Starting phenix.real_space_refine on Mon Aug 25 04:07:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgg_34738/08_2025/8hgg_34738.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgg_34738/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hgg_34738/08_2025/8hgg_34738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgg_34738/08_2025/8hgg_34738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgg_34738/08_2025/8hgg_34738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgg_34738/08_2025/8hgg_34738.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.17, per 1000 atoms: 0.24 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.30 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: 6.26 Time building geometry restraints manager: 2.88 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: 0.05 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: 1.070 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.830 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.000 ARG B 209 TYR 0.018 0.002 TYR D 841 PHE 0.016 0.002 PHE D1232 TRP 0.011 0.001 TRP C 943 HIS 0.006 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00349 (26096) covalent geometry : angle 0.61885 (35518) SS BOND : bond 0.00265 ( 82) SS BOND : angle 0.89620 ( 164) hydrogen bonds : bond 0.16723 ( 562) hydrogen bonds : angle 7.09538 ( 1572) metal coordination : bond 0.00559 ( 6) *********************** 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 : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 TRP cc_start: 0.8057 (t-100) cc_final: 0.7835 (t-100) REVERT: B 145 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8326 (mm) REVERT: B 180 TRP cc_start: 0.8169 (t-100) cc_final: 0.7888 (t-100) REVERT: C 22 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7184 (mmp80) REVERT: C 51 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7727 (mm-40) REVERT: C 70 ASP cc_start: 0.7592 (p0) cc_final: 0.7385 (p0) REVERT: C 204 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (tp) REVERT: C 222 ASP cc_start: 0.3973 (OUTLIER) cc_final: 0.3684 (t0) REVERT: C 330 ILE cc_start: 0.8252 (mm) cc_final: 0.7828 (mt) REVERT: C 534 ASP cc_start: 0.5954 (m-30) cc_final: 0.5636 (t0) REVERT: C 668 ASP cc_start: 0.7675 (p0) cc_final: 0.7405 (p0) REVERT: C 842 TRP cc_start: 0.7015 (p90) cc_final: 0.6768 (p90) REVERT: C 975 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7697 (p) REVERT: C 1102 ASP cc_start: 0.6598 (p0) cc_final: 0.6152 (p0) REVERT: D 51 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: D 204 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7919 (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: 0.7653 (m) REVERT: D 668 ASP cc_start: 0.7652 (p0) cc_final: 0.7396 (p0) REVERT: D 842 TRP cc_start: 0.7048 (p90) cc_final: 0.6812 (p90) REVERT: D 953 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6699 (t0) REVERT: D 975 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7629 (p) REVERT: D 1102 ASP cc_start: 0.6712 (p0) cc_final: 0.6297 (p0) outliers start: 155 outliers final: 49 residues processed: 516 average time/residue: 0.1684 time to fit residues: 139.1792 Evaluate side-chains 301 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 1336 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0970 overall best weight: 1.3740 ------------------------------------------------------------------------------- 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 198 HIS C 294 GLN C 374 ASN C 403 GLN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN C 985 HIS D 78 HIS D 153 GLN D 198 HIS D 294 GLN ** D 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN D 683 ASN D 985 HIS D1062 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.225248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.218371 restraints weight = 33189.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.217150 restraints weight = 71637.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.216251 restraints weight = 74585.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.215379 restraints weight = 58161.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.214919 restraints weight = 60872.978| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26184 Z= 0.131 Angle : 0.544 6.651 35682 Z= 0.283 Chirality : 0.044 0.169 3794 Planarity : 0.004 0.065 4686 Dihedral : 6.580 59.589 3586 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.70 % Allowed : 9.55 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3218 helix: -1.55 (0.26), residues: 302 sheet: 0.02 (0.20), residues: 684 loop : -0.82 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 215 TYR 0.018 0.001 TYR C1214 PHE 0.020 0.001 PHE D 236 TRP 0.022 0.001 TRP C 658 HIS 0.008 0.001 HIS D 529 Details of bonding type rmsd covalent geometry : bond 0.00306 (26096) covalent geometry : angle 0.53672 (35518) SS BOND : bond 0.00307 ( 82) SS BOND : angle 1.44372 ( 164) hydrogen bonds : bond 0.03367 ( 562) hydrogen bonds : angle 5.46934 ( 1572) metal coordination : bond 0.00635 ( 6) *********************** 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 366 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 261 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7815 (t0) REVERT: A 180 TRP cc_start: 0.8061 (t-100) cc_final: 0.7838 (t-100) REVERT: B 180 TRP cc_start: 0.8113 (t-100) cc_final: 0.7857 (t-100) REVERT: C 51 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7620 (mm-40) REVERT: C 330 ILE cc_start: 0.8167 (mm) cc_final: 0.7788 (mt) REVERT: C 668 ASP cc_start: 0.7849 (p0) cc_final: 0.7433 (p0) REVERT: C 770 VAL cc_start: 0.8832 (t) cc_final: 0.8496 (m) REVERT: C 842 TRP cc_start: 0.7247 (p90) cc_final: 0.6949 (p90) REVERT: C 853 GLU cc_start: 0.6905 (mp0) cc_final: 0.6641 (mp0) REVERT: C 975 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7799 (p) REVERT: C 1026 ASP cc_start: 0.7701 (m-30) cc_final: 0.7489 (m-30) REVERT: C 1030 TYR cc_start: 0.7112 (p90) cc_final: 0.6822 (p90) REVERT: D 51 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7629 (mm-40) REVERT: D 67 ILE cc_start: 0.5288 (OUTLIER) cc_final: 0.5033 (pt) REVERT: D 330 ILE cc_start: 0.8173 (mm) cc_final: 0.7823 (mt) REVERT: D 403 GLN cc_start: 0.6186 (tp40) cc_final: 0.5971 (tt0) REVERT: D 541 THR cc_start: 0.5850 (p) cc_final: 0.5414 (t) REVERT: D 770 VAL cc_start: 0.8890 (t) cc_final: 0.8539 (m) REVERT: D 842 TRP cc_start: 0.7305 (p90) cc_final: 0.6997 (p90) REVERT: D 1030 TYR cc_start: 0.7070 (p90) cc_final: 0.6792 (p90) REVERT: D 1518 MET cc_start: 0.4960 (tpt) cc_final: 0.4740 (tpt) outliers start: 105 outliers final: 60 residues processed: 343 average time/residue: 0.1516 time to fit residues: 87.9761 Evaluate side-chains 291 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 78 HIS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 250 THR 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 975 VAL 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 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 78 HIS 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 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 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 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 1231 SER Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1334 THR Chi-restraints excluded: chain D residue 1336 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 318 optimal weight: 10.0000 chunk 1 optimal weight: 0.0970 chunk 176 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 587 GLN C 687 ASN D 365 HIS D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 ASN D 969 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.220276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.213766 restraints weight = 32778.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.202116 restraints weight = 77514.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.197046 restraints weight = 65813.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.196234 restraints weight = 57528.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.195754 restraints weight = 53802.721| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26184 Z= 0.197 Angle : 0.582 6.928 35682 Z= 0.303 Chirality : 0.046 0.179 3794 Planarity : 0.004 0.053 4686 Dihedral : 6.098 55.587 3546 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.66 % Allowed : 11.13 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3218 helix: -1.14 (0.28), residues: 304 sheet: -0.15 (0.20), residues: 656 loop : -0.83 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.017 0.002 TYR C1214 PHE 0.019 0.002 PHE C 236 TRP 0.028 0.002 TRP C 658 HIS 0.006 0.001 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00466 (26096) covalent geometry : angle 0.57578 (35518) SS BOND : bond 0.00364 ( 82) SS BOND : angle 1.35669 ( 164) hydrogen bonds : bond 0.03275 ( 562) hydrogen bonds : angle 5.37192 ( 1572) metal coordination : bond 0.01035 ( 6) *********************** 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 338 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 234 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 TRP cc_start: 0.8144 (t-100) cc_final: 0.7884 (t-100) REVERT: B 180 TRP cc_start: 0.8190 (t-100) cc_final: 0.7863 (t-100) REVERT: C 51 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7601 (mm-40) REVERT: C 668 ASP cc_start: 0.7785 (p0) cc_final: 0.7574 (p0) REVERT: C 842 TRP cc_start: 0.7307 (p90) cc_final: 0.6787 (p90) REVERT: C 975 VAL cc_start: 0.7943 (p) cc_final: 0.7727 (p) REVERT: C 1026 ASP cc_start: 0.7851 (m-30) cc_final: 0.7592 (m-30) REVERT: C 1030 TYR cc_start: 0.7329 (p90) cc_final: 0.7016 (p90) REVERT: D 51 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7608 (mm-40) REVERT: D 67 ILE cc_start: 0.5330 (OUTLIER) cc_final: 0.5115 (pt) REVERT: D 330 ILE cc_start: 0.8229 (mm) cc_final: 0.7839 (mt) REVERT: D 359 ASP cc_start: 0.4817 (m-30) cc_final: 0.4554 (m-30) REVERT: D 658 TRP cc_start: 0.8142 (p-90) cc_final: 0.7941 (p-90) REVERT: D 842 TRP cc_start: 0.7376 (p90) cc_final: 0.6833 (p90) REVERT: D 1030 TYR cc_start: 0.7212 (p90) cc_final: 0.6841 (p90) REVERT: D 1518 MET cc_start: 0.5378 (tpt) cc_final: 0.5153 (tpt) outliers start: 104 outliers final: 61 residues processed: 317 average time/residue: 0.1495 time to fit residues: 80.7696 Evaluate side-chains 286 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 74 VAL 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 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 926 THR Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 1023 LEU 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 418 VAL 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 829 VAL 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 931 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 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 174 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 301 optimal weight: 0.0060 chunk 108 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 166 optimal weight: 0.3980 chunk 57 optimal weight: 9.9990 chunk 81 optimal weight: 0.2980 chunk 238 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN C 365 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 ASN C1491 ASN D 365 HIS D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1142 ASN ** 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 = 0.221864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.215451 restraints weight = 33035.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.214584 restraints weight = 65704.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.212672 restraints weight = 65341.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.204532 restraints weight = 79795.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.202047 restraints weight = 60707.509| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26184 Z= 0.124 Angle : 0.521 7.423 35682 Z= 0.269 Chirality : 0.044 0.183 3794 Planarity : 0.004 0.038 4686 Dihedral : 5.580 57.723 3535 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.35 % Allowed : 12.05 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3218 helix: -0.70 (0.30), residues: 304 sheet: -0.15 (0.21), residues: 656 loop : -0.73 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 170 TYR 0.017 0.001 TYR D1214 PHE 0.017 0.001 PHE D 236 TRP 0.030 0.001 TRP C 658 HIS 0.004 0.001 HIS D 529 Details of bonding type rmsd covalent geometry : bond 0.00292 (26096) covalent geometry : angle 0.51603 (35518) SS BOND : bond 0.00233 ( 82) SS BOND : angle 1.15023 ( 164) hydrogen bonds : bond 0.02731 ( 562) hydrogen bonds : angle 5.04500 ( 1572) metal coordination : bond 0.00568 ( 6) *********************** 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 330 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 235 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.6165 (mt0) cc_final: 0.5886 (mt0) REVERT: C 51 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7027 (mm-40) REVERT: C 183 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8088 (mtp180) REVERT: C 330 ILE cc_start: 0.8267 (mm) cc_final: 0.7838 (mt) REVERT: C 770 VAL cc_start: 0.8985 (t) cc_final: 0.8694 (m) REVERT: C 842 TRP cc_start: 0.7329 (p90) cc_final: 0.7058 (p90) REVERT: C 853 GLU cc_start: 0.7015 (mp0) cc_final: 0.6749 (mp0) REVERT: C 1026 ASP cc_start: 0.7871 (m-30) cc_final: 0.7553 (m-30) REVERT: C 1030 TYR cc_start: 0.7163 (p90) cc_final: 0.6913 (p90) REVERT: C 1195 ASN cc_start: 0.1836 (p0) cc_final: 0.1072 (m-40) REVERT: D 51 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7677 (mm-40) REVERT: D 183 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8079 (mtp180) REVERT: D 330 ILE cc_start: 0.8122 (mm) cc_final: 0.7678 (mt) REVERT: D 403 GLN cc_start: 0.5975 (tp40) cc_final: 0.5281 (tt0) REVERT: D 541 THR cc_start: 0.6392 (p) cc_final: 0.5842 (t) REVERT: D 658 TRP cc_start: 0.8119 (p-90) cc_final: 0.7855 (p-90) REVERT: D 770 VAL cc_start: 0.8930 (t) cc_final: 0.8610 (m) REVERT: D 842 TRP cc_start: 0.7376 (p90) cc_final: 0.7124 (p90) REVERT: D 1030 TYR cc_start: 0.7087 (p90) cc_final: 0.6844 (p90) REVERT: D 1195 ASN cc_start: 0.1693 (p0) cc_final: 0.1013 (m-40) REVERT: D 1201 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: D 1518 MET cc_start: 0.5400 (tpt) cc_final: 0.5123 (tpt) outliers start: 95 outliers final: 69 residues processed: 311 average time/residue: 0.1514 time to fit residues: 79.8080 Evaluate side-chains 290 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 216 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 120 GLN 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 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 418 VAL 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 824 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 931 CYS Chi-restraints excluded: chain C residue 941 ASP 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 199 THR Chi-restraints excluded: chain D residue 250 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 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 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 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 1334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 311 optimal weight: 20.0000 chunk 250 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN C 85 ASN C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.219684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.211594 restraints weight = 32948.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.204660 restraints weight = 79774.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.200864 restraints weight = 66769.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.199859 restraints weight = 62927.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.200034 restraints weight = 49016.853| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26184 Z= 0.147 Angle : 0.536 9.770 35682 Z= 0.275 Chirality : 0.044 0.181 3794 Planarity : 0.004 0.037 4686 Dihedral : 5.523 58.797 3529 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.56 % Allowed : 12.90 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.14), residues: 3218 helix: -0.71 (0.29), residues: 304 sheet: -0.17 (0.21), residues: 652 loop : -0.72 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.015 0.001 TYR D1214 PHE 0.017 0.001 PHE C 236 TRP 0.035 0.001 TRP C 658 HIS 0.004 0.001 HIS C1302 Details of bonding type rmsd covalent geometry : bond 0.00351 (26096) covalent geometry : angle 0.53023 (35518) SS BOND : bond 0.00284 ( 82) SS BOND : angle 1.31280 ( 164) hydrogen bonds : bond 0.02780 ( 562) hydrogen bonds : angle 4.99846 ( 1572) metal coordination : bond 0.00785 ( 6) *********************** 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 327 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 226 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.6153 (mt0) cc_final: 0.5910 (mt0) REVERT: C 51 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7676 (mm-40) REVERT: C 183 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8059 (mtp180) REVERT: C 330 ILE cc_start: 0.8265 (mm) cc_final: 0.7822 (mt) REVERT: C 770 VAL cc_start: 0.8933 (t) cc_final: 0.8646 (m) REVERT: C 842 TRP cc_start: 0.7329 (p90) cc_final: 0.7069 (p90) REVERT: C 853 GLU cc_start: 0.7148 (mp0) cc_final: 0.6848 (mp0) REVERT: C 1026 ASP cc_start: 0.7948 (m-30) cc_final: 0.7636 (m-30) REVERT: C 1030 TYR cc_start: 0.7218 (p90) cc_final: 0.6950 (p90) REVERT: D 51 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7718 (mm-40) REVERT: D 183 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8075 (mtp180) REVERT: D 658 TRP cc_start: 0.8209 (p-90) cc_final: 0.7939 (p-90) REVERT: D 770 VAL cc_start: 0.8972 (t) cc_final: 0.8618 (m) REVERT: D 842 TRP cc_start: 0.7417 (p90) cc_final: 0.6903 (p90) REVERT: D 1030 TYR cc_start: 0.7097 (p90) cc_final: 0.6831 (p90) REVERT: D 1195 ASN cc_start: 0.1597 (p0) cc_final: 0.1072 (m-40) REVERT: D 1201 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6207 (mp0) REVERT: D 1518 MET cc_start: 0.5453 (tpt) cc_final: 0.5166 (tpt) outliers start: 101 outliers final: 73 residues processed: 306 average time/residue: 0.1544 time to fit residues: 79.5168 Evaluate side-chains 289 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 211 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 120 GLN 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 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 824 LEU 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 926 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 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 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 291 optimal weight: 3.9990 chunk 300 optimal weight: 30.0000 chunk 271 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN C 85 ASN C 362 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 362 HIS D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4474 r_free = 0.4474 target = 0.219945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.212933 restraints weight = 32845.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.203035 restraints weight = 81469.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.198201 restraints weight = 65596.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197890 restraints weight = 55344.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.196890 restraints weight = 49776.483| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26184 Z= 0.134 Angle : 0.518 7.385 35682 Z= 0.267 Chirality : 0.044 0.162 3794 Planarity : 0.004 0.037 4686 Dihedral : 5.387 58.535 3527 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.88 % Allowed : 13.07 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.14), residues: 3218 helix: -0.55 (0.30), residues: 304 sheet: -0.24 (0.20), residues: 664 loop : -0.69 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 36 TYR 0.013 0.001 TYR C1486 PHE 0.016 0.001 PHE C 236 TRP 0.038 0.001 TRP C 658 HIS 0.004 0.001 HIS C1302 Details of bonding type rmsd covalent geometry : bond 0.00318 (26096) covalent geometry : angle 0.51536 (35518) SS BOND : bond 0.00240 ( 82) SS BOND : angle 0.96830 ( 164) hydrogen bonds : bond 0.02657 ( 562) hydrogen bonds : angle 4.91312 ( 1572) metal coordination : bond 0.00670 ( 6) *********************** 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 340 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 230 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.6232 (mt0) cc_final: 0.5877 (mt0) REVERT: A 180 TRP cc_start: 0.7996 (t-100) cc_final: 0.7693 (t-100) REVERT: C 183 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8046 (mtp180) REVERT: C 330 ILE cc_start: 0.8286 (mm) cc_final: 0.7829 (mt) REVERT: C 544 PHE cc_start: 0.6183 (m-10) cc_final: 0.5883 (m-10) REVERT: C 770 VAL cc_start: 0.8924 (t) cc_final: 0.8674 (m) REVERT: C 842 TRP cc_start: 0.7378 (p90) cc_final: 0.7116 (p90) REVERT: C 853 GLU cc_start: 0.7104 (mp0) cc_final: 0.6765 (mp0) REVERT: C 1026 ASP cc_start: 0.8018 (m-30) cc_final: 0.7689 (m-30) REVERT: C 1030 TYR cc_start: 0.7269 (p90) cc_final: 0.6979 (p90) REVERT: D 183 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8054 (mtp180) REVERT: D 330 ILE cc_start: 0.8201 (mm) cc_final: 0.7779 (mt) REVERT: D 658 TRP cc_start: 0.8136 (p-90) cc_final: 0.7884 (p-90) REVERT: D 756 ASP cc_start: 0.8134 (m-30) cc_final: 0.7871 (m-30) REVERT: D 770 VAL cc_start: 0.8895 (t) cc_final: 0.8615 (m) REVERT: D 842 TRP cc_start: 0.7384 (p90) cc_final: 0.6871 (p90) REVERT: D 1030 TYR cc_start: 0.7084 (p90) cc_final: 0.6800 (p90) REVERT: D 1201 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: D 1482 MET cc_start: 0.7115 (mmt) cc_final: 0.6874 (mmt) outliers start: 110 outliers final: 83 residues processed: 320 average time/residue: 0.1500 time to fit residues: 81.6326 Evaluate side-chains 302 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 216 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL 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 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 717 THR 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 859 THR Chi-restraints excluded: chain C residue 926 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 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 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 250 THR Chi-restraints excluded: chain D residue 278 VAL 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 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 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 941 ASP Chi-restraints excluded: chain D residue 976 ILE Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 992 ILE 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 1334 THR Chi-restraints excluded: chain D residue 1424 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 305 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 85 ASN C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 HIS 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 = 0.4454 r_free = 0.4454 target = 0.218254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.212398 restraints weight = 32656.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.199652 restraints weight = 71692.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.194924 restraints weight = 63437.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.193879 restraints weight = 57451.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.193889 restraints weight = 51413.453| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26184 Z= 0.180 Angle : 0.563 7.914 35682 Z= 0.290 Chirality : 0.045 0.234 3794 Planarity : 0.004 0.048 4686 Dihedral : 5.553 58.691 3527 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.70 % Allowed : 13.53 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3218 helix: -0.93 (0.28), residues: 328 sheet: -0.35 (0.21), residues: 660 loop : -0.78 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 896 TYR 0.014 0.002 TYR D 131 PHE 0.016 0.002 PHE C 236 TRP 0.047 0.001 TRP C 658 HIS 0.008 0.001 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00429 (26096) covalent geometry : angle 0.55762 (35518) SS BOND : bond 0.00282 ( 82) SS BOND : angle 1.30329 ( 164) hydrogen bonds : bond 0.02883 ( 562) hydrogen bonds : angle 5.03286 ( 1572) metal coordination : bond 0.00999 ( 6) *********************** 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 321 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 216 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.6339 (mt0) cc_final: 0.5941 (mt0) REVERT: A 180 TRP cc_start: 0.8012 (t-100) cc_final: 0.7723 (t-100) REVERT: B 156 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: C 183 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8088 (mtp180) REVERT: C 330 ILE cc_start: 0.8323 (mm) cc_final: 0.7885 (mt) REVERT: C 756 ASP cc_start: 0.8165 (m-30) cc_final: 0.7479 (m-30) REVERT: C 770 VAL cc_start: 0.8917 (t) cc_final: 0.8614 (m) REVERT: C 842 TRP cc_start: 0.7322 (p90) cc_final: 0.6836 (p90) REVERT: C 853 GLU cc_start: 0.7158 (mp0) cc_final: 0.6824 (mp0) REVERT: C 1026 ASP cc_start: 0.8000 (m-30) cc_final: 0.7652 (m-30) REVERT: C 1030 TYR cc_start: 0.7307 (p90) cc_final: 0.7052 (p90) REVERT: D 51 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7617 (mm-40) REVERT: D 183 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8083 (mtp180) REVERT: D 330 ILE cc_start: 0.8189 (mm) cc_final: 0.7804 (mt) REVERT: D 658 TRP cc_start: 0.8142 (p-90) cc_final: 0.7835 (p-90) REVERT: D 756 ASP cc_start: 0.8191 (m-30) cc_final: 0.7928 (m-30) REVERT: D 842 TRP cc_start: 0.7413 (p90) cc_final: 0.6930 (p90) REVERT: D 1030 TYR cc_start: 0.7242 (p90) cc_final: 0.6961 (p90) REVERT: D 1201 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6055 (mp0) outliers start: 105 outliers final: 80 residues processed: 301 average time/residue: 0.1527 time to fit residues: 77.7633 Evaluate side-chains 295 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 210 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 220 CYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 156 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 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 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 926 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 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 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 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 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 926 THR Chi-restraints excluded: chain D residue 931 CYS Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 976 ILE Chi-restraints excluded: chain D residue 990 CYS Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 992 ILE 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 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 224 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 148 optimal weight: 0.0970 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 156 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN C 85 ASN C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4484 r_free = 0.4484 target = 0.221501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.215577 restraints weight = 32755.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.203059 restraints weight = 71408.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197980 restraints weight = 66183.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.197503 restraints weight = 70932.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.197392 restraints weight = 56014.639| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26184 Z= 0.091 Angle : 0.496 7.773 35682 Z= 0.253 Chirality : 0.043 0.234 3794 Planarity : 0.003 0.041 4686 Dihedral : 5.128 58.908 3525 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.89 % Allowed : 14.62 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.14), residues: 3218 helix: -0.47 (0.30), residues: 316 sheet: -0.17 (0.21), residues: 666 loop : -0.60 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1007 TYR 0.014 0.001 TYR D1486 PHE 0.014 0.001 PHE C 236 TRP 0.036 0.001 TRP C 658 HIS 0.004 0.001 HIS D 529 Details of bonding type rmsd covalent geometry : bond 0.00215 (26096) covalent geometry : angle 0.49232 (35518) SS BOND : bond 0.00219 ( 82) SS BOND : angle 0.97650 ( 164) hydrogen bonds : bond 0.02411 ( 562) hydrogen bonds : angle 4.73168 ( 1572) metal coordination : bond 0.00248 ( 6) *********************** 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 313 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 231 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.6515 (mt0) cc_final: 0.6278 (mt0) REVERT: C 51 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7105 (mm-40) REVERT: C 183 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7945 (mmm-85) REVERT: C 541 THR cc_start: 0.6398 (p) cc_final: 0.5917 (t) REVERT: C 770 VAL cc_start: 0.8903 (t) cc_final: 0.8690 (m) REVERT: C 842 TRP cc_start: 0.7308 (p90) cc_final: 0.7074 (p90) REVERT: C 853 GLU cc_start: 0.6963 (mp0) cc_final: 0.6649 (mp0) REVERT: C 1026 ASP cc_start: 0.8013 (m-30) cc_final: 0.7674 (m-30) REVERT: C 1030 TYR cc_start: 0.7268 (p90) cc_final: 0.6973 (p90) REVERT: D 51 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7105 (mm-40) REVERT: D 183 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7953 (mmm-85) REVERT: D 330 ILE cc_start: 0.8168 (mm) cc_final: 0.7718 (mt) REVERT: D 658 TRP cc_start: 0.8044 (p-90) cc_final: 0.7760 (p-90) REVERT: D 842 TRP cc_start: 0.7335 (p90) cc_final: 0.7132 (p90) REVERT: D 1030 TYR cc_start: 0.7221 (p90) cc_final: 0.6885 (p90) REVERT: D 1201 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6004 (mp0) outliers start: 82 outliers final: 66 residues processed: 295 average time/residue: 0.1542 time to fit residues: 76.9153 Evaluate side-chains 290 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 85 ASN 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 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 821 ILE 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 926 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 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 1265 MET 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 102 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 VAL 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 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 918 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 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 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 188 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 280 optimal weight: 9.9990 chunk 262 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.198036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.193167 restraints weight = 32033.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.191847 restraints weight = 55336.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.190310 restraints weight = 56837.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.189645 restraints weight = 66136.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175901 restraints weight = 66363.022| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 26184 Z= 0.234 Angle : 0.622 8.807 35682 Z= 0.322 Chirality : 0.047 0.258 3794 Planarity : 0.005 0.071 4686 Dihedral : 5.626 58.646 3523 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.17 % Allowed : 14.34 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.14), residues: 3218 helix: -0.97 (0.28), residues: 328 sheet: -0.45 (0.21), residues: 632 loop : -0.84 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1007 TYR 0.015 0.002 TYR D 578 PHE 0.018 0.002 PHE C1516 TRP 0.061 0.002 TRP C 658 HIS 0.008 0.001 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00555 (26096) covalent geometry : angle 0.61802 (35518) SS BOND : bond 0.00365 ( 82) SS BOND : angle 1.20034 ( 164) hydrogen bonds : bond 0.03238 ( 562) hydrogen bonds : angle 5.21921 ( 1572) metal coordination : bond 0.01363 ( 6) *********************** 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 302 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 212 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 TRP cc_start: 0.8070 (t-100) cc_final: 0.7715 (t-100) REVERT: B 180 TRP cc_start: 0.8183 (t-100) cc_final: 0.7754 (t-100) REVERT: C 51 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7338 (mm-40) REVERT: C 183 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8115 (mtp180) REVERT: C 330 ILE cc_start: 0.8463 (mm) cc_final: 0.7989 (mt) REVERT: C 842 TRP cc_start: 0.7332 (p90) cc_final: 0.6825 (p90) REVERT: C 853 GLU cc_start: 0.7270 (mp0) cc_final: 0.6958 (mp0) REVERT: C 1026 ASP cc_start: 0.8069 (m-30) cc_final: 0.7759 (m-30) REVERT: C 1030 TYR cc_start: 0.7342 (p90) cc_final: 0.7091 (p90) REVERT: D 51 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7432 (mm-40) REVERT: D 183 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8158 (mtp180) REVERT: D 330 ILE cc_start: 0.8266 (mm) cc_final: 0.7834 (mt) REVERT: D 658 TRP cc_start: 0.8177 (p-90) cc_final: 0.7835 (p-90) REVERT: D 842 TRP cc_start: 0.7499 (p90) cc_final: 0.7003 (p90) REVERT: D 953 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6709 (t0) REVERT: D 1030 TYR cc_start: 0.7309 (p90) cc_final: 0.7056 (p90) REVERT: D 1201 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.5983 (mp0) REVERT: D 1482 MET cc_start: 0.7246 (mmt) cc_final: 0.6983 (mmt) outliers start: 90 outliers final: 71 residues processed: 287 average time/residue: 0.1663 time to fit residues: 79.8915 Evaluate side-chains 282 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 205 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 844 ILE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 926 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 1220 CYS Chi-restraints excluded: chain C residue 1265 MET 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 227 LYS Chi-restraints excluded: chain D residue 250 THR 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 844 ILE Chi-restraints excluded: chain D residue 858 VAL 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 941 ASP Chi-restraints excluded: chain D residue 953 ASP Chi-restraints excluded: chain D residue 976 ILE 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 1331 VAL 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 24 optimal weight: 4.9990 chunk 292 optimal weight: 0.0980 chunk 287 optimal weight: 20.0000 chunk 281 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 241 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.204794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.199697 restraints weight = 31961.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.198103 restraints weight = 63363.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.196153 restraints weight = 68418.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.194044 restraints weight = 64609.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.191802 restraints weight = 70509.472| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 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 : 0.002 0.036 26184 Z= 0.096 Angle : 0.510 7.974 35682 Z= 0.261 Chirality : 0.043 0.175 3794 Planarity : 0.003 0.042 4686 Dihedral : 5.215 57.510 3523 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.29 % Allowed : 15.33 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 3218 helix: -0.66 (0.29), residues: 328 sheet: -0.27 (0.21), residues: 660 loop : -0.64 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1007 TYR 0.011 0.001 TYR C1214 PHE 0.014 0.001 PHE C 236 TRP 0.049 0.001 TRP C 658 HIS 0.004 0.001 HIS D 529 Details of bonding type rmsd covalent geometry : bond 0.00227 (26096) covalent geometry : angle 0.50840 (35518) SS BOND : bond 0.00164 ( 82) SS BOND : angle 0.84923 ( 164) hydrogen bonds : bond 0.02516 ( 562) hydrogen bonds : angle 4.83728 ( 1572) metal coordination : bond 0.00331 ( 6) ********************** 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 289 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 TRP cc_start: 0.7967 (t-100) cc_final: 0.7673 (t-100) REVERT: C 51 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7242 (mm-40) REVERT: C 183 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7973 (mtp180) REVERT: C 330 ILE cc_start: 0.8342 (mm) cc_final: 0.7900 (mt) REVERT: C 842 TRP cc_start: 0.7278 (p90) cc_final: 0.7049 (p90) REVERT: C 853 GLU cc_start: 0.7125 (mp0) cc_final: 0.6789 (mp0) REVERT: C 1026 ASP cc_start: 0.8088 (m-30) cc_final: 0.7790 (m-30) REVERT: C 1030 TYR cc_start: 0.7292 (p90) cc_final: 0.7038 (p90) REVERT: D 51 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7300 (mm-40) REVERT: D 183 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7979 (mtp180) REVERT: D 330 ILE cc_start: 0.8198 (mm) cc_final: 0.7755 (mt) REVERT: D 658 TRP cc_start: 0.8061 (p-90) cc_final: 0.7785 (p-90) REVERT: D 842 TRP cc_start: 0.7365 (p90) cc_final: 0.7148 (p90) REVERT: D 1030 TYR cc_start: 0.7215 (p90) cc_final: 0.6954 (p90) REVERT: D 1201 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: D 1482 MET cc_start: 0.6823 (mmt) cc_final: 0.6617 (mmt) outliers start: 65 outliers final: 56 residues processed: 279 average time/residue: 0.1592 time to fit residues: 74.4083 Evaluate side-chains 273 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 374 ASN 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 926 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 1023 LEU Chi-restraints excluded: chain C residue 1044 ASP 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 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 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 844 ILE Chi-restraints excluded: chain D residue 858 VAL 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 976 ILE 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 1331 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 142 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 0.2980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1411 GLN D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN D1491 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.200113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.195080 restraints weight = 31781.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.193406 restraints weight = 60294.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185332 restraints weight = 66461.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181853 restraints weight = 59842.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.180636 restraints weight = 54434.349| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26184 Z= 0.107 Angle : 0.511 8.267 35682 Z= 0.260 Chirality : 0.043 0.165 3794 Planarity : 0.004 0.040 4686 Dihedral : 5.106 57.485 3523 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.40 % Allowed : 15.36 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.15), residues: 3218 helix: -0.56 (0.29), residues: 326 sheet: -0.24 (0.21), residues: 660 loop : -0.60 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1007 TYR 0.012 0.001 TYR D1214 PHE 0.014 0.001 PHE D 236 TRP 0.074 0.001 TRP C 658 HIS 0.011 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00255 (26096) covalent geometry : angle 0.50889 (35518) SS BOND : bond 0.00180 ( 82) SS BOND : angle 0.80604 ( 164) hydrogen bonds : bond 0.02518 ( 562) hydrogen bonds : angle 4.77807 ( 1572) metal coordination : bond 0.00507 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3819.66 seconds wall clock time: 67 minutes 14.55 seconds (4034.55 seconds total)