Starting phenix.real_space_refine on Fri Jul 3 08:15:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y5n_33621/07_2026/7y5n_33621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5n_33621/07_2026/7y5n_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_2026/7y5n_33621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2026/7y5n_33621.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2026/7y5n_33621.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2026/7y5n_33621.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2026/7y5n_33621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5n_33621/07_2026/7y5n_33621.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 chiralities: 1 Time building chain proxies: 2.35, per 1000 atoms: 0.18 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: 0.65 Conformation dependent library (CDL) restraints added in 407.7 milliseconds 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: 0.25 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: 2.48 Time building geometry restraints manager: 0.91 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 - 15.76: 7187 15.76 - 31.52: 591 31.52 - 47.29: 144 47.29 - 63.05: 41 63.05 - 78.81: 6 Dihedral angle restraints: 7969 sinusoidal: 3228 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 7966 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: 1.220 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 12.678 78.811 4793 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG C 274 TYR 0.017 0.002 TYR C 131 PHE 0.015 0.002 PHE C 92 TRP 0.011 0.002 TRP C 842 HIS 0.006 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 (13376) covalent geometry : angle 0.69264 / 0.38 (18202) SS BOND : bond 0.00289 / 0.16 ( 42) SS BOND : angle 0.91118 / 0.55 ( 84) hydrogen bonds : bond 0.15843 / 10.78 ( 292) hydrogen bonds : angle 6.89605 / 4.99 ( 801) metal coordination : bond 0.00646 / 0.33 ( 3) link_BETA1-4 : bond 0.00077 / 0.04 ( 1) link_BETA1-4 : angle 1.96016 / 1.08 ( 3) link_NAG-ASN : bond 0.00409 / 0.25 ( 11) link_NAG-ASN : angle 1.80184 / 1.40 ( 33) *********************** 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 : 0.313 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: 0.6687 (mtp85) cc_final: 0.6126 (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: 0.5611 (pt) REVERT: D 1177 ILE cc_start: 0.3542 (OUTLIER) cc_final: 0.3165 (mt) REVERT: D 1283 ARG cc_start: 0.6896 (mtt180) cc_final: 0.5528 (ttp80) REVERT: D 1388 PHE cc_start: 0.5103 (m-10) cc_final: 0.4810 (m-80) REVERT: D 1512 LYS cc_start: 0.8266 (tttt) cc_final: 0.7964 (ttpt) REVERT: D 1532 GLN cc_start: 0.5989 (mt0) cc_final: 0.5773 (mp10) outliers start: 78 outliers final: 23 residues processed: 274 average time/residue: 0.0932 time to fit residues: 37.7246 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 : 0.379 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 D1377 HIS ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.157443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122831 restraints weight = 18292.694| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.54 r_work: 0.3109 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13433 Z= 0.234 Angle : 0.647 8.066 18322 Z= 0.336 Chirality : 0.049 0.265 1979 Planarity : 0.005 0.041 2384 Dihedral : 7.298 59.015 1825 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.83 % Allowed : 11.20 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.20), residues: 1629 helix: -0.92 (0.39), residues: 140 sheet: -0.13 (0.28), residues: 362 loop : -1.00 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 203 TYR 0.020 0.002 TYR C 131 PHE 0.019 0.002 PHE D1342 TRP 0.013 0.002 TRP C 680 HIS 0.008 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (13376) covalent geometry : angle 0.63825 / 0.33 (18202) SS BOND : bond 0.00387 / 0.22 ( 42) SS BOND : angle 1.46312 / 0.92 ( 84) hydrogen bonds : bond 0.04350 / 2.84 ( 292) hydrogen bonds : angle 5.75992 / 4.21 ( 801) metal coordination : bond 0.00967 / 0.49 ( 3) link_BETA1-4 : bond 0.00205 / 0.11 ( 1) link_BETA1-4 : angle 0.96335 / 0.51 ( 3) link_NAG-ASN : bond 0.00513 / 0.27 ( 11) link_NAG-ASN : angle 1.49008 / 0.97 ( 33) *********************** 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 199 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 0.416 Fit side-chains REVERT: A 130 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7390 (tpm170) REVERT: C 221 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5351 (mmtm) REVERT: C 522 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8479 (m-30) REVERT: C 590 ARG cc_start: 0.7149 (mtp85) cc_final: 0.5915 (tpt170) REVERT: C 632 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 670 GLU cc_start: 0.7222 (mm-30) cc_final: 0.7008 (mm-30) REVERT: C 728 ASP cc_start: 0.5808 (m-30) cc_final: 0.5064 (t0) REVERT: C 961 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7766 (mp) REVERT: D 1170 ILE cc_start: 0.5328 (tt) cc_final: 0.4876 (pt) REVERT: D 1177 ILE cc_start: 0.1677 (OUTLIER) cc_final: 0.1396 (mt) REVERT: D 1283 ARG cc_start: 0.7318 (mtt180) cc_final: 0.5638 (ttp80) REVERT: D 1352 PHE cc_start: 0.5130 (m-80) cc_final: 0.4392 (m-10) REVERT: D 1388 PHE cc_start: 0.5683 (m-10) cc_final: 0.5212 (m-80) REVERT: D 1512 LYS cc_start: 0.8035 (tttt) cc_final: 0.7534 (ttpt) REVERT: D 1518 MET cc_start: 0.6223 (ttp) cc_final: 0.5684 (mmt) REVERT: D 1532 GLN cc_start: 0.6152 (mt0) cc_final: 0.5885 (mp10) outliers start: 55 outliers final: 35 residues processed: 189 average time/residue: 0.0885 time to fit residues: 25.1543 Evaluate side-chains 161 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 522 ASP 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 129 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1429 HIS ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.159430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125101 restraints weight = 18412.148| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.34 r_work: 0.3155 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13433 Z= 0.125 Angle : 0.564 8.279 18322 Z= 0.286 Chirality : 0.045 0.273 1979 Planarity : 0.004 0.035 2384 Dihedral : 6.482 58.597 1810 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.69 % Allowed : 11.62 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1629 helix: -0.21 (0.43), residues: 140 sheet: -0.14 (0.27), residues: 373 loop : -0.80 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1456 TYR 0.016 0.001 TYR C 131 PHE 0.020 0.001 PHE D1342 TRP 0.010 0.001 TRP C 842 HIS 0.004 0.001 HIS D1429 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (13376) covalent geometry : angle 0.55276 / 0.28 (18202) SS BOND : bond 0.00325 / 0.19 ( 42) SS BOND : angle 1.29008 / 0.85 ( 84) hydrogen bonds : bond 0.03463 / 2.24 ( 292) hydrogen bonds : angle 5.46752 / 4.00 ( 801) metal coordination : bond 0.00350 / 0.18 ( 3) link_BETA1-4 : bond 0.00207 / 0.11 ( 1) link_BETA1-4 : angle 1.01315 / 0.57 ( 3) link_NAG-ASN : bond 0.00670 / 0.36 ( 11) link_NAG-ASN : angle 1.90704 / 1.31 ( 33) *********************** 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 181 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7754 (mtp180) cc_final: 0.7461 (tpm170) REVERT: C 221 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5162 (mmtm) REVERT: C 319 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: C 384 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 590 ARG cc_start: 0.7096 (mtp85) cc_final: 0.5921 (tpt170) REVERT: C 728 ASP cc_start: 0.5435 (m-30) cc_final: 0.4822 (t0) REVERT: D 1170 ILE cc_start: 0.5455 (tt) cc_final: 0.4965 (pt) REVERT: D 1177 ILE cc_start: 0.2067 (OUTLIER) cc_final: 0.1772 (mt) REVERT: D 1283 ARG cc_start: 0.7364 (mtt180) cc_final: 0.5628 (ttp80) REVERT: D 1388 PHE cc_start: 0.5749 (m-10) cc_final: 0.5170 (m-80) REVERT: D 1491 ASN cc_start: 0.7210 (m110) cc_final: 0.6904 (m-40) REVERT: D 1512 LYS cc_start: 0.7970 (tttt) cc_final: 0.7389 (ttpt) REVERT: D 1532 GLN cc_start: 0.6282 (mt0) cc_final: 0.5961 (mp10) outliers start: 53 outliers final: 37 residues processed: 174 average time/residue: 0.0941 time to fit residues: 24.7397 Evaluate side-chains 159 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 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 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 63 optimal weight: 7.9990 chunk 140 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 32 optimal weight: 0.0980 chunk 86 optimal weight: 0.2980 chunk 143 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.160896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126163 restraints weight = 18393.785| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.45 r_work: 0.3186 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13433 Z= 0.094 Angle : 0.541 7.820 18322 Z= 0.272 Chirality : 0.045 0.435 1979 Planarity : 0.004 0.032 2384 Dihedral : 5.970 58.571 1803 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.99 % Allowed : 12.53 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1629 helix: 0.29 (0.46), residues: 134 sheet: 0.03 (0.28), residues: 355 loop : -0.70 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.014 0.001 TYR C 131 PHE 0.011 0.001 PHE D1342 TRP 0.009 0.001 TRP C 842 HIS 0.003 0.000 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (13376) covalent geometry : angle 0.53428 / 0.27 (18202) SS BOND : bond 0.00333 / 0.17 ( 42) SS BOND : angle 1.01979 / 0.63 ( 84) hydrogen bonds : bond 0.03048 / 1.96 ( 292) hydrogen bonds : angle 5.26127 / 3.85 ( 801) metal coordination : bond 0.00157 / 0.08 ( 3) link_BETA1-4 : bond 0.00195 / 0.10 ( 1) link_BETA1-4 : angle 1.02332 / 0.57 ( 3) link_NAG-ASN : bond 0.00673 / 0.30 ( 11) link_NAG-ASN : angle 1.48958 / 1.11 ( 33) *********************** 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 179 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7480 (tpm170) REVERT: C 221 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5369 (mmtm) REVERT: C 319 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: C 590 ARG cc_start: 0.7159 (mtp85) cc_final: 0.5945 (tpt170) REVERT: C 728 ASP cc_start: 0.5322 (m-30) cc_final: 0.4789 (t0) REVERT: D 1170 ILE cc_start: 0.5419 (OUTLIER) cc_final: 0.4955 (pt) REVERT: D 1177 ILE cc_start: 0.1986 (OUTLIER) cc_final: 0.1688 (mt) REVERT: D 1283 ARG cc_start: 0.7357 (mtt180) cc_final: 0.5599 (ttp80) REVERT: D 1388 PHE cc_start: 0.5739 (m-10) cc_final: 0.5161 (m-80) REVERT: D 1491 ASN cc_start: 0.7217 (m110) cc_final: 0.6872 (m-40) REVERT: D 1512 LYS cc_start: 0.7884 (tttt) cc_final: 0.7368 (ttpt) REVERT: D 1532 GLN cc_start: 0.6276 (mt0) cc_final: 0.5986 (mp10) outliers start: 43 outliers final: 33 residues processed: 174 average time/residue: 0.0942 time to fit residues: 24.1540 Evaluate side-chains 161 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 102 VAL 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 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 690 THR 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 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 1170 ILE 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 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 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 0.0770 chunk 77 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 143 optimal weight: 0.1980 chunk 148 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 118 optimal weight: 0.4980 chunk 146 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126790 restraints weight = 18515.960| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.41 r_work: 0.3174 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13433 Z= 0.101 Angle : 0.543 12.056 18322 Z= 0.266 Chirality : 0.045 0.342 1979 Planarity : 0.004 0.031 2384 Dihedral : 5.672 58.766 1796 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.34 % Allowed : 13.15 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1629 helix: 0.51 (0.47), residues: 134 sheet: 0.05 (0.28), residues: 356 loop : -0.66 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1538 TYR 0.013 0.001 TYR C 131 PHE 0.012 0.001 PHE D1342 TRP 0.009 0.001 TRP C 842 HIS 0.002 0.000 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (13376) covalent geometry : angle 0.52661 / 0.26 (18202) SS BOND : bond 0.00362 / 0.18 ( 42) SS BOND : angle 0.96371 / 0.52 ( 84) hydrogen bonds : bond 0.03090 / 2.00 ( 292) hydrogen bonds : angle 5.08127 / 3.72 ( 801) metal coordination : bond 0.00237 / 0.12 ( 3) link_BETA1-4 : bond 0.00181 / 0.10 ( 1) link_BETA1-4 : angle 1.02591 / 0.57 ( 3) link_NAG-ASN : bond 0.00622 / 0.28 ( 11) link_NAG-ASN : angle 2.92264 / 1.87 ( 33) *********************** 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 181 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7496 (tpm170) REVERT: C 221 LYS cc_start: 0.6359 (OUTLIER) cc_final: 0.5362 (mmtm) REVERT: C 319 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: C 384 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7285 (tm-30) REVERT: C 590 ARG cc_start: 0.7159 (mtp85) cc_final: 0.5929 (tpt170) REVERT: C 728 ASP cc_start: 0.5508 (m-30) cc_final: 0.4914 (t0) REVERT: D 1170 ILE cc_start: 0.5462 (OUTLIER) cc_final: 0.4980 (pt) REVERT: D 1177 ILE cc_start: 0.1993 (OUTLIER) cc_final: 0.1730 (mt) REVERT: D 1283 ARG cc_start: 0.7355 (mtt180) cc_final: 0.5686 (ttp80) REVERT: D 1352 PHE cc_start: 0.5330 (m-80) cc_final: 0.4681 (m-10) REVERT: D 1388 PHE cc_start: 0.5708 (m-10) cc_final: 0.5086 (m-80) REVERT: D 1491 ASN cc_start: 0.7301 (m110) cc_final: 0.6970 (m-40) REVERT: D 1512 LYS cc_start: 0.7933 (tttt) cc_final: 0.7259 (ttpt) REVERT: D 1532 GLN cc_start: 0.6224 (mt0) cc_final: 0.5943 (mp10) outliers start: 48 outliers final: 37 residues processed: 173 average time/residue: 0.0950 time to fit residues: 24.6319 Evaluate side-chains 165 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 67 ILE 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 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 835 LEU 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 1170 ILE 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 0.0050 chunk 98 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.158187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123508 restraints weight = 18320.252| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.13 r_work: 0.3168 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13433 Z= 0.111 Angle : 0.531 11.497 18322 Z= 0.263 Chirality : 0.045 0.390 1979 Planarity : 0.004 0.031 2384 Dihedral : 5.548 58.764 1793 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.41 % Allowed : 13.36 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1629 helix: 0.55 (0.46), residues: 134 sheet: -0.01 (0.28), residues: 358 loop : -0.61 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1538 TYR 0.014 0.001 TYR C 131 PHE 0.010 0.001 PHE D1342 TRP 0.009 0.001 TRP C 842 HIS 0.003 0.001 HIS C 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (13376) covalent geometry : angle 0.51947 / 0.26 (18202) SS BOND : bond 0.00215 / 0.12 ( 42) SS BOND : angle 0.87621 / 0.46 ( 84) hydrogen bonds : bond 0.03043 / 1.95 ( 292) hydrogen bonds : angle 4.95886 / 3.62 ( 801) metal coordination : bond 0.00325 / 0.17 ( 3) link_BETA1-4 : bond 0.00079 / 0.04 ( 1) link_BETA1-4 : angle 0.99892 / 0.55 ( 3) link_NAG-ASN : bond 0.00801 / 0.31 ( 11) link_NAG-ASN : angle 2.40024 / 1.61 ( 33) *********************** 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 180 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7514 (tpm170) REVERT: C 221 LYS cc_start: 0.6319 (OUTLIER) cc_final: 0.5394 (mmtm) REVERT: C 319 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: C 384 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7323 (tm-30) REVERT: C 590 ARG cc_start: 0.7172 (mtp85) cc_final: 0.5916 (tpt170) REVERT: C 728 ASP cc_start: 0.5198 (m-30) cc_final: 0.4677 (t0) REVERT: D 1170 ILE cc_start: 0.5422 (OUTLIER) cc_final: 0.4956 (pt) REVERT: D 1177 ILE cc_start: 0.1921 (OUTLIER) cc_final: 0.1684 (mt) REVERT: D 1283 ARG cc_start: 0.7415 (mtt180) cc_final: 0.5782 (ttp80) REVERT: D 1352 PHE cc_start: 0.5300 (m-80) cc_final: 0.4681 (m-10) REVERT: D 1388 PHE cc_start: 0.5727 (m-10) cc_final: 0.5079 (m-80) REVERT: D 1491 ASN cc_start: 0.7239 (m110) cc_final: 0.6943 (m-40) REVERT: D 1512 LYS cc_start: 0.7887 (tttt) cc_final: 0.7281 (ttpt) REVERT: D 1532 GLN cc_start: 0.6251 (mt0) cc_final: 0.5964 (mp10) outliers start: 49 outliers final: 35 residues processed: 171 average time/residue: 0.0943 time to fit residues: 24.1029 Evaluate side-chains 169 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU 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 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 835 LEU 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 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1006 LEU 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 1170 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 156 optimal weight: 0.0470 chunk 62 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D1389 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124520 restraints weight = 18333.038| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.49 r_work: 0.3157 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13433 Z= 0.126 Angle : 0.531 7.425 18322 Z= 0.266 Chirality : 0.046 0.314 1979 Planarity : 0.004 0.031 2384 Dihedral : 5.585 58.665 1792 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.41 % Allowed : 13.29 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1629 helix: 0.43 (0.45), residues: 141 sheet: -0.02 (0.28), residues: 358 loop : -0.57 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1538 TYR 0.014 0.001 TYR C 131 PHE 0.012 0.001 PHE D1342 TRP 0.009 0.001 TRP C 842 HIS 0.003 0.001 HIS C 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13376) covalent geometry : angle 0.52247 / 0.26 (18202) SS BOND : bond 0.00205 / 0.11 ( 42) SS BOND : angle 0.83052 / 0.46 ( 84) hydrogen bonds : bond 0.03104 / 1.99 ( 292) hydrogen bonds : angle 4.96360 / 3.63 ( 801) metal coordination : bond 0.00415 / 0.21 ( 3) link_BETA1-4 : bond 0.00167 / 0.09 ( 1) link_BETA1-4 : angle 1.02202 / 0.57 ( 3) link_NAG-ASN : bond 0.00778 / 0.34 ( 11) link_NAG-ASN : angle 1.96795 / 1.37 ( 33) *********************** 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 178 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7481 (tpm170) REVERT: C 221 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5364 (mmtm) REVERT: C 319 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7334 (mm-30) REVERT: C 384 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7344 (tm-30) REVERT: C 590 ARG cc_start: 0.7226 (mtp85) cc_final: 0.5904 (tpt170) REVERT: C 728 ASP cc_start: 0.5245 (m-30) cc_final: 0.4661 (t0) REVERT: C 759 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8718 (tp) REVERT: D 1170 ILE cc_start: 0.5398 (tt) cc_final: 0.4929 (pt) REVERT: D 1177 ILE cc_start: 0.1958 (OUTLIER) cc_final: 0.1700 (mt) REVERT: D 1283 ARG cc_start: 0.7395 (mtt180) cc_final: 0.5765 (ttp80) REVERT: D 1352 PHE cc_start: 0.5331 (m-80) cc_final: 0.4675 (m-10) REVERT: D 1388 PHE cc_start: 0.5745 (m-10) cc_final: 0.5116 (m-80) REVERT: D 1491 ASN cc_start: 0.7347 (m110) cc_final: 0.7064 (m-40) REVERT: D 1512 LYS cc_start: 0.7923 (tttt) cc_final: 0.7246 (ttpt) REVERT: D 1532 GLN cc_start: 0.6252 (mt0) cc_final: 0.5956 (mp10) outliers start: 49 outliers final: 40 residues processed: 171 average time/residue: 0.0991 time to fit residues: 25.0786 Evaluate side-chains 168 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 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 541 THR Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 835 LEU 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 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1006 LEU 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 1118 TYR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122324 restraints weight = 18365.001| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.08 r_work: 0.3103 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13433 Z= 0.194 Angle : 0.587 7.546 18322 Z= 0.296 Chirality : 0.048 0.335 1979 Planarity : 0.004 0.032 2384 Dihedral : 5.847 58.197 1792 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.13 % Allowed : 13.85 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1629 helix: 0.19 (0.43), residues: 141 sheet: -0.10 (0.27), residues: 364 loop : -0.65 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1538 TYR 0.016 0.002 TYR C 131 PHE 0.012 0.001 PHE C 92 TRP 0.011 0.001 TRP C 44 HIS 0.004 0.001 HIS C 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (13376) covalent geometry : angle 0.57877 / 0.29 (18202) SS BOND : bond 0.00273 / 0.14 ( 42) SS BOND : angle 0.98838 / 0.58 ( 84) hydrogen bonds : bond 0.03519 / 2.26 ( 292) hydrogen bonds : angle 5.13532 / 3.77 ( 801) metal coordination : bond 0.00807 / 0.41 ( 3) link_BETA1-4 : bond 0.00030 / 0.02 ( 1) link_BETA1-4 : angle 1.01151 / 0.57 ( 3) link_NAG-ASN : bond 0.00769 / 0.35 ( 11) link_NAG-ASN : angle 2.03710 / 1.34 ( 33) *********************** 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 177 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7486 (tpm170) REVERT: C 221 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.5510 (mmtm) REVERT: C 319 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: C 590 ARG cc_start: 0.7158 (mtp85) cc_final: 0.5914 (tpt170) REVERT: C 728 ASP cc_start: 0.4966 (m-30) cc_final: 0.4487 (t0) REVERT: C 759 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8802 (tp) REVERT: D 1170 ILE cc_start: 0.5443 (tt) cc_final: 0.4954 (pt) REVERT: D 1177 ILE cc_start: 0.2159 (OUTLIER) cc_final: 0.1858 (mt) REVERT: D 1283 ARG cc_start: 0.7379 (mtt180) cc_final: 0.5828 (ttp80) REVERT: D 1352 PHE cc_start: 0.5242 (m-80) cc_final: 0.4711 (m-10) REVERT: D 1388 PHE cc_start: 0.5784 (m-10) cc_final: 0.5155 (m-80) REVERT: D 1491 ASN cc_start: 0.7481 (m110) cc_final: 0.7230 (m-40) REVERT: D 1512 LYS cc_start: 0.7985 (tttt) cc_final: 0.7407 (ttpt) REVERT: D 1532 GLN cc_start: 0.6207 (mt0) cc_final: 0.5876 (mp10) outliers start: 45 outliers final: 38 residues processed: 169 average time/residue: 0.0869 time to fit residues: 22.4075 Evaluate side-chains 169 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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 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 835 LEU 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 1006 LEU 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 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 Chi-restraints excluded: chain D residue 1522 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.156556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121787 restraints weight = 18483.637| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.24 r_work: 0.3141 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13433 Z= 0.136 Angle : 0.544 7.665 18322 Z= 0.274 Chirality : 0.046 0.295 1979 Planarity : 0.004 0.033 2384 Dihedral : 5.707 58.167 1792 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.27 % Allowed : 13.92 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1629 helix: 0.35 (0.44), residues: 141 sheet: -0.11 (0.27), residues: 364 loop : -0.60 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1538 TYR 0.016 0.001 TYR C 131 PHE 0.010 0.001 PHE C 19 TRP 0.010 0.001 TRP C 179 HIS 0.003 0.001 HIS D1343 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13376) covalent geometry : angle 0.53645 / 0.27 (18202) SS BOND : bond 0.00209 / 0.11 ( 42) SS BOND : angle 0.85280 / 0.48 ( 84) hydrogen bonds : bond 0.03169 / 2.04 ( 292) hydrogen bonds : angle 5.04105 / 3.69 ( 801) metal coordination : bond 0.00434 / 0.22 ( 3) link_BETA1-4 : bond 0.00159 / 0.08 ( 1) link_BETA1-4 : angle 1.02577 / 0.58 ( 3) link_NAG-ASN : bond 0.00785 / 0.37 ( 11) link_NAG-ASN : angle 1.88090 / 1.23 ( 33) *********************** 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 175 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7795 (mtp180) cc_final: 0.7470 (tpm170) REVERT: C 221 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5507 (mmtm) REVERT: C 319 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: C 590 ARG cc_start: 0.7211 (mtp85) cc_final: 0.5916 (tpt170) REVERT: C 728 ASP cc_start: 0.5098 (m-30) cc_final: 0.4500 (t0) REVERT: C 759 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8792 (tp) REVERT: C 984 GLN cc_start: 0.8149 (mp10) cc_final: 0.7799 (mp10) REVERT: D 1170 ILE cc_start: 0.5455 (OUTLIER) cc_final: 0.4966 (pt) REVERT: D 1177 ILE cc_start: 0.1944 (OUTLIER) cc_final: 0.1724 (mt) REVERT: D 1283 ARG cc_start: 0.7369 (mtt180) cc_final: 0.5773 (ttp80) REVERT: D 1352 PHE cc_start: 0.5081 (m-80) cc_final: 0.4640 (m-10) REVERT: D 1388 PHE cc_start: 0.5742 (m-10) cc_final: 0.5135 (m-80) REVERT: D 1491 ASN cc_start: 0.7384 (m110) cc_final: 0.7141 (m-40) REVERT: D 1512 LYS cc_start: 0.7941 (tttt) cc_final: 0.7259 (ttpt) REVERT: D 1532 GLN cc_start: 0.6231 (mt0) cc_final: 0.5856 (mp10) outliers start: 47 outliers final: 39 residues processed: 169 average time/residue: 0.0971 time to fit residues: 24.8328 Evaluate side-chains 167 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 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 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 1006 LEU 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 1170 ILE 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 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 1458 VAL 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 32 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.159364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125021 restraints weight = 18375.809| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.26 r_work: 0.3163 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13433 Z= 0.114 Angle : 0.545 10.535 18322 Z= 0.272 Chirality : 0.046 0.416 1979 Planarity : 0.004 0.033 2384 Dihedral : 5.618 58.406 1792 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.20 % Allowed : 14.20 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1629 helix: 0.49 (0.45), residues: 141 sheet: -0.07 (0.28), residues: 364 loop : -0.57 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1538 TYR 0.014 0.001 TYR C 131 PHE 0.009 0.001 PHE C 19 TRP 0.010 0.001 TRP C 179 HIS 0.003 0.001 HIS D1468 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (13376) covalent geometry : angle 0.53841 / 0.27 (18202) SS BOND : bond 0.00180 / 0.09 ( 42) SS BOND : angle 0.81373 / 0.45 ( 84) hydrogen bonds : bond 0.03080 / 1.98 ( 292) hydrogen bonds : angle 4.95143 / 3.62 ( 801) metal coordination : bond 0.00300 / 0.15 ( 3) link_BETA1-4 : bond 0.00267 / 0.14 ( 1) link_BETA1-4 : angle 1.04352 / 0.58 ( 3) link_NAG-ASN : bond 0.01040 / 0.50 ( 11) link_NAG-ASN : angle 1.79636 / 1.17 ( 33) ********************** 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 173 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8141 (ptt180) cc_final: 0.7772 (ptt-90) REVERT: A 130 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7449 (tpm170) REVERT: C 221 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.5483 (mmtm) REVERT: C 319 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: C 590 ARG cc_start: 0.7219 (mtp85) cc_final: 0.5915 (tpt170) REVERT: C 728 ASP cc_start: 0.5025 (m-30) cc_final: 0.4475 (t0) REVERT: C 759 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8758 (tp) REVERT: C 984 GLN cc_start: 0.8087 (mp10) cc_final: 0.7721 (mp10) REVERT: D 1170 ILE cc_start: 0.5462 (OUTLIER) cc_final: 0.4981 (pt) REVERT: D 1177 ILE cc_start: 0.1951 (OUTLIER) cc_final: 0.1694 (mt) REVERT: D 1283 ARG cc_start: 0.7374 (mtt180) cc_final: 0.5776 (ttp80) REVERT: D 1301 TYR cc_start: 0.2500 (m-80) cc_final: 0.2298 (m-80) REVERT: D 1352 PHE cc_start: 0.5112 (m-80) cc_final: 0.4682 (m-10) REVERT: D 1388 PHE cc_start: 0.5726 (m-10) cc_final: 0.5109 (m-80) REVERT: D 1491 ASN cc_start: 0.7417 (m110) cc_final: 0.7195 (m-40) REVERT: D 1512 LYS cc_start: 0.7970 (tttt) cc_final: 0.7237 (ttpt) REVERT: D 1532 GLN cc_start: 0.6193 (mt0) cc_final: 0.5853 (mp10) outliers start: 46 outliers final: 39 residues processed: 167 average time/residue: 0.1017 time to fit residues: 25.2879 Evaluate side-chains 170 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 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 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 1006 LEU 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 1118 TYR Chi-restraints excluded: chain D residue 1170 ILE 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 1289 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 84 optimal weight: 0.0040 chunk 151 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 161 optimal weight: 0.0170 chunk 141 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.160814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126968 restraints weight = 18272.611| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.03 r_work: 0.3194 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13433 Z= 0.093 Angle : 0.528 9.352 18322 Z= 0.262 Chirality : 0.045 0.365 1979 Planarity : 0.004 0.033 2384 Dihedral : 5.448 58.790 1792 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.78 % Allowed : 14.61 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1629 helix: 0.65 (0.45), residues: 141 sheet: -0.03 (0.28), residues: 355 loop : -0.51 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1538 TYR 0.013 0.001 TYR C 131 PHE 0.008 0.001 PHE C 19 TRP 0.011 0.001 TRP C 179 HIS 0.003 0.000 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (13376) covalent geometry : angle 0.52099 / 0.26 (18202) SS BOND : bond 0.00203 / 0.13 ( 42) SS BOND : angle 0.91599 / 0.49 ( 84) hydrogen bonds : bond 0.02888 / 1.89 ( 292) hydrogen bonds : angle 4.82397 / 3.52 ( 801) metal coordination : bond 0.00163 / 0.08 ( 3) link_BETA1-4 : bond 0.00276 / 0.15 ( 1) link_BETA1-4 : angle 1.05714 / 0.59 ( 3) link_NAG-ASN : bond 0.00758 / 0.37 ( 11) link_NAG-ASN : angle 1.67121 / 1.09 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2528.58 seconds wall clock time: 44 minutes 9.26 seconds (2649.26 seconds total)