Starting phenix.real_space_refine on Thu Jul 31 03:26:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5n_33621/07_2025/7y5n_33621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5n_33621/07_2025/7y5n_33621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2025/7y5n_33621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2025/7y5n_33621.map" model { file = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2025/7y5n_33621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2025/7y5n_33621.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Zn 1 6.06 5 S 112 5.16 5 C 8147 2.51 5 N 2270 2.21 5 O 2497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13034 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1109 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "C" Number of atoms: 8767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8767 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 69, 'TRANS': 1045} Chain: "D" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2982 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 29, 'TRANS': 358} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Unusual residues: {' CA': 7, ' ZN': 1, 'NAG': 9} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.50, per 1000 atoms: 0.58 Number of scatterers: 13034 At special positions: 0 Unit cell: (146.228, 116.772, 127.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 7 19.99 S 112 16.00 O 2497 8.00 N 2270 7.00 C 8147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 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 C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 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=2.02 Simple disulfide: pdb=" SG CYS C 971 " - pdb=" SG CYS C1059 " distance=2.03 Simple disulfide: pdb=" SG CYS C1112 " - pdb=" SG CYS C1125 " 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=2.04 Simple disulfide: pdb=" SG CYS D1162 " - pdb=" SG CYS D1200 " distance=2.02 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=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 310 " " NAG C1601 " - " ASN C 322 " " NAG C1602 " - " ASN C 349 " " NAG C1603 " - " ASN C 400 " " NAG C1604 " - " ASN C 521 " " NAG C1605 " - " ASN C 645 " " NAG C1606 " - " ASN C 745 " " NAG C1607 " - " ASN C 946 " " NAG C1609 " - " ASN C 825 " " NAG C1610 " - " ASN C 539 " " NAG D1601 " - " ASN D1142 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1608 " pdb="ZN ZN C1608 " - pdb=" NE2 HIS C 482 " pdb="ZN ZN C1608 " - pdb=" NE2 HIS C 486 " pdb="ZN ZN C1608 " - pdb=" NE2 HIS C 492 " 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 24 sheets defined 12.0% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 212 through 216 removed outlier: 4.470A pdb=" N ALA C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 216' Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 335 through 339 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 391 removed outlier: 4.036A pdb=" N GLY C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.982A 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: 3.700A pdb=" N THR C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 Processing helix chain 'C' and resid 478 through 487 Processing helix chain 'C' and resid 492 through 496 removed outlier: 4.440A 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 583 through 587 removed outlier: 3.506A pdb=" N TRP C 586 " --> pdb=" O TYR C 583 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 587 " --> pdb=" O GLN C 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 587' Processing helix chain 'C' and resid 815 through 820 removed outlier: 3.949A pdb=" N SER C 820 " --> pdb=" O MET C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 877 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1105 through 1112 removed outlier: 3.510A pdb=" N SER C1111 " --> pdb=" O VAL C1107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C1112 " --> pdb=" O THR C1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1283 Processing helix chain 'D' and resid 1339 through 1343 removed outlier: 3.755A pdb=" N HIS D1343 " --> pdb=" O PRO D1340 " (cutoff:3.500A) Processing helix chain 'D' and resid 1493 through 1502 removed outlier: 3.809A pdb=" N ASN D1497 " --> pdb=" O ALA D1494 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR D1498 " --> pdb=" O PHE D1495 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D1502 " --> pdb=" O ASP D1499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 5.817A pdb=" N SER A 114 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 5.348A 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: 3.633A pdb=" N ILE A 159 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 198 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 135 through 140 removed outlier: 5.412A pdb=" N GLN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 132 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 176 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 135 through 140 removed outlier: 5.412A pdb=" N GLN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 132 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 106 removed outlier: 6.480A pdb=" N ILE C 77 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL C 56 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 79 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 321 removed outlier: 4.862A pdb=" N PHE C 437 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU C 280 " --> pdb=" O PHE C 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA8, first strand: chain 'C' and resid 600 through 604 removed outlier: 6.925A pdb=" N THR C 610 " --> pdb=" O LEU C 602 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 640 through 642 removed outlier: 6.648A pdb=" N ILE C 784 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 720 " --> pdb=" O ILE C 784 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 786 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE C 718 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET C 788 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU C 716 " --> pdb=" O MET C 788 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C 790 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 645 through 647 removed outlier: 11.614A pdb=" N LEU C 705 " --> pdb=" O TYR C 776 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N TYR C 776 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N PHE C 707 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 11.668A pdb=" N GLN C 774 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N TYR C 709 " --> pdb=" O GLY C 772 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLY C 772 " --> pdb=" O TYR C 709 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 735 " --> pdb=" O TYR C 776 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 736 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 805 through 810 Processing sheet with id=AB3, first strand: chain 'C' and resid 901 through 903 Processing sheet with id=AB4, first strand: chain 'C' and resid 939 through 943 removed outlier: 3.548A pdb=" N GLY C1095 " --> pdb=" O HIS C1022 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 948 through 949 removed outlier: 6.742A pdb=" N GLN C1080 " --> pdb=" O PHE C1010 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C1040 " --> pdb=" O GLY C1053 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C1053 " --> pdb=" O VAL C1040 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU C1042 " --> pdb=" O ASP C1051 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP C1051 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP C1044 " --> pdb=" O SER C1049 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER C1049 " --> pdb=" O ASP C1044 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AB7, first strand: chain 'D' and resid 1143 through 1147 removed outlier: 3.581A pdb=" N VAL D1185 " --> pdb=" O VAL D1160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1175 through 1176 removed outlier: 3.566A pdb=" N GLU D1175 " --> pdb=" O ARG D1172 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA D1199 " --> pdb=" O GLN D1169 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG D1171 " --> pdb=" O GLN D1197 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN D1197 " --> pdb=" O ARG D1171 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1216 through 1219 Processing sheet with id=AC1, first strand: chain 'D' and resid 1239 through 1242 Processing sheet with id=AC2, first strand: chain 'D' and resid 1275 through 1277 Processing sheet with id=AC3, first strand: chain 'D' and resid 1301 through 1302 removed outlier: 3.563A pdb=" N HIS D1302 " --> pdb=" O VAL D1331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1358 through 1359 removed outlier: 4.308A pdb=" N CYS D1358 " --> pdb=" O ILE D1376 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE D1376 " --> pdb=" O CYS D1358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 1408 through 1411 Processing sheet with id=AC6, first strand: chain 'D' and resid 1431 through 1435 308 hydrogen bonds defined for protein. 801 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: 4.90 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4233 1.34 - 1.46: 3086 1.46 - 1.58: 5923 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 13376 Sorted by residual: bond pdb=" N VAL D1513 " pdb=" CA VAL D1513 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" C1 NAG C1609 " pdb=" O5 NAG C1609 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.69e+00 bond pdb=" N PHE D1516 " pdb=" CA PHE D1516 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.15e+00 bond pdb=" N TRP A 207 " pdb=" CA TRP A 207 " ideal model delta sigma weight residual 1.453 1.489 -0.035 1.27e-02 6.20e+03 7.65e+00 bond pdb=" N LEU C 940 " pdb=" CA LEU C 940 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.26e-02 6.30e+03 7.08e+00 ... (remaining 13371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 17650 1.77 - 3.54: 489 3.54 - 5.31: 41 5.31 - 7.08: 14 7.08 - 8.86: 8 Bond angle restraints: 18202 Sorted by residual: angle pdb=" C THR D1334 " pdb=" N CYS D1335 " pdb=" CA CYS D1335 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.98e+01 angle pdb=" CA MET C 473 " pdb=" C MET C 473 " pdb=" O MET C 473 " ideal model delta sigma weight residual 120.19 116.61 3.58 8.40e-01 1.42e+00 1.81e+01 angle pdb=" N GLN A 189 " pdb=" CA GLN A 189 " pdb=" C GLN A 189 " ideal model delta sigma weight residual 109.81 118.28 -8.47 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C GLU C 442 " pdb=" N GLU C 443 " pdb=" CA GLU C 443 " ideal model delta sigma weight residual 122.08 127.54 -5.46 1.47e+00 4.63e-01 1.38e+01 angle pdb=" C TRP C 727 " pdb=" N ASP C 728 " pdb=" CA ASP C 728 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.28e+01 ... (remaining 18197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 7775 22.77 - 45.54: 360 45.54 - 68.31: 64 68.31 - 91.08: 8 91.08 - 113.85: 14 Dihedral angle restraints: 8221 sinusoidal: 3480 harmonic: 4741 Sorted by residual: dihedral pdb=" CB CYS C 252 " pdb=" SG CYS C 252 " pdb=" SG CYS C 577 " pdb=" CB CYS C 577 " ideal model delta sinusoidal sigma weight residual 93.00 155.15 -62.15 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS C 867 " pdb=" SG CYS C 867 " pdb=" SG CYS C 895 " pdb=" CB CYS C 895 " ideal model delta sinusoidal sigma weight residual -86.00 -141.45 55.45 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CA ASP C 811 " pdb=" C ASP C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 8218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1424 0.049 - 0.099: 408 0.099 - 0.148: 127 0.148 - 0.197: 16 0.197 - 0.247: 4 Chirality restraints: 1979 Sorted by residual: chirality pdb=" C1 NAG C1610 " pdb=" ND2 ASN C 539 " pdb=" C2 NAG C1610 " pdb=" O5 NAG C1610 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA GLN A 189 " pdb=" N GLN A 189 " pdb=" C GLN A 189 " pdb=" CB GLN A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LEU C 940 " pdb=" N LEU C 940 " pdb=" C LEU C 940 " pdb=" CB LEU C 940 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1976 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 988 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO C 989 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 989 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 681 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO C 682 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 682 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 682 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 101 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A 102 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.029 5.00e-02 4.00e+02 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2709 2.78 - 3.31: 10699 3.31 - 3.84: 21453 3.84 - 4.37: 24874 4.37 - 4.90: 43251 Nonbonded interactions: 102986 Sorted by model distance: nonbonded pdb=" O GLY D1300 " pdb=" OG1 THR D1334 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP C 87 " pdb=" OG SER C 110 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR D1320 " pdb=" OD1 ASP D1322 " model vdw 2.322 3.040 nonbonded pdb=" O GLY C 49 " pdb=" OH TYR C 111 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASN C 322 " pdb=" OG SER C 324 " model vdw 2.331 3.040 ... (remaining 102981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 0.005 0.066 13433 Z= 0.232 Angle : 0.698 8.855 18322 Z= 0.376 Chirality : 0.051 0.247 1979 Planarity : 0.006 0.055 2384 Dihedral : 14.101 113.850 5045 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.43 % Allowed : 7.24 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1629 helix: -2.27 (0.31), residues: 153 sheet: 0.18 (0.28), residues: 354 loop : -1.27 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 842 HIS 0.006 0.001 HIS C 78 PHE 0.015 0.002 PHE C 92 TYR 0.017 0.002 TYR C 131 ARG 0.003 0.000 ARG C 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 11) link_NAG-ASN : angle 1.80184 ( 33) link_BETA1-4 : bond 0.00077 ( 1) link_BETA1-4 : angle 1.96016 ( 3) hydrogen bonds : bond 0.15843 ( 292) hydrogen bonds : angle 6.89605 ( 801) metal coordination : bond 0.00646 ( 3) SS BOND : bond 0.00289 ( 42) SS BOND : angle 0.91118 ( 84) covalent geometry : bond 0.00480 (13376) covalent geometry : angle 0.69264 (18202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 210 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8713 (p) cc_final: 0.8505 (p) REVERT: C 221 LYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5253 (mmtm) REVERT: C 590 ARG cc_start: 0.6686 (mtp85) cc_final: 0.6127 (tpt170) REVERT: C 632 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8376 (mt) REVERT: C 728 ASP cc_start: 0.5535 (m-30) cc_final: 0.4961 (t0) REVERT: C 745 ASN cc_start: 0.7008 (OUTLIER) cc_final: 0.6773 (m-40) REVERT: C 778 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7970 (mp) REVERT: C 889 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7338 (m-30) REVERT: C 961 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7383 (mp) REVERT: C 1109 LEU cc_start: 0.8180 (mt) cc_final: 0.7961 (mm) REVERT: D 1170 ILE cc_start: 0.5968 (OUTLIER) cc_final: 0.5612 (pt) REVERT: D 1177 ILE cc_start: 0.3542 (OUTLIER) cc_final: 0.3166 (mt) REVERT: D 1283 ARG cc_start: 0.6896 (mtt180) cc_final: 0.5530 (ttp80) REVERT: D 1388 PHE cc_start: 0.5103 (m-10) cc_final: 0.4809 (m-80) REVERT: D 1512 LYS cc_start: 0.8266 (tttt) cc_final: 0.7965 (ttpt) REVERT: D 1532 GLN cc_start: 0.5989 (mt0) cc_final: 0.5774 (mp10) outliers start: 78 outliers final: 23 residues processed: 274 average time/residue: 0.2600 time to fit residues: 103.3246 Evaluate side-chains 173 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 173 GLN A 188 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 78 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 HIS C1062 ASN D1154 HIS D1211 HIS D1274 ASN D1377 HIS D1389 HIS ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.157243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122620 restraints weight = 18184.327| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.42 r_work: 0.3118 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13433 Z= 0.239 Angle : 0.664 9.295 18322 Z= 0.341 Chirality : 0.049 0.262 1979 Planarity : 0.005 0.042 2384 Dihedral : 10.947 107.633 2077 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.62 % Allowed : 11.34 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1629 helix: -0.93 (0.39), residues: 140 sheet: -0.14 (0.28), residues: 362 loop : -1.00 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 680 HIS 0.008 0.001 HIS C 78 PHE 0.018 0.002 PHE D1342 TYR 0.020 0.002 TYR C 131 ARG 0.003 0.001 ARG A 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 11) link_NAG-ASN : angle 1.72956 ( 33) link_BETA1-4 : bond 0.00019 ( 1) link_BETA1-4 : angle 1.05244 ( 3) hydrogen bonds : bond 0.04411 ( 292) hydrogen bonds : angle 5.76130 ( 801) metal coordination : bond 0.00991 ( 3) SS BOND : bond 0.00490 ( 42) SS BOND : angle 1.58940 ( 84) covalent geometry : bond 0.00565 (13376) covalent geometry : angle 0.65280 (18202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 1.677 Fit side-chains REVERT: A 130 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7387 (tpm170) REVERT: C 221 LYS cc_start: 0.6307 (OUTLIER) cc_final: 0.5332 (mmtm) REVERT: C 590 ARG cc_start: 0.7154 (mtp85) cc_final: 0.5909 (tpt170) REVERT: C 632 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8707 (mt) REVERT: C 670 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6980 (mm-30) REVERT: C 728 ASP cc_start: 0.5819 (m-30) cc_final: 0.5071 (t0) REVERT: C 961 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7777 (mp) REVERT: D 1170 ILE cc_start: 0.5379 (tt) cc_final: 0.4880 (pt) REVERT: D 1177 ILE cc_start: 0.1650 (OUTLIER) cc_final: 0.1371 (mt) REVERT: D 1283 ARG cc_start: 0.7302 (mtt180) cc_final: 0.5760 (ttp80) REVERT: D 1352 PHE cc_start: 0.5248 (m-80) cc_final: 0.4519 (m-10) REVERT: D 1388 PHE cc_start: 0.5691 (m-10) cc_final: 0.5227 (m-80) REVERT: D 1512 LYS cc_start: 0.8032 (tttt) cc_final: 0.7518 (ttpt) REVERT: D 1518 MET cc_start: 0.6286 (ttp) cc_final: 0.5748 (mmt) REVERT: D 1532 GLN cc_start: 0.6201 (mt0) cc_final: 0.5900 (mp10) outliers start: 52 outliers final: 35 residues processed: 188 average time/residue: 0.3127 time to fit residues: 89.2734 Evaluate side-chains 158 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 69 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 0.0020 chunk 29 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 85 ASN C 269 GLN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.160016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125515 restraints weight = 18274.417| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.40 r_work: 0.3172 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13433 Z= 0.110 Angle : 0.566 8.111 18322 Z= 0.283 Chirality : 0.045 0.301 1979 Planarity : 0.004 0.034 2384 Dihedral : 9.073 104.408 2062 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.41 % Allowed : 12.04 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1629 helix: -0.15 (0.43), residues: 140 sheet: -0.19 (0.28), residues: 356 loop : -0.78 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 842 HIS 0.005 0.001 HIS D1429 PHE 0.019 0.001 PHE D1342 TYR 0.016 0.001 TYR C 131 ARG 0.004 0.000 ARG D1456 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 11) link_NAG-ASN : angle 2.20713 ( 33) link_BETA1-4 : bond 0.00138 ( 1) link_BETA1-4 : angle 1.18004 ( 3) hydrogen bonds : bond 0.03386 ( 292) hydrogen bonds : angle 5.43462 ( 801) metal coordination : bond 0.00238 ( 3) SS BOND : bond 0.00269 ( 42) SS BOND : angle 1.29043 ( 84) covalent geometry : bond 0.00253 (13376) covalent geometry : angle 0.55254 (18202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7466 (tpm170) REVERT: C 221 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5148 (mmtm) REVERT: C 319 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7352 (mm-30) REVERT: C 384 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7182 (tm-30) REVERT: C 590 ARG cc_start: 0.7184 (mtp85) cc_final: 0.5948 (tpt170) REVERT: C 670 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6960 (mm-30) REVERT: C 728 ASP cc_start: 0.5534 (m-30) cc_final: 0.4872 (t0) REVERT: D 1170 ILE cc_start: 0.5399 (tt) cc_final: 0.4919 (pt) REVERT: D 1177 ILE cc_start: 0.1951 (OUTLIER) cc_final: 0.1666 (mt) REVERT: D 1283 ARG cc_start: 0.7377 (mtt180) cc_final: 0.5633 (ttp80) REVERT: D 1352 PHE cc_start: 0.5393 (m-80) cc_final: 0.4596 (m-10) REVERT: D 1388 PHE cc_start: 0.5709 (m-10) cc_final: 0.5137 (m-80) REVERT: D 1512 LYS cc_start: 0.7927 (tttt) cc_final: 0.7364 (ttpt) REVERT: D 1532 GLN cc_start: 0.6274 (mt0) cc_final: 0.5959 (mp10) outliers start: 49 outliers final: 34 residues processed: 177 average time/residue: 0.2470 time to fit residues: 65.5875 Evaluate side-chains 156 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1319 CYS Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 92 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 70 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 234 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120468 restraints weight = 18396.416| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.55 r_work: 0.3067 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 13433 Z= 0.279 Angle : 0.686 8.249 18322 Z= 0.350 Chirality : 0.050 0.404 1979 Planarity : 0.005 0.039 2384 Dihedral : 8.562 95.397 2053 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.11 % Allowed : 12.60 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1629 helix: -0.32 (0.44), residues: 134 sheet: -0.37 (0.27), residues: 373 loop : -0.83 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 658 HIS 0.007 0.001 HIS C 492 PHE 0.016 0.002 PHE C 19 TYR 0.019 0.002 TYR C 471 ARG 0.004 0.001 ARG C 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 11) link_NAG-ASN : angle 2.41880 ( 33) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 1.23777 ( 3) hydrogen bonds : bond 0.04258 ( 292) hydrogen bonds : angle 5.62971 ( 801) metal coordination : bond 0.01111 ( 3) SS BOND : bond 0.00436 ( 42) SS BOND : angle 1.33856 ( 84) covalent geometry : bond 0.00664 (13376) covalent geometry : angle 0.67373 (18202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7430 (tpm170) REVERT: C 221 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5224 (mmtm) REVERT: C 319 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: C 418 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8662 (p) REVERT: C 590 ARG cc_start: 0.7192 (mtp85) cc_final: 0.6033 (tpt170) REVERT: C 728 ASP cc_start: 0.5198 (m-30) cc_final: 0.4628 (t0) REVERT: C 759 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8755 (tp) REVERT: D 1283 ARG cc_start: 0.7430 (mtt180) cc_final: 0.5878 (ttp80) REVERT: D 1352 PHE cc_start: 0.5284 (m-80) cc_final: 0.4730 (m-10) REVERT: D 1388 PHE cc_start: 0.5755 (m-10) cc_final: 0.5190 (m-80) REVERT: D 1491 ASN cc_start: 0.7495 (m110) cc_final: 0.7161 (m-40) REVERT: D 1512 LYS cc_start: 0.8085 (tttt) cc_final: 0.7539 (ttpt) REVERT: D 1532 GLN cc_start: 0.6212 (mt0) cc_final: 0.5863 (mp10) outliers start: 59 outliers final: 46 residues processed: 179 average time/residue: 0.2740 time to fit residues: 74.3003 Evaluate side-chains 174 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1319 CYS Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1452 THR Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 85 optimal weight: 0.0770 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.158552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124281 restraints weight = 18300.245| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.37 r_work: 0.3139 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13433 Z= 0.112 Angle : 0.593 18.240 18322 Z= 0.290 Chirality : 0.046 0.490 1979 Planarity : 0.004 0.035 2384 Dihedral : 8.073 94.762 2051 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.41 % Allowed : 14.34 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1629 helix: -0.14 (0.43), residues: 147 sheet: -0.18 (0.27), residues: 363 loop : -0.72 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 842 HIS 0.013 0.001 HIS C 234 PHE 0.026 0.001 PHE C 236 TYR 0.015 0.001 TYR C 131 ARG 0.005 0.000 ARG D1538 Details of bonding type rmsd link_NAG-ASN : bond 0.00823 ( 11) link_NAG-ASN : angle 4.66178 ( 33) link_BETA1-4 : bond 0.00062 ( 1) link_BETA1-4 : angle 1.11433 ( 3) hydrogen bonds : bond 0.03327 ( 292) hydrogen bonds : angle 5.32936 ( 801) metal coordination : bond 0.00287 ( 3) SS BOND : bond 0.00316 ( 42) SS BOND : angle 1.12076 ( 84) covalent geometry : bond 0.00256 (13376) covalent geometry : angle 0.55501 (18202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 1.628 Fit side-chains revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7418 (tpm170) REVERT: C 221 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5198 (mmtm) REVERT: C 319 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: C 590 ARG cc_start: 0.7130 (mtp85) cc_final: 0.5863 (tpt170) REVERT: C 728 ASP cc_start: 0.5100 (m-30) cc_final: 0.4604 (t0) REVERT: D 1151 ASP cc_start: 0.3093 (t0) cc_final: 0.2872 (t0) REVERT: D 1283 ARG cc_start: 0.7449 (mtt180) cc_final: 0.5762 (ttp80) REVERT: D 1352 PHE cc_start: 0.5307 (m-80) cc_final: 0.4743 (m-10) REVERT: D 1388 PHE cc_start: 0.5709 (m-10) cc_final: 0.5105 (m-80) REVERT: D 1491 ASN cc_start: 0.7343 (m110) cc_final: 0.7001 (m-40) REVERT: D 1505 THR cc_start: 0.7027 (OUTLIER) cc_final: 0.6827 (p) REVERT: D 1512 LYS cc_start: 0.7931 (tttt) cc_final: 0.7272 (ttpt) REVERT: D 1532 GLN cc_start: 0.6134 (mt0) cc_final: 0.5808 (mp10) outliers start: 49 outliers final: 35 residues processed: 171 average time/residue: 0.2987 time to fit residues: 77.5617 Evaluate side-chains 156 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1505 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 0.0050 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.157924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123505 restraints weight = 18562.397| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.41 r_work: 0.3143 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13433 Z= 0.142 Angle : 0.584 14.712 18322 Z= 0.288 Chirality : 0.046 0.285 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.868 93.924 2049 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.13 % Allowed : 14.89 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1629 helix: -0.06 (0.43), residues: 147 sheet: -0.23 (0.27), residues: 364 loop : -0.70 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 842 HIS 0.004 0.001 HIS D1468 PHE 0.019 0.001 PHE C 236 TYR 0.015 0.001 TYR C 131 ARG 0.007 0.000 ARG D1538 Details of bonding type rmsd link_NAG-ASN : bond 0.00914 ( 11) link_NAG-ASN : angle 4.00611 ( 33) link_BETA1-4 : bond 0.00104 ( 1) link_BETA1-4 : angle 1.22350 ( 3) hydrogen bonds : bond 0.03360 ( 292) hydrogen bonds : angle 5.24975 ( 801) metal coordination : bond 0.00480 ( 3) SS BOND : bond 0.00238 ( 42) SS BOND : angle 1.14798 ( 84) covalent geometry : bond 0.00333 (13376) covalent geometry : angle 0.55462 (18202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7426 (tpm170) REVERT: C 221 LYS cc_start: 0.6152 (OUTLIER) cc_final: 0.5200 (mmtm) REVERT: C 319 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: C 590 ARG cc_start: 0.7132 (mtp85) cc_final: 0.5864 (tpt170) REVERT: C 728 ASP cc_start: 0.5059 (m-30) cc_final: 0.4519 (t0) REVERT: D 1246 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7363 (tp) REVERT: D 1283 ARG cc_start: 0.7394 (mtt180) cc_final: 0.5792 (ttp80) REVERT: D 1352 PHE cc_start: 0.5224 (m-80) cc_final: 0.4646 (m-10) REVERT: D 1388 PHE cc_start: 0.5755 (m-10) cc_final: 0.5157 (m-80) REVERT: D 1491 ASN cc_start: 0.7427 (m110) cc_final: 0.7104 (m-40) REVERT: D 1512 LYS cc_start: 0.7937 (tttt) cc_final: 0.7265 (ttpt) REVERT: D 1532 GLN cc_start: 0.6135 (mt0) cc_final: 0.5809 (mp10) outliers start: 45 outliers final: 36 residues processed: 160 average time/residue: 0.2466 time to fit residues: 59.2205 Evaluate side-chains 159 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 0.0030 chunk 145 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.155826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121516 restraints weight = 18653.730| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.55 r_work: 0.3088 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13433 Z= 0.213 Angle : 0.629 13.851 18322 Z= 0.313 Chirality : 0.048 0.259 1979 Planarity : 0.004 0.036 2384 Dihedral : 7.982 93.410 2048 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.90 % Allowed : 14.54 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1629 helix: -0.24 (0.42), residues: 148 sheet: -0.31 (0.27), residues: 366 loop : -0.81 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 842 HIS 0.005 0.001 HIS D1468 PHE 0.019 0.002 PHE C 236 TYR 0.016 0.002 TYR C 131 ARG 0.007 0.001 ARG D1538 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 11) link_NAG-ASN : angle 3.88791 ( 33) link_BETA1-4 : bond 0.00040 ( 1) link_BETA1-4 : angle 1.25047 ( 3) hydrogen bonds : bond 0.03767 ( 292) hydrogen bonds : angle 5.36075 ( 801) metal coordination : bond 0.00861 ( 3) SS BOND : bond 0.00302 ( 42) SS BOND : angle 1.11349 ( 84) covalent geometry : bond 0.00506 (13376) covalent geometry : angle 0.60404 (18202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7403 (tpm170) REVERT: C 221 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5217 (mmtm) REVERT: C 319 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: C 590 ARG cc_start: 0.7187 (mtp85) cc_final: 0.5917 (tpt170) REVERT: C 728 ASP cc_start: 0.5209 (m-30) cc_final: 0.4578 (t0) REVERT: C 759 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8808 (tp) REVERT: D 1283 ARG cc_start: 0.7375 (mtt180) cc_final: 0.5837 (ttp80) REVERT: D 1352 PHE cc_start: 0.5066 (m-80) cc_final: 0.4679 (m-10) REVERT: D 1388 PHE cc_start: 0.5737 (m-10) cc_final: 0.5141 (m-80) REVERT: D 1491 ASN cc_start: 0.7567 (m110) cc_final: 0.7252 (m-40) REVERT: D 1512 LYS cc_start: 0.7996 (tttt) cc_final: 0.7375 (ttpt) REVERT: D 1532 GLN cc_start: 0.6325 (mt0) cc_final: 0.5896 (mp10) outliers start: 56 outliers final: 43 residues processed: 169 average time/residue: 0.2448 time to fit residues: 61.7770 Evaluate side-chains 163 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 106 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120966 restraints weight = 18610.988| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.35 r_work: 0.3110 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13433 Z= 0.141 Angle : 0.582 11.232 18322 Z= 0.289 Chirality : 0.045 0.244 1979 Planarity : 0.004 0.037 2384 Dihedral : 7.813 92.888 2048 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.48 % Allowed : 15.17 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1629 helix: -0.01 (0.43), residues: 147 sheet: -0.25 (0.27), residues: 365 loop : -0.73 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 179 HIS 0.004 0.001 HIS D1468 PHE 0.016 0.001 PHE C 236 TYR 0.016 0.001 TYR C 131 ARG 0.008 0.000 ARG D1538 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 11) link_NAG-ASN : angle 3.00553 ( 33) link_BETA1-4 : bond 0.00000 ( 1) link_BETA1-4 : angle 1.25207 ( 3) hydrogen bonds : bond 0.03324 ( 292) hydrogen bonds : angle 5.23384 ( 801) metal coordination : bond 0.00437 ( 3) SS BOND : bond 0.00238 ( 42) SS BOND : angle 1.50479 ( 84) covalent geometry : bond 0.00329 (13376) covalent geometry : angle 0.56020 (18202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7447 (tpm170) REVERT: C 221 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5158 (mmtm) REVERT: C 319 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: C 590 ARG cc_start: 0.7142 (mtp85) cc_final: 0.5861 (tpt170) REVERT: C 728 ASP cc_start: 0.4949 (m-30) cc_final: 0.4377 (t0) REVERT: C 759 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8788 (tp) REVERT: D 1283 ARG cc_start: 0.7382 (mtt180) cc_final: 0.5791 (ttp80) REVERT: D 1352 PHE cc_start: 0.5240 (m-80) cc_final: 0.4796 (m-10) REVERT: D 1388 PHE cc_start: 0.5707 (m-10) cc_final: 0.5125 (m-80) REVERT: D 1491 ASN cc_start: 0.7478 (m110) cc_final: 0.7164 (m-40) REVERT: D 1512 LYS cc_start: 0.7938 (tttt) cc_final: 0.7360 (ttpt) REVERT: D 1532 GLN cc_start: 0.6288 (mt0) cc_final: 0.5846 (mp10) outliers start: 50 outliers final: 42 residues processed: 163 average time/residue: 0.3174 time to fit residues: 80.1308 Evaluate side-chains 163 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 23 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 128 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 156 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120224 restraints weight = 18469.769| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.62 r_work: 0.3114 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13433 Z= 0.153 Angle : 0.582 10.910 18322 Z= 0.290 Chirality : 0.045 0.239 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.728 91.865 2046 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.27 % Allowed : 15.38 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1629 helix: 0.05 (0.43), residues: 147 sheet: -0.21 (0.27), residues: 363 loop : -0.73 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 179 HIS 0.005 0.001 HIS C 985 PHE 0.018 0.001 PHE D1342 TYR 0.015 0.001 TYR C 131 ARG 0.008 0.000 ARG D1538 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 11) link_NAG-ASN : angle 3.07191 ( 33) link_BETA1-4 : bond 0.00050 ( 1) link_BETA1-4 : angle 1.26914 ( 3) hydrogen bonds : bond 0.03367 ( 292) hydrogen bonds : angle 5.19638 ( 801) metal coordination : bond 0.00527 ( 3) SS BOND : bond 0.00237 ( 42) SS BOND : angle 1.31101 ( 84) covalent geometry : bond 0.00361 (13376) covalent geometry : angle 0.56139 (18202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.7725 (mp10) cc_final: 0.7492 (mp10) REVERT: A 130 ARG cc_start: 0.7795 (mtp180) cc_final: 0.7446 (tpm170) REVERT: C 221 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5079 (mmtm) REVERT: C 319 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: C 590 ARG cc_start: 0.7189 (mtp85) cc_final: 0.5896 (tpt170) REVERT: C 728 ASP cc_start: 0.4797 (m-30) cc_final: 0.4231 (t0) REVERT: C 759 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8790 (tp) REVERT: D 1177 ILE cc_start: 0.1979 (OUTLIER) cc_final: 0.1760 (mt) REVERT: D 1283 ARG cc_start: 0.7386 (mtt180) cc_final: 0.5849 (ttp80) REVERT: D 1352 PHE cc_start: 0.5335 (m-80) cc_final: 0.4893 (m-10) REVERT: D 1491 ASN cc_start: 0.7484 (m110) cc_final: 0.7209 (m-40) REVERT: D 1512 LYS cc_start: 0.7994 (tttt) cc_final: 0.7414 (ttpt) REVERT: D 1532 GLN cc_start: 0.6312 (mt0) cc_final: 0.5864 (mp10) outliers start: 47 outliers final: 40 residues processed: 163 average time/residue: 0.3065 time to fit residues: 75.3883 Evaluate side-chains 163 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120766 restraints weight = 18490.443| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.29 r_work: 0.3122 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13433 Z= 0.141 Angle : 0.571 10.568 18322 Z= 0.284 Chirality : 0.045 0.234 1979 Planarity : 0.004 0.036 2384 Dihedral : 7.643 91.321 2045 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.34 % Allowed : 15.45 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1629 helix: 0.23 (0.44), residues: 141 sheet: -0.19 (0.27), residues: 363 loop : -0.67 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 179 HIS 0.004 0.001 HIS D1468 PHE 0.024 0.001 PHE C 236 TYR 0.015 0.001 TYR C 131 ARG 0.007 0.000 ARG D1538 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 11) link_NAG-ASN : angle 3.01876 ( 33) link_BETA1-4 : bond 0.00085 ( 1) link_BETA1-4 : angle 1.24525 ( 3) hydrogen bonds : bond 0.03261 ( 292) hydrogen bonds : angle 5.15999 ( 801) metal coordination : bond 0.00456 ( 3) SS BOND : bond 0.00225 ( 42) SS BOND : angle 1.13877 ( 84) covalent geometry : bond 0.00331 (13376) covalent geometry : angle 0.55215 (18202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8147 (ptt180) cc_final: 0.7907 (ptt-90) REVERT: A 130 ARG cc_start: 0.7747 (mtp180) cc_final: 0.7436 (tpm170) REVERT: C 221 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5058 (mmtm) REVERT: C 319 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: C 590 ARG cc_start: 0.7149 (mtp85) cc_final: 0.5888 (tpt170) REVERT: C 728 ASP cc_start: 0.4812 (m-30) cc_final: 0.4159 (t0) REVERT: C 759 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 1177 ILE cc_start: 0.2063 (OUTLIER) cc_final: 0.1855 (mt) REVERT: D 1283 ARG cc_start: 0.7382 (mtt180) cc_final: 0.5847 (ttp80) REVERT: D 1352 PHE cc_start: 0.5306 (m-80) cc_final: 0.4912 (m-10) REVERT: D 1388 PHE cc_start: 0.5758 (m-10) cc_final: 0.5114 (m-80) REVERT: D 1491 ASN cc_start: 0.7492 (m110) cc_final: 0.7204 (m-40) REVERT: D 1512 LYS cc_start: 0.7938 (tttt) cc_final: 0.7389 (ttpt) REVERT: D 1532 GLN cc_start: 0.6272 (mt0) cc_final: 0.5846 (mp10) outliers start: 48 outliers final: 41 residues processed: 160 average time/residue: 0.2541 time to fit residues: 60.8491 Evaluate side-chains 162 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 132 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 160 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 0.0060 chunk 127 optimal weight: 9.9990 overall best weight: 0.5014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125019 restraints weight = 18168.061| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.01 r_work: 0.3186 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13433 Z= 0.097 Angle : 0.546 10.147 18322 Z= 0.269 Chirality : 0.044 0.225 1979 Planarity : 0.004 0.036 2384 Dihedral : 7.436 90.143 2045 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.85 % Allowed : 15.87 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1629 helix: 0.46 (0.45), residues: 141 sheet: -0.12 (0.27), residues: 363 loop : -0.60 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 158 HIS 0.004 0.000 HIS D1468 PHE 0.009 0.001 PHE C 19 TYR 0.014 0.001 TYR C 131 ARG 0.006 0.000 ARG D1538 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 11) link_NAG-ASN : angle 2.84697 ( 33) link_BETA1-4 : bond 0.00142 ( 1) link_BETA1-4 : angle 1.23949 ( 3) hydrogen bonds : bond 0.02937 ( 292) hydrogen bonds : angle 5.01061 ( 801) metal coordination : bond 0.00142 ( 3) SS BOND : bond 0.00173 ( 42) SS BOND : angle 1.02117 ( 84) covalent geometry : bond 0.00223 (13376) covalent geometry : angle 0.52950 (18202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6594.26 seconds wall clock time: 119 minutes 3.78 seconds (7143.78 seconds total)