle 7.17740 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 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 382 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 305 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: C 741 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7649 (p-80) REVERT: C 986 MET cc_start: 0.8711 (ttm) cc_final: 0.8442 (tpp) REVERT: C 1014 TYR cc_start: 0.9117 (t80) cc_final: 0.8895 (t80) REVERT: D 415 GLN cc_start: 0.7923 (tt0) cc_final: 0.7597 (tt0) REVERT: D 957 ARG cc_start: 0.8632 (ttm170) cc_final: 0.8414 (ttm170) REVERT: D 1254 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7523 (ttp80) outliers start: 77 outliers final: 51 residues processed: 354 average time/residue: 0.2245 time to fit residues: 131.6023 Evaluate side-chains 343 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 398 ILE 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 741 HIS Chi-restraints excluded: chain C residue 743 VAL 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 818 VAL 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 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 787 ASN 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 82 SER Chi-restraints excluded: chain F residue 280 GLU 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 154 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 69 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 404 optimal weight: 10.0000 chunk 370 optimal weight: 8.9990 chunk 112 optimal weight: 0.0020 chunk 178 optimal weight: 0.0470 chunk 255 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 GLN C1020 HIS D 949 HIS F 308 ASN ** G 82 HIS ** 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 = 0.4318 r_free = 0.4318 target = 0.194286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158613 restraints weight = 45851.738| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.77 r_work: 0.3566 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34728 Z= 0.118 Angle : 0.579 15.609 47497 Z= 0.290 Chirality : 0.040 0.161 5404 Planarity : 0.004 0.058 5820 Dihedral : 16.605 178.402 5747 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.76 % Allowed : 15.30 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.13), residues: 4019 helix: 1.43 (0.12), residues: 1769 sheet: -0.35 (0.26), residues: 407 loop : -0.65 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1174 TYR 0.017 0.001 TYR I 236 PHE 0.014 0.001 PHE A 30 TRP 0.028 0.001 TRP I 154 HIS 0.024 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00267 (34720) covalent geometry : angle 0.56984 (47485) hydrogen bonds : bond 0.03516 ( 1592) hydrogen bonds : angle 4.21621 ( 4484) metal coordination : bond 0.00518 ( 8) metal coordination : angle 6.40085 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 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 367 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: C 202 MET cc_start: 0.8378 (mtt) cc_final: 0.8127 (mtt) REVERT: C 359 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8531 (t80) REVERT: C 741 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.7632 (p-80) REVERT: D 415 GLN cc_start: 0.7672 (tt0) cc_final: 0.7452 (tt0) REVERT: E 68 LEU cc_start: 0.8888 (tp) cc_final: 0.8668 (tp) REVERT: F 278 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7024 (tp) outliers start: 59 outliers final: 36 residues processed: 346 average time/residue: 0.2230 time to fit residues: 127.3961 Evaluate side-chains 328 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 359 PHE 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 741 HIS Chi-restraints excluded: chain C residue 743 VAL 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 C residue 978 ILE 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 504 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 1021 GLN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 280 GLU 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 154 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 394 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 chunk 367 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 ASN C 361 ASN C 421 GLN C 493 ASN C 916 GLN ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** 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 = 0.4288 r_free = 0.4288 target = 0.191472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.157224 restraints weight = 45951.469| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.66 r_work: 0.3531 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34728 Z= 0.184 Angle : 0.632 16.826 47497 Z= 0.314 Chirality : 0.043 0.376 5404 Planarity : 0.004 0.048 5820 Dihedral : 16.644 177.309 5747 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.21 % Allowed : 15.16 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.13), residues: 4019 helix: 1.39 (0.12), residues: 1760 sheet: -0.36 (0.25), residues: 430 loop : -0.69 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1174 TYR 0.018 0.001 TYR I 236 PHE 0.016 0.001 PHE A 30 TRP 0.024 0.002 TRP F 333 HIS 0.008 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00444 (34720) covalent geometry : angle 0.62157 (47485) hydrogen bonds : bond 0.03861 ( 1592) hydrogen bonds : angle 4.28695 ( 4484) metal coordination : bond 0.01009 ( 8) metal coordination : angle 7.19122 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 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 371 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 297 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7258 (pt0) REVERT: C 202 MET cc_start: 0.8346 (mtt) cc_final: 0.8127 (mtt) REVERT: C 359 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8571 (t80) REVERT: C 579 MET cc_start: 0.8418 (mmm) cc_final: 0.8037 (mtp) REVERT: C 741 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.7667 (p-80) REVERT: C 1042 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7929 (pp) REVERT: D 415 GLN cc_start: 0.7826 (tt0) cc_final: 0.7575 (tt0) REVERT: D 1254 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7404 (ttp80) REVERT: F 278 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7105 (tp) outliers start: 74 outliers final: 49 residues processed: 345 average time/residue: 0.2278 time to fit residues: 129.4025 Evaluate side-chains 343 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 289 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE 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 741 HIS Chi-restraints excluded: chain C residue 743 VAL 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 818 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 963 ASP Chi-restraints excluded: chain C residue 978 ILE Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 849 HIS Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 308 ASN 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 G residue 75 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 204 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1020 HIS D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** 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 = 0.4295 r_free = 0.4295 target = 0.192132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157344 restraints weight = 45658.655| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.72 r_work: 0.3540 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34728 Z= 0.155 Angle : 0.613 16.924 47497 Z= 0.306 Chirality : 0.042 0.236 5404 Planarity : 0.004 0.047 5820 Dihedral : 16.630 177.065 5747 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.85 % Allowed : 15.78 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.13), residues: 4019 helix: 1.38 (0.12), residues: 1763 sheet: -0.37 (0.25), residues: 422 loop : -0.67 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 262 TYR 0.018 0.001 TYR I 236 PHE 0.020 0.001 PHE A 30 TRP 0.035 0.002 TRP F 333 HIS 0.018 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00370 (34720) covalent geometry : angle 0.60300 (47485) hydrogen bonds : bond 0.03684 ( 1592) hydrogen bonds : angle 4.26499 ( 4484) metal coordination : bond 0.00815 ( 8) metal coordination : angle 6.83706 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 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 357 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: C 202 MET cc_start: 0.8337 (mtt) cc_final: 0.8107 (mtt) REVERT: C 213 ARG cc_start: 0.6387 (mmp-170) cc_final: 0.6186 (mmp-170) REVERT: C 359 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8628 (t80) REVERT: C 579 MET cc_start: 0.8464 (mmm) cc_final: 0.8045 (mtp) REVERT: C 741 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.7709 (p-80) REVERT: C 1042 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7888 (pp) REVERT: D 415 GLN cc_start: 0.7788 (tt0) cc_final: 0.7548 (tt0) REVERT: D 1254 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7431 (ttp80) REVERT: F 278 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7045 (tp) REVERT: G 87 MET cc_start: 0.7569 (mpp) cc_final: 0.7324 (mpp) outliers start: 62 outliers final: 51 residues processed: 337 average time/residue: 0.2237 time to fit residues: 124.7482 Evaluate side-chains 343 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 367 VAL 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 741 HIS Chi-restraints excluded: chain C residue 743 VAL 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 818 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 978 ILE Chi-restraints excluded: chain C residue 1042 LEU 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 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 849 HIS Chi-restraints excluded: chain D residue 1021 GLN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 298 MET 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 G residue 62 GLN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 240 optimal weight: 1.9990 chunk 391 optimal weight: 30.0000 chunk 123 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 279 optimal weight: 0.0970 chunk 370 optimal weight: 20.0000 chunk 257 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1020 HIS D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** G 82 HIS ** 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 = 0.4294 r_free = 0.4294 target = 0.192171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.156016 restraints weight = 45622.787| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.81 r_work: 0.3509 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2280 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= 0.151 Angle : 0.620 16.501 47497 Z= 0.307 Chirality : 0.042 0.257 5404 Planarity : 0.004 0.047 5820 Dihedral : 16.613 176.808 5747 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.88 % Allowed : 15.90 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.13), residues: 4019 helix: 1.40 (0.12), residues: 1763 sheet: -0.49 (0.25), residues: 430 loop : -0.64 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 262 TYR 0.018 0.001 TYR I 236 PHE 0.022 0.001 PHE A 30 TRP 0.030 0.002 TRP F 333 HIS 0.004 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00359 (34720) covalent geometry : angle 0.61087 (47485) hydrogen bonds : bond 0.03653 ( 1592) hydrogen bonds : angle 4.25498 ( 4484) metal coordination : bond 0.00779 ( 8) metal coordination : angle 6.73651 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 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 365 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: C 202 MET cc_start: 0.8354 (mtt) cc_final: 0.8124 (mtt) REVERT: C 213 ARG cc_start: 0.6490 (mmp-170) cc_final: 0.6288 (mmp-170) REVERT: C 359 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8624 (t80) REVERT: C 579 MET cc_start: 0.8477 (mmm) cc_final: 0.8043 (mtp) REVERT: C 741 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.7677 (p-80) REVERT: C 1042 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7888 (pp) REVERT: D 415 GLN cc_start: 0.7810 (tt0) cc_final: 0.7579 (tt0) REVERT: D 1006 MET cc_start: 0.5702 (tpp) cc_final: 0.3453 (mtt) REVERT: D 1254 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7444 (ttp80) REVERT: F 278 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7148 (tp) outliers start: 63 outliers final: 54 residues processed: 344 average time/residue: 0.2264 time to fit residues: 128.9498 Evaluate side-chains 348 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 289 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 367 VAL 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 741 HIS Chi-restraints excluded: chain C residue 743 VAL 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 C residue 978 ILE Chi-restraints excluded: chain C residue 1042 LEU 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 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 849 HIS Chi-restraints excluded: chain D residue 1021 GLN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1233 GLU Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 298 MET 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 G residue 62 GLN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 214 optimal weight: 1.9990 chunk 387 optimal weight: 50.0000 chunk 153 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 chunk 194 optimal weight: 0.0670 chunk 169 optimal weight: 5.9990 chunk 391 optimal weight: 30.0000 chunk 327 optimal weight: 0.0270 chunk 351 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1020 HIS D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.194089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159982 restraints weight = 46234.273| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.66 r_work: 0.3582 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34728 Z= 0.122 Angle : 0.608 16.043 47497 Z= 0.303 Chirality : 0.041 0.225 5404 Planarity : 0.004 0.059 5820 Dihedral : 16.561 176.728 5747 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.79 % Allowed : 16.41 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.13), residues: 4019 helix: 1.43 (0.12), residues: 1774 sheet: -0.39 (0.25), residues: 422 loop : -0.60 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D1174 TYR 0.017 0.001 TYR I 236 PHE 0.014 0.001 PHE C 141 TRP 0.049 0.002 TRP F 333 HIS 0.007 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00277 (34720) covalent geometry : angle 0.59984 (47485) hydrogen bonds : bond 0.03444 ( 1592) hydrogen bonds : angle 4.21113 ( 4484) metal coordination : bond 0.00542 ( 8) metal coordination : angle 6.32109 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 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: 60 poor density : 310 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7666 (t) REVERT: B 217 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7084 (pt0) REVERT: C 213 ARG cc_start: 0.6358 (mmp-170) cc_final: 0.6157 (mmp-170) REVERT: C 359 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8609 (t80) REVERT: C 719 ASP cc_start: 0.6748 (t0) cc_final: 0.6542 (t0) REVERT: C 741 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.7646 (p-80) REVERT: C 1014 TYR cc_start: 0.9019 (t80) cc_final: 0.8796 (t80) REVERT: C 1042 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7728 (pp) REVERT: D 415 GLN cc_start: 0.7600 (tt0) cc_final: 0.7369 (tt0) REVERT: D 504 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8908 (mt) REVERT: D 1006 MET cc_start: 0.5576 (tpp) cc_final: 0.3420 (mtt) REVERT: D 1254 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.7402 (ttp80) REVERT: F 278 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7009 (tp) outliers start: 60 outliers final: 50 residues processed: 348 average time/residue: 0.2260 time to fit residues: 129.5765 Evaluate side-chains 354 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 367 VAL 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 741 HIS Chi-restraints excluded: chain C residue 743 VAL 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 C residue 978 ILE Chi-restraints excluded: chain C residue 1042 LEU 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 366 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 849 HIS Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1233 GLU Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 298 MET Chi-restraints excluded: chain F residue 308 ASN Chi-restraints excluded: chain F residue 333 TRP 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 G residue 62 GLN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 259 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 279 optimal weight: 0.0020 chunk 340 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 185 optimal weight: 0.5980 chunk 299 optimal weight: 9.9990 chunk 344 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 944 GLN C1020 HIS D 849 HIS D 949 HIS ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.194130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161640 restraints weight = 45876.103| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.51 r_work: 0.3625 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34728 Z= 0.123 Angle : 0.607 15.938 47497 Z= 0.303 Chirality : 0.041 0.198 5404 Planarity : 0.004 0.055 5820 Dihedral : 16.532 176.455 5747 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.82 % Allowed : 16.47 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.13), residues: 4019 helix: 1.45 (0.13), residues: 1774 sheet: -0.35 (0.25), residues: 412 loop : -0.57 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D1174 TYR 0.018 0.001 TYR I 236 PHE 0.028 0.001 PHE A 30 TRP 0.045 0.002 TRP F 333 HIS 0.011 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00281 (34720) covalent geometry : angle 0.59937 (47485) hydrogen bonds : bond 0.03439 ( 1592) hydrogen bonds : angle 4.19496 ( 4484) metal coordination : bond 0.00557 ( 8) metal coordination : angle 6.22744 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7291.57 seconds wall clock time: 126 minutes 27.10 seconds (7587.10 seconds total)