Starting phenix.real_space_refine on Sat Jun 21 18:59:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgg_34738/06_2025/8hgg_34738.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgg_34738/06_2025/8hgg_34738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgg_34738/06_2025/8hgg_34738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgg_34738/06_2025/8hgg_34738.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgg_34738/06_2025/8hgg_34738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgg_34738/06_2025/8hgg_34738.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 220 5.16 5 C 15916 2.51 5 N 4454 2.21 5 O 4812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25404 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "B" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "C" Number of atoms: 11600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1484, 11600 Classifications: {'peptide': 1484} Link IDs: {'PTRANS': 97, 'TRANS': 1386} Chain breaks: 3 Chain: "D" Number of atoms: 11600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1484, 11600 Classifications: {'peptide': 1484} Link IDs: {'PTRANS': 97, 'TRANS': 1386} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.29, per 1000 atoms: 0.56 Number of scatterers: 25404 At special positions: 0 Unit cell: (247.22, 160.956, 124.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 220 16.00 O 4812 8.00 N 4454 7.00 C 15916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=82, symmetry=0 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.04 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS D 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 107 " distance=2.04 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 247 " - pdb=" SG CYS C 507 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 633 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 673 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 695 " - pdb=" SG CYS C 701 " distance=2.03 Simple disulfide: pdb=" SG CYS C 867 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 880 " - pdb=" SG CYS C 891 " distance=2.03 Simple disulfide: pdb=" SG CYS C 903 " - pdb=" SG CYS C 910 " distance=2.04 Simple disulfide: pdb=" SG CYS C 919 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C 956 " - pdb=" SG CYS C 990 " distance=2.03 Simple disulfide: pdb=" SG CYS C 971 " - pdb=" SG CYS C1059 " distance=2.03 Simple disulfide: pdb=" SG CYS C1135 " - pdb=" SG CYS C1189 " distance=2.03 Simple disulfide: pdb=" SG CYS C1147 " - pdb=" SG CYS C1158 " distance=2.03 Simple disulfide: pdb=" SG CYS C1162 " - pdb=" SG CYS C1200 " distance=2.03 Simple disulfide: pdb=" SG CYS C1205 " - pdb=" SG CYS C1249 " distance=2.03 Simple disulfide: pdb=" SG CYS C1220 " - pdb=" SG CYS C1230 " distance=2.03 Simple disulfide: pdb=" SG CYS C1234 " - pdb=" SG CYS C1262 " distance=2.03 Simple disulfide: pdb=" SG CYS C1266 " - pdb=" SG CYS C1319 " distance=2.03 Simple disulfide: pdb=" SG CYS C1282 " - pdb=" SG CYS C1293 " distance=2.03 Simple disulfide: pdb=" SG CYS C1297 " - pdb=" SG CYS C1330 " distance=2.03 Simple disulfide: pdb=" SG CYS C1335 " - pdb=" SG CYS C1378 " distance=2.03 Simple disulfide: pdb=" SG CYS C1348 " - pdb=" SG CYS C1358 " distance=2.03 Simple disulfide: pdb=" SG CYS C1412 " - pdb=" SG CYS C1422 " distance=2.03 Simple disulfide: pdb=" SG CYS C1426 " - pdb=" SG CYS C1474 " distance=2.04 Simple disulfide: pdb=" SG CYS C1478 " - pdb=" SG CYS C1496 " distance=2.03 Simple disulfide: pdb=" SG CYS C1487 " - pdb=" SG CYS C1503 " distance=2.03 Simple disulfide: pdb=" SG CYS C1504 " - pdb=" SG CYS C1528 " distance=2.03 Simple disulfide: pdb=" SG CYS C1520 " - pdb=" SG CYS C1526 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 155 " distance=2.03 Simple disulfide: pdb=" SG CYS D 247 " - pdb=" SG CYS D 507 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 334 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 360 " distance=2.03 Simple disulfide: pdb=" SG CYS D 377 " - pdb=" SG CYS D 393 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 405 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 532 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 630 " - pdb=" SG CYS D 801 " distance=2.03 Simple disulfide: pdb=" SG CYS D 633 " - pdb=" SG CYS D 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 673 " - pdb=" SG CYS D 755 " distance=2.03 Simple disulfide: pdb=" SG CYS D 695 " - pdb=" SG CYS D 701 " distance=2.03 Simple disulfide: pdb=" SG CYS D 867 " - pdb=" SG CYS D 895 " distance=2.03 Simple disulfide: pdb=" SG CYS D 880 " - pdb=" SG CYS D 891 " distance=2.03 Simple disulfide: pdb=" SG CYS D 903 " - pdb=" SG CYS D 910 " distance=2.03 Simple disulfide: pdb=" SG CYS D 919 " - pdb=" SG CYS D 931 " distance=2.03 Simple disulfide: pdb=" SG CYS D 956 " - pdb=" SG CYS D 990 " distance=2.03 Simple disulfide: pdb=" SG CYS D 971 " - pdb=" SG CYS D1059 " distance=2.03 Simple disulfide: pdb=" SG CYS D1135 " - pdb=" SG CYS D1189 " distance=2.03 Simple disulfide: pdb=" SG CYS D1147 " - pdb=" SG CYS D1158 " distance=2.03 Simple disulfide: pdb=" SG CYS D1162 " - pdb=" SG CYS D1200 " distance=2.03 Simple disulfide: pdb=" SG CYS D1205 " - pdb=" SG CYS D1249 " distance=2.03 Simple disulfide: pdb=" SG CYS D1220 " - pdb=" SG CYS D1230 " distance=2.03 Simple disulfide: pdb=" SG CYS D1234 " - pdb=" SG CYS D1262 " distance=2.03 Simple disulfide: pdb=" SG CYS D1266 " - pdb=" SG CYS D1319 " distance=2.03 Simple disulfide: pdb=" SG CYS D1282 " - pdb=" SG CYS D1293 " distance=2.03 Simple disulfide: pdb=" SG CYS D1297 " - pdb=" SG CYS D1330 " distance=2.03 Simple disulfide: pdb=" SG CYS D1335 " - pdb=" SG CYS D1378 " distance=2.03 Simple disulfide: pdb=" SG CYS D1348 " - pdb=" SG CYS D1358 " distance=2.03 Simple disulfide: pdb=" SG CYS D1412 " - pdb=" SG CYS D1422 " distance=2.03 Simple disulfide: pdb=" SG CYS D1426 " - pdb=" SG CYS D1474 " distance=2.04 Simple disulfide: pdb=" SG CYS D1478 " - pdb=" SG CYS D1496 " distance=2.03 Simple disulfide: pdb=" SG CYS D1487 " - pdb=" SG CYS D1503 " distance=2.03 Simple disulfide: pdb=" SG CYS D1504 " - pdb=" SG CYS D1528 " distance=2.03 Simple disulfide: pdb=" SG CYS D1520 " - pdb=" SG CYS D1526 " distance=2.04 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: 5.51 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1601 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 492 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 482 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 486 " pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" NE2 HIS D 492 " pdb="ZN ZN D1601 " - pdb=" NE2 HIS D 482 " pdb="ZN ZN D1601 " - pdb=" NE2 HIS D 486 " 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 12.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.781A pdb=" N ASN A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.777A pdb=" N ASN B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.541A pdb=" N GLN C 153 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 254 through 264 removed outlier: 3.853A pdb=" N SER C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 322 through 328 removed outlier: 3.562A pdb=" N ARG C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.672A pdb=" N ILE C 339 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.655A pdb=" N GLY C 357 " --> pdb=" O THR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 removed outlier: 4.012A pdb=" N GLY C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 391' Processing helix chain 'C' and resid 400 through 405 removed outlier: 3.586A pdb=" N THR C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.803A pdb=" N ASN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 478 through 488 Processing helix chain 'C' and resid 492 through 496 removed outlier: 4.273A pdb=" N GLY C 496 " --> pdb=" O VAL C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 582 Processing helix chain 'C' and resid 815 through 821 removed outlier: 3.539A pdb=" N ILE C 821 " --> pdb=" O ASP C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 877 removed outlier: 3.621A pdb=" N GLN C 876 " --> pdb=" O GLN C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 924 removed outlier: 3.824A pdb=" N GLN C 924 " --> pdb=" O GLU C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 985 removed outlier: 3.842A pdb=" N GLN C 984 " --> pdb=" O GLY C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1105 through 1110 removed outlier: 3.726A pdb=" N SER C1110 " --> pdb=" O PRO C1106 " (cutoff:3.500A) Processing helix chain 'C' and resid 1280 through 1284 removed outlier: 3.522A pdb=" N GLU C1284 " --> pdb=" O ARG C1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 1339 through 1343 Processing helix chain 'C' and resid 1493 through 1495 No H-bonds generated for 'chain 'C' and resid 1493 through 1495' Processing helix chain 'C' and resid 1496 through 1502 removed outlier: 3.502A pdb=" N ASP C1502 " --> pdb=" O TYR C1498 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.537A pdb=" N GLN D 153 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.827A pdb=" N SER D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 322 through 328 removed outlier: 3.566A pdb=" N ARG D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.670A pdb=" N ILE D 339 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 358 removed outlier: 3.687A pdb=" N GLY D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 391 removed outlier: 4.030A pdb=" N GLY D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 391 " --> pdb=" O ASN D 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 391' Processing helix chain 'D' and resid 400 through 405 removed outlier: 3.598A pdb=" N THR D 404 " --> pdb=" O ASN D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 426 removed outlier: 3.796A pdb=" N ASN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 424 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 Processing helix chain 'D' and resid 478 through 488 Processing helix chain 'D' and resid 492 through 496 removed outlier: 4.285A pdb=" N GLY D 496 " --> pdb=" O VAL D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 582 Processing helix chain 'D' and resid 815 through 821 removed outlier: 3.544A pdb=" N ILE D 821 " --> pdb=" O ASP D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 877 removed outlier: 3.628A pdb=" N GLN D 876 " --> pdb=" O GLN D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 924 removed outlier: 3.779A pdb=" N GLN D 924 " --> pdb=" O GLU D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 985 removed outlier: 3.843A pdb=" N GLN D 984 " --> pdb=" O GLY D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1000 Processing helix chain 'D' and resid 1105 through 1110 removed outlier: 3.719A pdb=" N SER D1110 " --> pdb=" O PRO D1106 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1284 removed outlier: 3.517A pdb=" N GLU D1284 " --> pdb=" O ARG D1281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1339 through 1343 removed outlier: 3.625A pdb=" N HIS D1343 " --> pdb=" O PRO D1340 " (cutoff:3.500A) Processing helix chain 'D' and resid 1493 through 1495 No H-bonds generated for 'chain 'D' and resid 1493 through 1495' Processing helix chain 'D' and resid 1496 through 1501 removed outlier: 3.520A pdb=" N GLY D1500 " --> pdb=" O CYS D1496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 5.626A pdb=" N SER A 114 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A 216 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.758A pdb=" N ILE A 159 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL A 198 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 98 removed outlier: 5.626A pdb=" N SER B 114 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU B 216 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 174 removed outlier: 3.754A pdb=" N ILE B 159 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL B 198 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 135 through 140 removed outlier: 5.413A pdb=" N GLN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 132 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 138 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 135 through 140 removed outlier: 5.413A pdb=" N GLN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 132 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 138 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS C 227 " --> pdb=" O TYR C 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.566A pdb=" N TRP C 73 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 77 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL C 56 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 311 through 321 removed outlier: 5.154A pdb=" N PHE C 437 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU C 280 " --> pdb=" O PHE C 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 331 removed outlier: 5.893A pdb=" N LEU C 329 " --> pdb=" O LEU C 416 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 600 through 604 removed outlier: 5.217A pdb=" N VAL C 601 " --> pdb=" O GLU C 612 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 612 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 603 " --> pdb=" O THR C 610 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 609 " --> pdb=" O ASP C 830 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 830 " --> pdb=" O VAL C 609 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 640 through 642 removed outlier: 6.572A pdb=" N GLU C 783 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP C 719 " --> pdb=" O ASP C 785 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA C 787 " --> pdb=" O THR C 717 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 717 " --> pdb=" O ALA C 787 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 789 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 715 " --> pdb=" O LEU C 789 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER C 791 " --> pdb=" O PRO C 713 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 645 through 647 removed outlier: 6.163A pdb=" N TYR C 771 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY C 772 " --> pdb=" O LEU C 739 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 735 " --> pdb=" O TYR C 776 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 736 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 805 through 810 Processing sheet with id=AB5, first strand: chain 'C' and resid 901 through 903 Processing sheet with id=AB6, first strand: chain 'C' and resid 939 through 943 removed outlier: 5.688A pdb=" N VAL C1091 " --> pdb=" O ASP C1026 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASP C1026 " --> pdb=" O VAL C1091 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE C1093 " --> pdb=" O VAL C1024 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C1024 " --> pdb=" O ILE C1093 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C1095 " --> pdb=" O HIS C1022 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C1018 " --> pdb=" O ARG C1099 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 945 through 949 removed outlier: 4.989A pdb=" N ASN C 946 " --> pdb=" O TYR C1009 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR C1009 " --> pdb=" O ASN C 946 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N ALA C1008 " --> pdb=" O SER C1085 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N SER C1085 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 12.371A pdb=" N PHE C1010 " --> pdb=" O ARG C1083 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ARG C1083 " --> pdb=" O PHE C1010 " (cutoff:3.500A) removed outlier: 11.308A pdb=" N GLN C1012 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA C1081 " --> pdb=" O GLN C1012 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET C1014 " --> pdb=" O SER C1079 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C1040 " --> pdb=" O GLY C1053 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C1053 " --> pdb=" O VAL C1040 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C1042 " --> pdb=" O ASP C1051 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASP C1051 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP C1044 " --> pdb=" O SER C1049 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER C1049 " --> pdb=" O ASP C1044 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1069 through 1071 Processing sheet with id=AB9, first strand: chain 'C' and resid 1143 through 1147 Processing sheet with id=AC1, first strand: chain 'C' and resid 1175 through 1176 removed outlier: 3.641A pdb=" N ALA C1199 " --> pdb=" O GLN C1169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1216 through 1219 Processing sheet with id=AC3, first strand: chain 'C' and resid 1238 through 1242 Processing sheet with id=AC4, first strand: chain 'C' and resid 1275 through 1277 Processing sheet with id=AC5, first strand: chain 'C' and resid 1346 through 1348 Processing sheet with id=AC6, first strand: chain 'C' and resid 1408 through 1411 Processing sheet with id=AC7, first strand: chain 'C' and resid 1431 through 1435 Processing sheet with id=AC8, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.421A pdb=" N GLN D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 132 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 138 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.421A pdb=" N GLN D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 132 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 138 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 227 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 103 through 106 removed outlier: 3.568A pdb=" N TRP D 73 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 77 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL D 56 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 311 through 321 removed outlier: 5.141A pdb=" N PHE D 437 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU D 280 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 329 through 331 removed outlier: 5.877A pdb=" N LEU D 329 " --> pdb=" O LEU D 416 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 600 through 604 removed outlier: 5.221A pdb=" N VAL D 601 " --> pdb=" O GLU D 612 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU D 612 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY D 603 " --> pdb=" O THR D 610 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 609 " --> pdb=" O ASP D 830 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP D 830 " --> pdb=" O VAL D 609 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 640 through 642 removed outlier: 6.584A pdb=" N GLU D 783 " --> pdb=" O THR D 721 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP D 719 " --> pdb=" O ASP D 785 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 787 " --> pdb=" O THR D 717 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 717 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU D 789 " --> pdb=" O SER D 715 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER D 715 " --> pdb=" O LEU D 789 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 791 " --> pdb=" O PRO D 713 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 645 through 647 removed outlier: 6.171A pdb=" N TYR D 771 " --> pdb=" O PHE D 707 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 772 " --> pdb=" O LEU D 739 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D 735 " --> pdb=" O TYR D 776 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 736 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 805 through 810 Processing sheet with id=AD8, first strand: chain 'D' and resid 901 through 903 Processing sheet with id=AD9, first strand: chain 'D' and resid 939 through 943 removed outlier: 5.666A pdb=" N VAL D1091 " --> pdb=" O ASP D1026 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASP D1026 " --> pdb=" O VAL D1091 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE D1093 " --> pdb=" O VAL D1024 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL D1024 " --> pdb=" O ILE D1093 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D1095 " --> pdb=" O HIS D1022 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D1018 " --> pdb=" O ARG D1099 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 945 through 949 removed outlier: 4.987A pdb=" N ASN D 946 " --> pdb=" O TYR D1009 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR D1009 " --> pdb=" O ASN D 946 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N ALA D1008 " --> pdb=" O SER D1085 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N SER D1085 " --> pdb=" O ALA D1008 " (cutoff:3.500A) removed outlier: 12.337A pdb=" N PHE D1010 " --> pdb=" O ARG D1083 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ARG D1083 " --> pdb=" O PHE D1010 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N GLN D1012 " --> pdb=" O ALA D1081 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA D1081 " --> pdb=" O GLN D1012 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D1014 " --> pdb=" O SER D1079 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D1040 " --> pdb=" O GLY D1053 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY D1053 " --> pdb=" O VAL D1040 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU D1042 " --> pdb=" O ASP D1051 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASP D1051 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASP D1044 " --> pdb=" O SER D1049 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER D1049 " --> pdb=" O ASP D1044 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1143 through 1147 Processing sheet with id=AE3, first strand: chain 'D' and resid 1175 through 1176 removed outlier: 3.646A pdb=" N ALA D1199 " --> pdb=" O GLN D1169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1216 through 1219 Processing sheet with id=AE5, first strand: chain 'D' and resid 1239 through 1242 removed outlier: 3.760A pdb=" N LYS D1241 " --> pdb=" O LEU D1261 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1275 through 1277 Processing sheet with id=AE7, first strand: chain 'D' and resid 1346 through 1348 Processing sheet with id=AE8, first strand: chain 'D' and resid 1408 through 1411 Processing sheet with id=AE9, first strand: chain 'D' and resid 1431 through 1435 592 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.24 Time building geometry restraints manager: 6.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8173 1.34 - 1.46: 6090 1.46 - 1.58: 11569 1.58 - 1.71: 0 1.71 - 1.83: 264 Bond restraints: 26096 Sorted by residual: bond pdb=" N ILE C1066 " pdb=" CA ILE C1066 " ideal model delta sigma weight residual 1.458 1.489 -0.031 7.70e-03 1.69e+04 1.61e+01 bond pdb=" N TYR D1466 " pdb=" CA TYR D1466 " ideal model delta sigma weight residual 1.462 1.489 -0.026 7.70e-03 1.69e+04 1.18e+01 bond pdb=" N ILE D1472 " pdb=" CA ILE D1472 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" N TYR C1466 " pdb=" CA TYR C1466 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.07e+00 bond pdb=" N TRP C1465 " pdb=" CA TRP C1465 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.57e+00 ... (remaining 26091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 34684 1.72 - 3.44: 736 3.44 - 5.16: 56 5.16 - 6.88: 24 6.88 - 8.60: 18 Bond angle restraints: 35518 Sorted by residual: angle pdb=" CA MET C 473 " pdb=" C MET C 473 " pdb=" O MET C 473 " ideal model delta sigma weight residual 120.19 116.81 3.38 9.30e-01 1.16e+00 1.32e+01 angle pdb=" CA MET D 473 " pdb=" C MET D 473 " pdb=" O MET D 473 " ideal model delta sigma weight residual 120.19 116.83 3.36 9.30e-01 1.16e+00 1.30e+01 angle pdb=" N PRO C1467 " pdb=" CA PRO C1467 " pdb=" C PRO C1467 " ideal model delta sigma weight residual 112.47 105.16 7.31 2.06e+00 2.36e-01 1.26e+01 angle pdb=" C GLU D 442 " pdb=" N GLU D 443 " pdb=" CA GLU D 443 " ideal model delta sigma weight residual 122.61 127.93 -5.32 1.56e+00 4.11e-01 1.16e+01 angle pdb=" C GLU C 442 " pdb=" N GLU C 443 " pdb=" CA GLU C 443 " ideal model delta sigma weight residual 122.61 127.92 -5.31 1.56e+00 4.11e-01 1.16e+01 ... (remaining 35513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.50: 14044 13.50 - 26.99: 1183 26.99 - 40.49: 348 40.49 - 53.98: 121 53.98 - 67.48: 34 Dihedral angle restraints: 15730 sinusoidal: 6366 harmonic: 9364 Sorted by residual: dihedral pdb=" CB CYS B 104 " pdb=" SG CYS B 104 " pdb=" SG CYS B 107 " pdb=" CB CYS B 107 " ideal model delta sinusoidal sigma weight residual 93.00 153.21 -60.21 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 107 " pdb=" CB CYS A 107 " ideal model delta sinusoidal sigma weight residual 93.00 153.18 -60.18 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CB CYS D 252 " pdb=" SG CYS D 252 " pdb=" SG CYS D 577 " pdb=" CB CYS D 577 " ideal model delta sinusoidal sigma weight residual 93.00 152.44 -59.44 1 1.00e+01 1.00e-02 4.72e+01 ... (remaining 15727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2860 0.049 - 0.098: 684 0.098 - 0.147: 224 0.147 - 0.196: 23 0.196 - 0.245: 3 Chirality restraints: 3794 Sorted by residual: chirality pdb=" CA ILE C1065 " pdb=" N ILE C1065 " pdb=" C ILE C1065 " pdb=" CB ILE C1065 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LEU C1064 " pdb=" N LEU C1064 " pdb=" C LEU C1064 " pdb=" CB LEU C1064 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE C1066 " pdb=" N ILE C1066 " pdb=" C ILE C1066 " pdb=" CB ILE C1066 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3791 not shown) Planarity restraints: 4686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C1062 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C ASN C1062 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN C1062 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C1063 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 988 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO C 989 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 989 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 988 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO D 989 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 989 " -0.030 5.00e-02 4.00e+02 ... (remaining 4683 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7236 2.82 - 3.34: 20066 3.34 - 3.86: 41875 3.86 - 4.38: 47884 4.38 - 4.90: 83610 Nonbonded interactions: 200671 Sorted by model distance: nonbonded pdb=" OD1 ASP D 87 " pdb=" OG SER D 110 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP C 87 " pdb=" OG SER C 110 " model vdw 2.299 3.040 nonbonded pdb=" OE1 GLN B 156 " pdb=" OH TYR D1486 " model vdw 2.308 3.040 nonbonded pdb=" O HIS B 188 " pdb=" OG SER B 192 " model vdw 2.327 3.040 nonbonded pdb=" O ASN C 400 " pdb=" OG1 THR C 404 " model vdw 2.327 3.040 ... (remaining 200666 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 61.820 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 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 : 0.003 0.055 26184 Z= 0.176 Angle : 0.620 8.596 35682 Z= 0.340 Chirality : 0.048 0.245 3794 Planarity : 0.006 0.054 4686 Dihedral : 11.942 67.476 9460 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 5.46 % Allowed : 6.69 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3218 helix: -2.74 (0.20), residues: 288 sheet: 0.26 (0.20), residues: 676 loop : -1.08 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 943 HIS 0.006 0.001 HIS D 78 PHE 0.016 0.002 PHE D1232 TYR 0.018 0.002 TYR D 841 ARG 0.003 0.000 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.16723 ( 562) hydrogen bonds : angle 7.09538 ( 1572) metal coordination : bond 0.00559 ( 6) SS BOND : bond 0.00265 ( 82) SS BOND : angle 0.89620 ( 164) covalent geometry : bond 0.00349 (26096) covalent geometry : angle 0.61885 (35518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 390 time to evaluate : 2.490 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: A 180 TRP cc_start: 0.8057 (t-100) cc_final: 0.7834 (t-100) REVERT: B 145 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8325 (mm) REVERT: B 180 TRP cc_start: 0.8169 (t-100) cc_final: 0.7885 (t-100) REVERT: C 22 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7183 (mmp80) REVERT: C 51 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7723 (mm-40) REVERT: C 70 ASP cc_start: 0.7592 (p0) cc_final: 0.7387 (p0) REVERT: C 204 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8014 (tp) REVERT: C 222 ASP cc_start: 0.3973 (OUTLIER) cc_final: 0.3683 (t0) REVERT: C 330 ILE cc_start: 0.8252 (mm) cc_final: 0.7825 (mt) REVERT: C 534 ASP cc_start: 0.5954 (m-30) cc_final: 0.5637 (t0) REVERT: C 668 ASP cc_start: 0.7675 (p0) cc_final: 0.7409 (p0) REVERT: C 842 TRP cc_start: 0.7015 (p90) cc_final: 0.6766 (p90) REVERT: C 975 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7694 (p) REVERT: C 1102 ASP cc_start: 0.6598 (p0) cc_final: 0.6153 (p0) REVERT: D 51 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7327 (mm-40) REVERT: D 204 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7917 (tp) REVERT: D 330 ILE cc_start: 0.8287 (mm) cc_final: 0.7886 (mt) REVERT: D 644 SER cc_start: 0.7933 (m) cc_final: 0.7655 (m) REVERT: D 668 ASP cc_start: 0.7652 (p0) cc_final: 0.7394 (p0) REVERT: D 842 TRP cc_start: 0.7048 (p90) cc_final: 0.6810 (p90) REVERT: D 953 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6698 (t0) REVERT: D 975 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7622 (p) REVERT: D 1102 ASP cc_start: 0.6712 (p0) cc_final: 0.6296 (p0) outliers start: 155 outliers final: 48 residues processed: 516 average time/residue: 0.3563 time to fit residues: 292.7800 Evaluate side-chains 300 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1252 ASP Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 558 TYR Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 953 ASP Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 976 ILE Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1331 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 292 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 156 GLN B 142 ASN B 156 GLN C 78 HIS C 85 ASN C 294 GLN C 374 ASN C 403 GLN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN C 683 ASN C 985 HIS D 78 HIS D 153 GLN D 294 GLN D 365 HIS D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN D 683 ASN D 985 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.222442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.215953 restraints weight = 32929.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.202006 restraints weight = 63495.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.198216 restraints weight = 56312.727| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 26184 Z= 0.199 Angle : 0.602 7.684 35682 Z= 0.314 Chirality : 0.046 0.156 3794 Planarity : 0.005 0.066 4686 Dihedral : 6.795 57.927 3584 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.81 % Allowed : 10.15 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3218 helix: -1.68 (0.26), residues: 304 sheet: -0.06 (0.20), residues: 660 loop : -0.89 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 658 HIS 0.008 0.001 HIS D 529 PHE 0.021 0.002 PHE D 236 TYR 0.022 0.002 TYR C 471 ARG 0.005 0.000 ARG D1007 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 562) hydrogen bonds : angle 5.57440 ( 1572) metal coordination : bond 0.01022 ( 6) SS BOND : bond 0.00388 ( 82) SS BOND : angle 1.46428 ( 164) covalent geometry : bond 0.00467 (26096) covalent geometry : angle 0.59477 (35518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 247 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 TRP cc_start: 0.8134 (t-100) cc_final: 0.7915 (t-100) REVERT: C 51 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7611 (mm-40) REVERT: C 67 ILE cc_start: 0.5165 (OUTLIER) cc_final: 0.4951 (pt) REVERT: C 330 ILE cc_start: 0.8241 (mm) cc_final: 0.7826 (mt) REVERT: C 403 GLN cc_start: 0.6376 (tp40) cc_final: 0.6063 (tt0) REVERT: C 842 TRP cc_start: 0.7354 (p90) cc_final: 0.7060 (p90) REVERT: C 975 VAL cc_start: 0.7951 (p) cc_final: 0.7737 (p) REVERT: C 1026 ASP cc_start: 0.7787 (m-30) cc_final: 0.7585 (m-30) REVERT: C 1030 TYR cc_start: 0.7295 (p90) cc_final: 0.7013 (p90) REVERT: C 1518 MET cc_start: 0.5351 (tpt) cc_final: 0.5150 (tpt) REVERT: D 51 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7492 (mm-40) REVERT: D 67 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.5018 (pt) REVERT: D 330 ILE cc_start: 0.8224 (mm) cc_final: 0.7846 (mt) REVERT: D 389 ASP cc_start: 0.5076 (t0) cc_final: 0.4840 (t0) REVERT: D 403 GLN cc_start: 0.6345 (tp40) cc_final: 0.5961 (tt0) REVERT: D 842 TRP cc_start: 0.7342 (p90) cc_final: 0.7054 (p90) REVERT: D 1030 TYR cc_start: 0.7264 (p90) cc_final: 0.6980 (p90) REVERT: D 1518 MET cc_start: 0.5226 (tpt) cc_final: 0.5017 (tpt) outliers start: 108 outliers final: 58 residues processed: 333 average time/residue: 0.3244 time to fit residues: 181.3136 Evaluate side-chains 280 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 218 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 558 TYR Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1231 SER Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1334 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 129 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 156 GLN B 142 ASN B 156 GLN C 153 GLN C 365 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 ASN D 365 HIS D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 ASN D1318 GLN ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.220847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.215307 restraints weight = 32966.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.199617 restraints weight = 63992.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.195616 restraints weight = 65905.944| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26184 Z= 0.185 Angle : 0.571 6.818 35682 Z= 0.297 Chirality : 0.045 0.178 3794 Planarity : 0.004 0.047 4686 Dihedral : 6.051 59.901 3541 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.66 % Allowed : 11.52 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3218 helix: -1.16 (0.28), residues: 304 sheet: -0.20 (0.20), residues: 656 loop : -0.85 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 658 HIS 0.006 0.001 HIS C1302 PHE 0.018 0.002 PHE C 236 TYR 0.020 0.002 TYR C 471 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 562) hydrogen bonds : angle 5.35852 ( 1572) metal coordination : bond 0.00935 ( 6) SS BOND : bond 0.00340 ( 82) SS BOND : angle 1.33460 ( 164) covalent geometry : bond 0.00436 (26096) covalent geometry : angle 0.56480 (35518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 237 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 TRP cc_start: 0.8135 (t-100) cc_final: 0.7863 (t-100) REVERT: B 180 TRP cc_start: 0.8146 (t-100) cc_final: 0.7832 (t-100) REVERT: C 51 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7697 (mm-40) REVERT: C 183 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8103 (mtp180) REVERT: C 770 VAL cc_start: 0.8904 (t) cc_final: 0.8608 (m) REVERT: C 842 TRP cc_start: 0.7388 (p90) cc_final: 0.6851 (p90) REVERT: C 853 GLU cc_start: 0.7047 (mp0) cc_final: 0.6788 (mp0) REVERT: C 975 VAL cc_start: 0.7990 (p) cc_final: 0.7769 (p) REVERT: C 1026 ASP cc_start: 0.7864 (m-30) cc_final: 0.7608 (m-30) REVERT: C 1030 TYR cc_start: 0.7281 (p90) cc_final: 0.7004 (p90) REVERT: C 1518 MET cc_start: 0.5552 (tpt) cc_final: 0.5315 (tpt) REVERT: D 51 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7668 (mm-40) REVERT: D 183 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8108 (mtp180) REVERT: D 330 ILE cc_start: 0.8241 (mm) cc_final: 0.7826 (mt) REVERT: D 770 VAL cc_start: 0.8940 (t) cc_final: 0.8641 (m) REVERT: D 842 TRP cc_start: 0.7397 (p90) cc_final: 0.6869 (p90) REVERT: D 1030 TYR cc_start: 0.7237 (p90) cc_final: 0.6859 (p90) REVERT: D 1518 MET cc_start: 0.5559 (tpt) cc_final: 0.5334 (tpt) outliers start: 104 outliers final: 67 residues processed: 321 average time/residue: 0.3165 time to fit residues: 171.4676 Evaluate side-chains 291 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 183 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 604 HIS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 604 HIS Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 976 ILE Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1231 SER Chi-restraints excluded: chain D residue 1331 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 35 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 144 optimal weight: 0.0770 chunk 13 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 300 optimal weight: 20.0000 chunk 222 optimal weight: 0.0170 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN C 365 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 ASN D 365 HIS D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1318 GLN ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.216105 restraints weight = 33096.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.201013 restraints weight = 66444.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.196868 restraints weight = 65388.351| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26184 Z= 0.112 Angle : 0.520 7.712 35682 Z= 0.267 Chirality : 0.044 0.155 3794 Planarity : 0.004 0.034 4686 Dihedral : 5.591 59.724 3534 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.49 % Allowed : 12.51 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3218 helix: -0.77 (0.29), residues: 304 sheet: -0.18 (0.21), residues: 660 loop : -0.74 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 658 HIS 0.004 0.001 HIS D 529 PHE 0.017 0.001 PHE C 236 TYR 0.017 0.001 TYR D1214 ARG 0.005 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.02700 ( 562) hydrogen bonds : angle 5.02521 ( 1572) metal coordination : bond 0.00463 ( 6) SS BOND : bond 0.00212 ( 82) SS BOND : angle 1.19138 ( 164) covalent geometry : bond 0.00261 (26096) covalent geometry : angle 0.51538 (35518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 237 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7063 (mm-40) REVERT: C 183 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8039 (mtp180) REVERT: C 330 ILE cc_start: 0.8411 (mm) cc_final: 0.7949 (mt) REVERT: C 770 VAL cc_start: 0.8878 (t) cc_final: 0.8641 (m) REVERT: C 842 TRP cc_start: 0.7316 (p90) cc_final: 0.7053 (p90) REVERT: C 853 GLU cc_start: 0.7111 (mp0) cc_final: 0.6804 (mp0) REVERT: C 975 VAL cc_start: 0.8076 (p) cc_final: 0.7777 (p) REVERT: C 1026 ASP cc_start: 0.7830 (m-30) cc_final: 0.7552 (m-30) REVERT: C 1030 TYR cc_start: 0.7209 (p90) cc_final: 0.6873 (p90) REVERT: C 1200 CYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6482 (m) REVERT: D 51 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7143 (mm-40) REVERT: D 183 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8065 (mtp180) REVERT: D 389 ASP cc_start: 0.5100 (t0) cc_final: 0.4383 (t0) REVERT: D 403 GLN cc_start: 0.6180 (tp40) cc_final: 0.5370 (tt0) REVERT: D 770 VAL cc_start: 0.8843 (t) cc_final: 0.8578 (m) REVERT: D 842 TRP cc_start: 0.7355 (p90) cc_final: 0.7111 (p90) REVERT: D 1195 ASN cc_start: 0.1341 (p0) cc_final: 0.0661 (m-40) REVERT: D 1201 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: D 1518 MET cc_start: 0.5534 (tpt) cc_final: 0.5259 (tpt) outliers start: 99 outliers final: 71 residues processed: 317 average time/residue: 0.3272 time to fit residues: 174.7446 Evaluate side-chains 292 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 215 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 183 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1200 CYS Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1231 SER Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain C residue 1424 THR Chi-restraints excluded: chain C residue 1522 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 558 TYR Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 976 ILE Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1201 GLU Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 229 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 274 optimal weight: 0.0470 chunk 155 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 overall best weight: 2.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 142 ASN C 362 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1491 ASN ** 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 = 0.4469 r_free = 0.4469 target = 0.219971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.212846 restraints weight = 32902.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.211896 restraints weight = 79607.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.202669 restraints weight = 71787.584| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26184 Z= 0.181 Angle : 0.576 15.310 35682 Z= 0.294 Chirality : 0.046 0.173 3794 Planarity : 0.004 0.045 4686 Dihedral : 5.714 57.374 3530 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.70 % Allowed : 13.11 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3218 helix: -0.99 (0.28), residues: 316 sheet: -0.32 (0.21), residues: 660 loop : -0.80 (0.12), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 658 HIS 0.006 0.001 HIS C1302 PHE 0.017 0.002 PHE C 236 TYR 0.016 0.002 TYR D1030 ARG 0.005 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 562) hydrogen bonds : angle 5.11034 ( 1572) metal coordination : bond 0.00984 ( 6) SS BOND : bond 0.00300 ( 82) SS BOND : angle 1.37881 ( 164) covalent geometry : bond 0.00429 (26096) covalent geometry : angle 0.56946 (35518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 219 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7363 (mt0) REVERT: C 183 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8046 (mtp180) REVERT: C 330 ILE cc_start: 0.8341 (mm) cc_final: 0.7891 (mt) REVERT: C 544 PHE cc_start: 0.6173 (m-10) cc_final: 0.5892 (m-10) REVERT: C 770 VAL cc_start: 0.8862 (t) cc_final: 0.8570 (m) REVERT: C 842 TRP cc_start: 0.7274 (p90) cc_final: 0.6765 (p90) REVERT: C 975 VAL cc_start: 0.8075 (p) cc_final: 0.7799 (p) REVERT: C 1026 ASP cc_start: 0.7969 (m-30) cc_final: 0.7631 (m-30) REVERT: C 1030 TYR cc_start: 0.7245 (p90) cc_final: 0.6967 (p90) REVERT: C 1482 MET cc_start: 0.6653 (mtm) cc_final: 0.6352 (mtt) REVERT: D 51 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7898 (mm-40) REVERT: D 183 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8082 (mtp180) REVERT: D 330 ILE cc_start: 0.8226 (mm) cc_final: 0.7852 (mt) REVERT: D 770 VAL cc_start: 0.8854 (t) cc_final: 0.8582 (m) REVERT: D 842 TRP cc_start: 0.7364 (p90) cc_final: 0.6864 (p90) REVERT: D 1195 ASN cc_start: 0.1602 (p0) cc_final: 0.1040 (m-40) REVERT: D 1201 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: D 1518 MET cc_start: 0.5609 (tpt) cc_final: 0.5329 (tpt) outliers start: 105 outliers final: 79 residues processed: 304 average time/residue: 0.3137 time to fit residues: 161.5596 Evaluate side-chains 293 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 209 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 183 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 604 HIS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1231 SER Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain C residue 1424 THR Chi-restraints excluded: chain C residue 1502 ASP Chi-restraints excluded: chain C residue 1522 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 558 TYR Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 604 HIS Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1201 GLU Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1231 SER Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1424 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 126 optimal weight: 0.0020 chunk 150 optimal weight: 0.0170 chunk 2 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 127 optimal weight: 0.0020 chunk 44 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 230 optimal weight: 0.8980 chunk 267 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 156 GLN C 168 ASN C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1491 ASN D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.222752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.217480 restraints weight = 32608.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.202474 restraints weight = 63886.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.199177 restraints weight = 76711.442| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26184 Z= 0.085 Angle : 0.489 8.209 35682 Z= 0.249 Chirality : 0.043 0.199 3794 Planarity : 0.003 0.033 4686 Dihedral : 5.241 59.755 3529 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.07 % Allowed : 13.99 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3218 helix: -0.35 (0.30), residues: 304 sheet: -0.17 (0.21), residues: 670 loop : -0.59 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 658 HIS 0.003 0.000 HIS D 529 PHE 0.015 0.001 PHE C 236 TYR 0.018 0.001 TYR D1030 ARG 0.006 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.02364 ( 562) hydrogen bonds : angle 4.74750 ( 1572) metal coordination : bond 0.00008 ( 6) SS BOND : bond 0.00170 ( 82) SS BOND : angle 0.87676 ( 164) covalent geometry : bond 0.00199 (26096) covalent geometry : angle 0.48609 (35518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 241 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.6002 (mt0) REVERT: C 51 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.6885 (mm-40) REVERT: C 541 THR cc_start: 0.6564 (p) cc_final: 0.6013 (t) REVERT: C 770 VAL cc_start: 0.8867 (t) cc_final: 0.8646 (m) REVERT: C 842 TRP cc_start: 0.7322 (p90) cc_final: 0.7085 (p90) REVERT: C 853 GLU cc_start: 0.6979 (mp0) cc_final: 0.6685 (mp0) REVERT: C 975 VAL cc_start: 0.8074 (p) cc_final: 0.7846 (p) REVERT: C 1026 ASP cc_start: 0.7977 (m-30) cc_final: 0.7684 (m-30) REVERT: C 1030 TYR cc_start: 0.7105 (p90) cc_final: 0.6814 (p90) REVERT: D 51 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6913 (mm-40) REVERT: D 183 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7923 (mmm-85) REVERT: D 330 ILE cc_start: 0.8186 (mm) cc_final: 0.7732 (mt) REVERT: D 770 VAL cc_start: 0.8905 (t) cc_final: 0.8703 (m) REVERT: D 842 TRP cc_start: 0.7381 (p90) cc_final: 0.7144 (p90) REVERT: D 1195 ASN cc_start: 0.1712 (p0) cc_final: 0.1202 (m-40) REVERT: D 1201 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6235 (mp0) outliers start: 87 outliers final: 58 residues processed: 311 average time/residue: 0.3163 time to fit residues: 167.0349 Evaluate side-chains 281 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain C residue 1522 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 558 TYR Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1201 GLU Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1250 MET Chi-restraints excluded: chain D residue 1331 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 32 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 117 optimal weight: 0.4980 chunk 212 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 236 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN C 85 ASN C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1411 GLN D 85 ASN D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.217294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.209535 restraints weight = 32960.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198853 restraints weight = 75112.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.195831 restraints weight = 70666.614| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 26184 Z= 0.244 Angle : 0.616 8.371 35682 Z= 0.320 Chirality : 0.047 0.178 3794 Planarity : 0.005 0.068 4686 Dihedral : 5.718 57.233 3527 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.70 % Allowed : 13.71 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3218 helix: -0.90 (0.28), residues: 314 sheet: -0.50 (0.21), residues: 662 loop : -0.79 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 658 HIS 0.008 0.001 HIS D 492 PHE 0.018 0.002 PHE D1516 TYR 0.017 0.002 TYR D 578 ARG 0.006 0.001 ARG D1007 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 562) hydrogen bonds : angle 5.19379 ( 1572) metal coordination : bond 0.01338 ( 6) SS BOND : bond 0.00374 ( 82) SS BOND : angle 1.26647 ( 164) covalent geometry : bond 0.00580 (26096) covalent geometry : angle 0.61165 (35518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 223 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7707 (tt0) cc_final: 0.7490 (tt0) REVERT: C 51 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: C 183 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8122 (mtp180) REVERT: C 756 ASP cc_start: 0.8167 (m-30) cc_final: 0.7918 (m-30) REVERT: C 842 TRP cc_start: 0.7356 (p90) cc_final: 0.6865 (p90) REVERT: C 853 GLU cc_start: 0.7132 (mp0) cc_final: 0.6824 (mp0) REVERT: C 975 VAL cc_start: 0.8104 (p) cc_final: 0.7818 (p) REVERT: C 1026 ASP cc_start: 0.7999 (m-30) cc_final: 0.7693 (m-30) REVERT: C 1030 TYR cc_start: 0.7246 (p90) cc_final: 0.6992 (p90) REVERT: D 51 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: D 183 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8158 (mtp180) REVERT: D 330 ILE cc_start: 0.8108 (mm) cc_final: 0.7704 (mt) REVERT: D 756 ASP cc_start: 0.8196 (m-30) cc_final: 0.7978 (m-30) REVERT: D 842 TRP cc_start: 0.7444 (p90) cc_final: 0.6953 (p90) REVERT: D 1030 TYR cc_start: 0.7009 (p90) cc_final: 0.6655 (p90) REVERT: D 1201 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: D 1250 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6854 (mtt) outliers start: 105 outliers final: 74 residues processed: 308 average time/residue: 0.3196 time to fit residues: 166.0945 Evaluate side-chains 289 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 209 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 183 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 604 HIS Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain C residue 1424 THR Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 374 ASN Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 558 TYR Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 604 HIS Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 918 VAL Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1201 GLU Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1231 SER Chi-restraints excluded: chain D residue 1250 MET Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1334 THR Chi-restraints excluded: chain D residue 1424 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 193 optimal weight: 0.2980 chunk 223 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 HIS C1411 GLN D 333 ASN D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN ** D1491 ASN ** 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 = 0.4468 r_free = 0.4468 target = 0.219543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.213786 restraints weight = 32696.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.199450 restraints weight = 70115.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.194492 restraints weight = 61571.326| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26184 Z= 0.117 Angle : 0.521 7.217 35682 Z= 0.268 Chirality : 0.044 0.211 3794 Planarity : 0.004 0.051 4686 Dihedral : 5.339 59.784 3524 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.61 % Allowed : 15.05 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3218 helix: -0.79 (0.29), residues: 326 sheet: -0.25 (0.21), residues: 660 loop : -0.69 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 658 HIS 0.009 0.001 HIS C 529 PHE 0.015 0.001 PHE C 236 TYR 0.018 0.001 TYR D1030 ARG 0.004 0.000 ARG D1007 Details of bonding type rmsd hydrogen bonds : bond 0.02619 ( 562) hydrogen bonds : angle 4.91760 ( 1572) metal coordination : bond 0.00458 ( 6) SS BOND : bond 0.00210 ( 82) SS BOND : angle 1.04865 ( 164) covalent geometry : bond 0.00276 (26096) covalent geometry : angle 0.51725 (35518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 224 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7118 (mm-40) REVERT: C 183 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7438 (mmm-85) REVERT: C 330 ILE cc_start: 0.8270 (mm) cc_final: 0.7902 (mt) REVERT: C 842 TRP cc_start: 0.7344 (p90) cc_final: 0.7124 (p90) REVERT: C 853 GLU cc_start: 0.7137 (mp0) cc_final: 0.6846 (mp0) REVERT: C 975 VAL cc_start: 0.8125 (p) cc_final: 0.7867 (p) REVERT: C 1026 ASP cc_start: 0.8018 (m-30) cc_final: 0.7723 (m-30) REVERT: C 1030 TYR cc_start: 0.7286 (p90) cc_final: 0.7037 (p90) REVERT: D 183 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8044 (mtp180) REVERT: D 330 ILE cc_start: 0.8168 (mm) cc_final: 0.7740 (mt) REVERT: D 842 TRP cc_start: 0.7433 (p90) cc_final: 0.7164 (p90) REVERT: D 1201 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.5854 (mp0) REVERT: D 1250 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7003 (mtt) outliers start: 74 outliers final: 58 residues processed: 281 average time/residue: 0.3306 time to fit residues: 156.3804 Evaluate side-chains 278 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 183 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain C residue 1424 THR Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 558 TYR Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1201 GLU Chi-restraints excluded: chain D residue 1231 SER Chi-restraints excluded: chain D residue 1250 MET Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1334 THR Chi-restraints excluded: chain D residue 1424 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 137 optimal weight: 7.9990 chunk 227 optimal weight: 0.4980 chunk 72 optimal weight: 0.0980 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1411 GLN D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN ** D1491 ASN ** 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 = 0.4268 r_free = 0.4268 target = 0.198462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.193683 restraints weight = 32108.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.192000 restraints weight = 56797.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.190464 restraints weight = 63920.649| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26184 Z= 0.144 Angle : 0.540 8.470 35682 Z= 0.277 Chirality : 0.044 0.180 3794 Planarity : 0.004 0.047 4686 Dihedral : 5.332 59.681 3524 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.68 % Allowed : 15.01 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3218 helix: -0.75 (0.29), residues: 326 sheet: -0.33 (0.21), residues: 660 loop : -0.72 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP C 658 HIS 0.005 0.001 HIS D 529 PHE 0.015 0.001 PHE D 236 TYR 0.017 0.001 TYR D1030 ARG 0.004 0.000 ARG D1007 Details of bonding type rmsd hydrogen bonds : bond 0.02750 ( 562) hydrogen bonds : angle 4.94830 ( 1572) metal coordination : bond 0.00758 ( 6) SS BOND : bond 0.00234 ( 82) SS BOND : angle 1.00979 ( 164) covalent geometry : bond 0.00342 (26096) covalent geometry : angle 0.53736 (35518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 213 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7995 (mtp180) REVERT: C 330 ILE cc_start: 0.8237 (mm) cc_final: 0.7865 (mt) REVERT: C 842 TRP cc_start: 0.7268 (p90) cc_final: 0.7044 (p90) REVERT: C 853 GLU cc_start: 0.7117 (mp0) cc_final: 0.6806 (mp0) REVERT: C 1026 ASP cc_start: 0.8070 (m-30) cc_final: 0.7756 (m-30) REVERT: D 183 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8021 (mtp180) REVERT: D 330 ILE cc_start: 0.8136 (mm) cc_final: 0.7687 (mt) REVERT: D 842 TRP cc_start: 0.7346 (p90) cc_final: 0.6913 (p90) REVERT: D 1201 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: D 1250 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6818 (mtt) outliers start: 76 outliers final: 65 residues processed: 274 average time/residue: 0.3322 time to fit residues: 153.2176 Evaluate side-chains 277 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 183 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1045 THR Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1231 SER Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain C residue 1424 THR Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1201 GLU Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1231 SER Chi-restraints excluded: chain D residue 1250 MET Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1334 THR Chi-restraints excluded: chain D residue 1424 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 66 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 309 optimal weight: 20.0000 chunk 39 optimal weight: 0.6980 chunk 303 optimal weight: 9.9990 chunk 113 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 140 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1411 GLN D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN D1411 GLN D1491 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.222588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.215607 restraints weight = 33115.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.203388 restraints weight = 70228.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.200990 restraints weight = 63995.879| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26184 Z= 0.088 Angle : 0.495 8.198 35682 Z= 0.252 Chirality : 0.043 0.197 3794 Planarity : 0.003 0.041 4686 Dihedral : 5.010 57.305 3524 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.47 % Allowed : 15.19 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3218 helix: -0.61 (0.29), residues: 326 sheet: -0.16 (0.21), residues: 666 loop : -0.58 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 658 HIS 0.004 0.001 HIS D 529 PHE 0.013 0.001 PHE D 236 TYR 0.017 0.001 TYR D1030 ARG 0.004 0.000 ARG D1007 Details of bonding type rmsd hydrogen bonds : bond 0.02414 ( 562) hydrogen bonds : angle 4.70572 ( 1572) metal coordination : bond 0.00213 ( 6) SS BOND : bond 0.00166 ( 82) SS BOND : angle 0.78935 ( 164) covalent geometry : bond 0.00207 (26096) covalent geometry : angle 0.49278 (35518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 TRP cc_start: 0.8017 (t-100) cc_final: 0.7667 (t-100) REVERT: B 180 TRP cc_start: 0.8077 (t-100) cc_final: 0.7641 (t-100) REVERT: C 51 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7139 (mm-40) REVERT: C 183 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7920 (mmm-85) REVERT: C 330 ILE cc_start: 0.8308 (mm) cc_final: 0.7957 (mt) REVERT: C 541 THR cc_start: 0.6157 (p) cc_final: 0.5741 (t) REVERT: C 842 TRP cc_start: 0.7311 (p90) cc_final: 0.7102 (p90) REVERT: C 853 GLU cc_start: 0.7116 (mp0) cc_final: 0.6815 (mp0) REVERT: C 1026 ASP cc_start: 0.8033 (m-30) cc_final: 0.7760 (m-30) REVERT: D 51 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7030 (mm-40) REVERT: D 183 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7950 (mmm-85) REVERT: D 842 TRP cc_start: 0.7353 (p90) cc_final: 0.7137 (p90) REVERT: D 1201 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: D 1250 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6866 (mtt) outliers start: 70 outliers final: 56 residues processed: 274 average time/residue: 0.3245 time to fit residues: 150.0978 Evaluate side-chains 266 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 183 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 701 CYS Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1220 CYS Chi-restraints excluded: chain C residue 1331 VAL Chi-restraints excluded: chain C residue 1424 THR Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 374 ASN Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 701 CYS Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1044 ASP Chi-restraints excluded: chain D residue 1069 VAL Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1201 GLU Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1231 SER Chi-restraints excluded: chain D residue 1250 MET Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1334 THR Chi-restraints excluded: chain D residue 1424 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 31 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 321 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 118 optimal weight: 0.0370 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1411 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN D1411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.221726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.216550 restraints weight = 32832.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.199899 restraints weight = 62196.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.197264 restraints weight = 68248.107| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.231 26184 Z= 0.150 Angle : 0.652 59.128 35682 Z= 0.373 Chirality : 0.045 0.965 3794 Planarity : 0.004 0.057 4686 Dihedral : 4.988 57.360 3522 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.40 % Allowed : 15.29 % Favored : 82.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3218 helix: -0.60 (0.29), residues: 326 sheet: -0.15 (0.21), residues: 666 loop : -0.57 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 658 HIS 0.004 0.001 HIS D 529 PHE 0.013 0.001 PHE D 236 TYR 0.015 0.001 TYR D1030 ARG 0.003 0.000 ARG D1007 Details of bonding type rmsd hydrogen bonds : bond 0.02414 ( 562) hydrogen bonds : angle 4.70406 ( 1572) metal coordination : bond 0.00232 ( 6) SS BOND : bond 0.00162 ( 82) SS BOND : angle 0.76090 ( 164) covalent geometry : bond 0.00303 (26096) covalent geometry : angle 0.65113 (35518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7332.76 seconds wall clock time: 128 minutes 26.74 seconds (7706.74 seconds total)