Starting phenix.real_space_refine on Wed Mar 4 10:57:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5n_33621/03_2026/7y5n_33621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5n_33621/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7y5n_33621/03_2026/7y5n_33621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5n_33621/03_2026/7y5n_33621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5n_33621/03_2026/7y5n_33621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5n_33621/03_2026/7y5n_33621.map" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Unusual residues: {' CA': 7, ' ZN': 1, 'NAG': 9} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.76, per 1000 atoms: 0.21 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: 1.08 Conformation dependent library (CDL) restraints added in 624.3 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: 0.58 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: 2.11 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4233 1.34 - 1.46: 3086 1.46 - 1.58: 5923 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 13376 Sorted by residual: bond pdb=" N VAL D1513 " pdb=" CA VAL D1513 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" C1 NAG C1609 " pdb=" O5 NAG C1609 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.69e+00 bond pdb=" N PHE D1516 " pdb=" CA PHE D1516 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.15e+00 bond pdb=" N TRP A 207 " pdb=" CA TRP A 207 " ideal model delta sigma weight residual 1.453 1.489 -0.035 1.27e-02 6.20e+03 7.65e+00 bond pdb=" N LEU C 940 " pdb=" CA LEU C 940 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.26e-02 6.30e+03 7.08e+00 ... (remaining 13371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 17650 1.77 - 3.54: 489 3.54 - 5.31: 41 5.31 - 7.08: 14 7.08 - 8.86: 8 Bond angle restraints: 18202 Sorted by residual: angle pdb=" C THR D1334 " pdb=" N CYS D1335 " pdb=" CA CYS D1335 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.98e+01 angle pdb=" CA MET C 473 " pdb=" C MET C 473 " pdb=" O MET C 473 " ideal model delta sigma weight residual 120.19 116.61 3.58 8.40e-01 1.42e+00 1.81e+01 angle pdb=" N GLN A 189 " pdb=" CA GLN A 189 " pdb=" C GLN A 189 " ideal model delta sigma weight residual 109.81 118.28 -8.47 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C GLU C 442 " pdb=" N GLU C 443 " pdb=" CA GLU C 443 " ideal model delta sigma weight residual 122.08 127.54 -5.46 1.47e+00 4.63e-01 1.38e+01 angle pdb=" C TRP C 727 " pdb=" N ASP C 728 " pdb=" CA ASP C 728 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.28e+01 ... (remaining 18197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 7775 22.77 - 45.54: 360 45.54 - 68.31: 64 68.31 - 91.08: 8 91.08 - 113.85: 14 Dihedral angle restraints: 8221 sinusoidal: 3480 harmonic: 4741 Sorted by residual: dihedral pdb=" CB CYS C 252 " pdb=" SG CYS C 252 " pdb=" SG CYS C 577 " pdb=" CB CYS C 577 " ideal model delta sinusoidal sigma weight residual 93.00 155.15 -62.15 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS C 867 " pdb=" SG CYS C 867 " pdb=" SG CYS C 895 " pdb=" CB CYS C 895 " ideal model delta sinusoidal sigma weight residual -86.00 -141.45 55.45 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CA ASP C 811 " pdb=" C ASP C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 8218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1424 0.049 - 0.099: 408 0.099 - 0.148: 127 0.148 - 0.197: 16 0.197 - 0.247: 4 Chirality restraints: 1979 Sorted by residual: chirality pdb=" C1 NAG C1610 " pdb=" ND2 ASN C 539 " pdb=" C2 NAG C1610 " pdb=" O5 NAG C1610 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA GLN A 189 " pdb=" N GLN A 189 " pdb=" C GLN A 189 " pdb=" CB GLN A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LEU C 940 " pdb=" N LEU C 940 " pdb=" C LEU C 940 " pdb=" CB LEU C 940 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1976 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 988 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO C 989 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 989 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 681 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO C 682 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 682 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 682 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 101 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A 102 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.029 5.00e-02 4.00e+02 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2709 2.78 - 3.31: 10699 3.31 - 3.84: 21453 3.84 - 4.37: 24874 4.37 - 4.90: 43251 Nonbonded interactions: 102986 Sorted by model distance: nonbonded pdb=" O GLY D1300 " pdb=" OG1 THR D1334 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP C 87 " pdb=" OG SER C 110 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR D1320 " pdb=" OD1 ASP D1322 " model vdw 2.322 3.040 nonbonded pdb=" O GLY C 49 " pdb=" OH TYR C 111 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASN C 322 " pdb=" OG SER C 324 " model vdw 2.331 3.040 ... (remaining 102981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.850 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13433 Z= 0.232 Angle : 0.698 8.855 18322 Z= 0.376 Chirality : 0.051 0.247 1979 Planarity : 0.006 0.055 2384 Dihedral : 14.101 113.850 5045 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.43 % Allowed : 7.24 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00480 (13376) covalent geometry : angle 0.69264 (18202) SS BOND : bond 0.00289 ( 42) SS BOND : angle 0.91118 ( 84) hydrogen bonds : bond 0.15843 ( 292) hydrogen bonds : angle 6.89605 ( 801) metal coordination : bond 0.00646 ( 3) link_BETA1-4 : bond 0.00077 ( 1) link_BETA1-4 : angle 1.96016 ( 3) link_NAG-ASN : bond 0.00409 ( 11) link_NAG-ASN : angle 1.80184 ( 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 : 0.446 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: 0.8504 (p) REVERT: C 221 LYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5254 (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: 0.7339 (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: 0.4809 (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: 0.5772 (mp10) outliers start: 78 outliers final: 23 residues processed: 274 average time/residue: 0.1102 time to fit residues: 44.0188 Evaluate side-chains 174 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 173 GLN A 188 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 78 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 HIS C1062 ASN D1154 HIS D1211 HIS 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 = 0.3934 r_free = 0.3934 target = 0.157139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121991 restraints weight = 18336.137| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.64 r_work: 0.3101 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13433 Z= 0.237 Angle : 0.663 9.257 18322 Z= 0.341 Chirality : 0.049 0.269 1979 Planarity : 0.005 0.043 2384 Dihedral : 10.801 107.202 2077 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.97 % Allowed : 11.00 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.90 (0.40), residues: 140 sheet: -0.19 (0.28), residues: 364 loop : -0.98 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 69 TYR 0.020 0.002 TYR C 131 PHE 0.019 0.002 PHE D1342 TRP 0.015 0.002 TRP C 680 HIS 0.008 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00555 (13376) covalent geometry : angle 0.65398 (18202) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.41940 ( 84) hydrogen bonds : bond 0.04289 ( 292) hydrogen bonds : angle 5.74620 ( 801) metal coordination : bond 0.00962 ( 3) link_BETA1-4 : bond 0.00068 ( 1) link_BETA1-4 : angle 1.07651 ( 3) link_NAG-ASN : bond 0.00346 ( 11) link_NAG-ASN : angle 1.79410 ( 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 200 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7396 (tpm170) REVERT: C 221 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.5348 (mmtm) REVERT: C 522 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8508 (m-30) REVERT: C 590 ARG cc_start: 0.7172 (mtp85) cc_final: 0.5912 (tpt170) REVERT: C 632 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8715 (mt) REVERT: C 670 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7019 (mm-30) REVERT: C 728 ASP cc_start: 0.5657 (m-30) cc_final: 0.5011 (t0) REVERT: D 1170 ILE cc_start: 0.5404 (tt) cc_final: 0.4887 (pt) REVERT: D 1177 ILE cc_start: 0.1658 (OUTLIER) cc_final: 0.1380 (mt) REVERT: D 1283 ARG cc_start: 0.7301 (mtt180) cc_final: 0.5763 (ttp80) REVERT: D 1388 PHE cc_start: 0.5613 (m-10) cc_final: 0.5136 (m-80) REVERT: D 1512 LYS cc_start: 0.8029 (tttt) cc_final: 0.7480 (ttpt) REVERT: D 1518 MET cc_start: 0.6353 (ttp) cc_final: 0.5804 (mmt) REVERT: D 1532 GLN cc_start: 0.6189 (mt0) cc_final: 0.5892 (mp10) outliers start: 57 outliers final: 37 residues processed: 192 average time/residue: 0.1083 time to fit residues: 31.0061 Evaluate side-chains 161 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 319 GLU 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 991 THR 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: 1.9990 chunk 161 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 234 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 HIS D1429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123573 restraints weight = 18453.353| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.44 r_work: 0.3132 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13433 Z= 0.153 Angle : 0.592 8.408 18322 Z= 0.299 Chirality : 0.046 0.263 1979 Planarity : 0.004 0.036 2384 Dihedral : 9.041 103.615 2060 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.48 % Allowed : 12.04 % 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: -0.95 (0.20), residues: 1629 helix: -0.27 (0.43), residues: 140 sheet: -0.24 (0.27), residues: 375 loop : -0.83 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 69 TYR 0.017 0.001 TYR C 131 PHE 0.012 0.001 PHE C 236 TRP 0.009 0.001 TRP C 842 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00358 (13376) covalent geometry : angle 0.58141 (18202) SS BOND : bond 0.00291 ( 42) SS BOND : angle 1.20264 ( 84) hydrogen bonds : bond 0.03645 ( 292) hydrogen bonds : angle 5.50659 ( 801) metal coordination : bond 0.00493 ( 3) link_BETA1-4 : bond 0.00042 ( 1) link_BETA1-4 : angle 1.18666 ( 3) link_NAG-ASN : bond 0.00522 ( 11) link_NAG-ASN : angle 2.14326 ( 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 177 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7762 (mtp180) cc_final: 0.7449 (tpm170) REVERT: C 221 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5193 (mmtm) REVERT: C 384 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 590 ARG cc_start: 0.7103 (mtp85) cc_final: 0.5880 (tpt170) REVERT: C 728 ASP cc_start: 0.5296 (m-30) cc_final: 0.4725 (t0) REVERT: D 1283 ARG cc_start: 0.7310 (mtt180) cc_final: 0.5648 (ttp80) REVERT: D 1388 PHE cc_start: 0.5617 (m-10) cc_final: 0.5075 (m-80) REVERT: D 1512 LYS cc_start: 0.7986 (tttt) cc_final: 0.7407 (ttpt) REVERT: D 1532 GLN cc_start: 0.6290 (mt0) cc_final: 0.5956 (mp10) outliers start: 50 outliers final: 38 residues processed: 170 average time/residue: 0.1028 time to fit residues: 26.2983 Evaluate side-chains 157 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 550 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 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1452 THR 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: 6.9990 chunk 140 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 86 optimal weight: 0.0670 chunk 143 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 85 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 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 = 0.3951 r_free = 0.3951 target = 0.158576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125121 restraints weight = 18470.902| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.42 r_work: 0.3120 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13433 Z= 0.144 Angle : 0.581 8.112 18322 Z= 0.292 Chirality : 0.047 0.494 1979 Planarity : 0.004 0.034 2384 Dihedral : 8.157 95.074 2054 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.04 % Allowed : 12.39 % Favored : 83.58 % 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: -0.82 (0.20), residues: 1629 helix: 0.12 (0.46), residues: 134 sheet: -0.18 (0.27), residues: 364 loop : -0.76 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 69 TYR 0.016 0.001 TYR C 131 PHE 0.012 0.001 PHE C1076 TRP 0.009 0.001 TRP C 842 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00338 (13376) covalent geometry : angle 0.56966 (18202) SS BOND : bond 0.00256 ( 42) SS BOND : angle 1.13373 ( 84) hydrogen bonds : bond 0.03401 ( 292) hydrogen bonds : angle 5.36435 ( 801) metal coordination : bond 0.00482 ( 3) link_BETA1-4 : bond 0.00114 ( 1) link_BETA1-4 : angle 1.20608 ( 3) link_NAG-ASN : bond 0.00455 ( 11) link_NAG-ASN : angle 2.16930 ( 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 187 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7767 (mtp180) cc_final: 0.7443 (tpm170) REVERT: C 221 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5208 (mmtm) REVERT: C 319 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: C 590 ARG cc_start: 0.7144 (mtp85) cc_final: 0.5898 (tpt170) REVERT: C 728 ASP cc_start: 0.5266 (m-30) cc_final: 0.4725 (t0) REVERT: C 759 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8767 (tp) REVERT: D 1283 ARG cc_start: 0.7305 (mtt180) cc_final: 0.5836 (ttp80) REVERT: D 1352 PHE cc_start: 0.5284 (m-80) cc_final: 0.4642 (m-10) REVERT: D 1388 PHE cc_start: 0.5656 (m-10) cc_final: 0.5082 (m-80) REVERT: D 1491 ASN cc_start: 0.7326 (m110) cc_final: 0.6998 (m-40) REVERT: D 1512 LYS cc_start: 0.7965 (tttt) cc_final: 0.7385 (ttpt) REVERT: D 1532 GLN cc_start: 0.6264 (mt0) cc_final: 0.5924 (mp10) outliers start: 58 outliers final: 42 residues processed: 179 average time/residue: 0.1052 time to fit residues: 27.9722 Evaluate side-chains 160 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain 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 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 690 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1319 CYS Chi-restraints excluded: chain D residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 0.0370 chunk 148 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 146 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123952 restraints weight = 18575.980| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.52 r_work: 0.3135 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13433 Z= 0.142 Angle : 0.573 7.638 18322 Z= 0.288 Chirality : 0.047 0.447 1979 Planarity : 0.004 0.035 2384 Dihedral : 8.032 94.388 2053 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.62 % Allowed : 13.71 % Favored : 82.67 % 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: -0.84 (0.20), residues: 1629 helix: -0.07 (0.43), residues: 147 sheet: -0.22 (0.27), residues: 364 loop : -0.74 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1538 TYR 0.015 0.001 TYR C 131 PHE 0.014 0.001 PHE C 236 TRP 0.009 0.001 TRP C 842 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00332 (13376) covalent geometry : angle 0.56204 (18202) SS BOND : bond 0.00424 ( 42) SS BOND : angle 1.06249 ( 84) hydrogen bonds : bond 0.03338 ( 292) hydrogen bonds : angle 5.30238 ( 801) metal coordination : bond 0.00457 ( 3) link_BETA1-4 : bond 0.00002 ( 1) link_BETA1-4 : angle 1.17834 ( 3) link_NAG-ASN : bond 0.00821 ( 11) link_NAG-ASN : angle 2.23467 ( 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 170 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7435 (tpm170) REVERT: C 221 LYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5200 (mmtm) REVERT: C 319 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: C 590 ARG cc_start: 0.7138 (mtp85) cc_final: 0.5891 (tpt170) REVERT: C 728 ASP cc_start: 0.5218 (m-30) cc_final: 0.4719 (t0) REVERT: D 1283 ARG cc_start: 0.7416 (mtt180) cc_final: 0.5782 (ttp80) REVERT: D 1352 PHE cc_start: 0.5311 (m-80) cc_final: 0.4718 (m-10) REVERT: D 1388 PHE cc_start: 0.5665 (m-10) cc_final: 0.5114 (m-80) REVERT: D 1491 ASN cc_start: 0.7365 (m110) cc_final: 0.7041 (m-40) REVERT: D 1512 LYS cc_start: 0.7975 (tttt) cc_final: 0.7282 (ttpt) REVERT: D 1532 GLN cc_start: 0.6116 (mt0) cc_final: 0.5800 (mp10) outliers start: 52 outliers final: 44 residues processed: 164 average time/residue: 0.1001 time to fit residues: 24.6828 Evaluate side-chains 162 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 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 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 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 960 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 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 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 85 optimal weight: 0.0010 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.159997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125131 restraints weight = 18276.530| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.58 r_work: 0.3153 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13433 Z= 0.107 Angle : 0.532 7.302 18322 Z= 0.267 Chirality : 0.044 0.219 1979 Planarity : 0.004 0.034 2384 Dihedral : 7.706 92.847 2052 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.13 % Allowed : 14.61 % Favored : 82.25 % 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: -0.72 (0.21), residues: 1629 helix: 0.12 (0.44), residues: 147 sheet: -0.12 (0.28), residues: 363 loop : -0.68 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1538 TYR 0.014 0.001 TYR C 131 PHE 0.020 0.001 PHE D1342 TRP 0.009 0.001 TRP C 842 HIS 0.003 0.000 HIS D1468 Details of bonding type rmsd covalent geometry : bond 0.00247 (13376) covalent geometry : angle 0.52244 (18202) SS BOND : bond 0.00205 ( 42) SS BOND : angle 1.11006 ( 84) hydrogen bonds : bond 0.03049 ( 292) hydrogen bonds : angle 5.13289 ( 801) metal coordination : bond 0.00289 ( 3) link_BETA1-4 : bond 0.00117 ( 1) link_BETA1-4 : angle 1.21064 ( 3) link_NAG-ASN : bond 0.00647 ( 11) link_NAG-ASN : angle 1.81600 ( 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 175 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7457 (tpm170) REVERT: C 221 LYS cc_start: 0.6382 (OUTLIER) cc_final: 0.5329 (mmtm) REVERT: C 319 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: C 384 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7428 (tm-30) REVERT: C 590 ARG cc_start: 0.7206 (mtp85) cc_final: 0.5919 (tpt170) REVERT: C 728 ASP cc_start: 0.5011 (m-30) cc_final: 0.4500 (t0) REVERT: C 759 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8714 (tp) REVERT: D 1177 ILE cc_start: 0.1956 (OUTLIER) cc_final: 0.1756 (mt) REVERT: D 1283 ARG cc_start: 0.7461 (mtt180) cc_final: 0.5824 (ttp80) REVERT: D 1352 PHE cc_start: 0.5200 (m-80) cc_final: 0.4577 (m-10) REVERT: D 1388 PHE cc_start: 0.5797 (m-10) cc_final: 0.5119 (m-80) REVERT: D 1491 ASN cc_start: 0.7381 (m110) cc_final: 0.7055 (m-40) REVERT: D 1512 LYS cc_start: 0.7908 (tttt) cc_final: 0.7318 (ttpt) REVERT: D 1532 GLN cc_start: 0.6251 (mt0) cc_final: 0.5927 (mp10) outliers start: 45 outliers final: 31 residues processed: 169 average time/residue: 0.1082 time to fit residues: 27.1650 Evaluate side-chains 159 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 991 THR 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 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 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.157020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123463 restraints weight = 18412.866| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.49 r_work: 0.3100 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13433 Z= 0.198 Angle : 0.600 8.305 18322 Z= 0.303 Chirality : 0.048 0.445 1979 Planarity : 0.004 0.033 2384 Dihedral : 7.811 92.387 2043 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.97 % Allowed : 13.99 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1629 helix: -0.12 (0.42), residues: 148 sheet: -0.22 (0.27), residues: 364 loop : -0.74 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1538 TYR 0.015 0.002 TYR C 131 PHE 0.013 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 covalent geometry : bond 0.00466 (13376) covalent geometry : angle 0.58724 (18202) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.09904 ( 84) hydrogen bonds : bond 0.03589 ( 292) hydrogen bonds : angle 5.29584 ( 801) metal coordination : bond 0.00767 ( 3) link_BETA1-4 : bond 0.00046 ( 1) link_BETA1-4 : angle 1.15071 ( 3) link_NAG-ASN : bond 0.01090 ( 11) link_NAG-ASN : angle 2.58013 ( 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 183 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7430 (tpm170) REVERT: C 221 LYS cc_start: 0.6466 (OUTLIER) cc_final: 0.5404 (mmtm) REVERT: C 319 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: C 418 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8663 (p) REVERT: C 590 ARG cc_start: 0.7167 (mtp85) cc_final: 0.5877 (tpt170) REVERT: C 728 ASP cc_start: 0.5106 (m-30) cc_final: 0.4550 (t0) REVERT: C 759 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8794 (tp) REVERT: D 1283 ARG cc_start: 0.7383 (mtt180) cc_final: 0.5829 (ttp80) REVERT: D 1352 PHE cc_start: 0.5221 (m-80) cc_final: 0.4701 (m-10) REVERT: D 1388 PHE cc_start: 0.5806 (m-10) cc_final: 0.5176 (m-80) REVERT: D 1491 ASN cc_start: 0.7488 (m110) cc_final: 0.7202 (m-40) REVERT: D 1512 LYS cc_start: 0.7975 (tttt) cc_final: 0.7468 (ttpt) REVERT: D 1532 GLN cc_start: 0.6184 (mt0) cc_final: 0.5826 (mp10) outliers start: 57 outliers final: 41 residues processed: 174 average time/residue: 0.1031 time to fit residues: 27.0107 Evaluate side-chains 164 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 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 418 VAL 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 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 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 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.120368 restraints weight = 18380.721| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.31 r_work: 0.3104 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13433 Z= 0.179 Angle : 0.585 9.235 18322 Z= 0.297 Chirality : 0.047 0.330 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.856 91.963 2043 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.48 % Allowed : 14.68 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1629 helix: -0.01 (0.43), residues: 142 sheet: -0.25 (0.27), residues: 364 loop : -0.71 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1538 TYR 0.016 0.001 TYR C 131 PHE 0.018 0.001 PHE D1342 TRP 0.010 0.001 TRP C 842 HIS 0.003 0.001 HIS C 482 Details of bonding type rmsd covalent geometry : bond 0.00423 (13376) covalent geometry : angle 0.57015 (18202) SS BOND : bond 0.00250 ( 42) SS BOND : angle 1.53493 ( 84) hydrogen bonds : bond 0.03420 ( 292) hydrogen bonds : angle 5.27476 ( 801) metal coordination : bond 0.00666 ( 3) link_BETA1-4 : bond 0.00045 ( 1) link_BETA1-4 : angle 1.22034 ( 3) link_NAG-ASN : bond 0.00766 ( 11) link_NAG-ASN : angle 2.20416 ( 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: 50 poor density : 127 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7727 (mtp180) cc_final: 0.7450 (tpm170) REVERT: C 221 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5228 (mmtm) REVERT: C 319 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: C 590 ARG cc_start: 0.7142 (mtp85) cc_final: 0.5866 (tpt170) REVERT: C 728 ASP cc_start: 0.5007 (m-30) cc_final: 0.4504 (t0) REVERT: C 759 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8794 (tp) REVERT: D 1283 ARG cc_start: 0.7378 (mtt180) cc_final: 0.5839 (ttp80) REVERT: D 1352 PHE cc_start: 0.5052 (m-80) cc_final: 0.4646 (m-10) REVERT: D 1388 PHE cc_start: 0.5767 (m-10) cc_final: 0.5058 (m-80) REVERT: D 1491 ASN cc_start: 0.7448 (m110) cc_final: 0.7179 (m-40) REVERT: D 1512 LYS cc_start: 0.7929 (tttt) cc_final: 0.7397 (ttpt) REVERT: D 1532 GLN cc_start: 0.6305 (mt0) cc_final: 0.5854 (mp10) outliers start: 50 outliers final: 40 residues processed: 168 average time/residue: 0.1074 time to fit residues: 27.1201 Evaluate side-chains 162 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL 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 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 1100 SER Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL 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: 5.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120748 restraints weight = 18502.254| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.28 r_work: 0.3109 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13433 Z= 0.166 Angle : 0.583 7.730 18322 Z= 0.295 Chirality : 0.046 0.311 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.836 91.680 2043 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.27 % Allowed : 14.89 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1629 helix: 0.10 (0.43), residues: 141 sheet: -0.32 (0.27), residues: 366 loop : -0.70 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1538 TYR 0.015 0.001 TYR C 131 PHE 0.011 0.001 PHE C 19 TRP 0.010 0.001 TRP C 179 HIS 0.004 0.001 HIS D1468 Details of bonding type rmsd covalent geometry : bond 0.00392 (13376) covalent geometry : angle 0.56976 (18202) SS BOND : bond 0.00293 ( 42) SS BOND : angle 1.36986 ( 84) hydrogen bonds : bond 0.03385 ( 292) hydrogen bonds : angle 5.25728 ( 801) metal coordination : bond 0.00585 ( 3) link_BETA1-4 : bond 0.00141 ( 1) link_BETA1-4 : angle 1.24615 ( 3) link_NAG-ASN : bond 0.00670 ( 11) link_NAG-ASN : angle 2.17546 ( 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 169 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8167 (ptt180) cc_final: 0.7807 (ptt-90) REVERT: A 130 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7441 (tpm170) REVERT: C 221 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5173 (mmtm) REVERT: C 319 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: C 418 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 590 ARG cc_start: 0.7142 (mtp85) cc_final: 0.5882 (tpt170) REVERT: C 728 ASP cc_start: 0.4780 (m-30) cc_final: 0.4276 (t0) REVERT: C 759 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8793 (tp) REVERT: D 1246 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7454 (tp) REVERT: D 1283 ARG cc_start: 0.7379 (mtt180) cc_final: 0.5839 (ttp80) REVERT: D 1352 PHE cc_start: 0.5315 (m-80) cc_final: 0.4892 (m-10) REVERT: D 1388 PHE cc_start: 0.5778 (m-10) cc_final: 0.5115 (m-80) REVERT: D 1491 ASN cc_start: 0.7447 (m110) cc_final: 0.7225 (m-40) REVERT: D 1512 LYS cc_start: 0.7939 (tttt) cc_final: 0.7410 (ttpt) REVERT: D 1532 GLN cc_start: 0.6318 (mt0) cc_final: 0.5856 (mp10) outliers start: 47 outliers final: 39 residues processed: 160 average time/residue: 0.1120 time to fit residues: 26.6601 Evaluate side-chains 163 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 418 VAL 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 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 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 32 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.156952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121264 restraints weight = 18436.216| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.38 r_work: 0.3130 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13433 Z= 0.115 Angle : 0.543 7.703 18322 Z= 0.274 Chirality : 0.045 0.276 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.634 90.282 2042 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.85 % Allowed : 15.31 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1629 helix: 0.31 (0.44), residues: 141 sheet: -0.24 (0.28), residues: 351 loop : -0.62 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1538 TYR 0.015 0.001 TYR C 131 PHE 0.025 0.001 PHE C 236 TRP 0.011 0.001 TRP C 179 HIS 0.003 0.001 HIS D1468 Details of bonding type rmsd covalent geometry : bond 0.00267 (13376) covalent geometry : angle 0.53150 (18202) SS BOND : bond 0.00193 ( 42) SS BOND : angle 1.14563 ( 84) hydrogen bonds : bond 0.03038 ( 292) hydrogen bonds : angle 5.09592 ( 801) metal coordination : bond 0.00264 ( 3) link_BETA1-4 : bond 0.00085 ( 1) link_BETA1-4 : angle 1.24196 ( 3) link_NAG-ASN : bond 0.00631 ( 11) link_NAG-ASN : angle 2.06170 ( 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 162 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7455 (tpm170) REVERT: C 221 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5464 (mmtm) REVERT: C 319 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: C 590 ARG cc_start: 0.7211 (mtp85) cc_final: 0.5888 (tpt170) REVERT: C 728 ASP cc_start: 0.4796 (m-30) cc_final: 0.4227 (t0) REVERT: C 759 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8790 (tp) REVERT: D 1283 ARG cc_start: 0.7378 (mtt180) cc_final: 0.5785 (ttp80) REVERT: D 1352 PHE cc_start: 0.5101 (m-80) cc_final: 0.4690 (m-10) REVERT: D 1491 ASN cc_start: 0.7366 (m110) cc_final: 0.7135 (m-40) REVERT: D 1512 LYS cc_start: 0.7891 (tttt) cc_final: 0.7359 (ttpt) REVERT: D 1532 GLN cc_start: 0.6168 (mt0) cc_final: 0.5792 (mp10) outliers start: 41 outliers final: 36 residues processed: 157 average time/residue: 0.0995 time to fit residues: 23.1233 Evaluate side-chains 159 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1209 ASP Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 84 optimal weight: 0.0670 chunk 151 optimal weight: 30.0000 chunk 78 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 161 optimal weight: 0.0370 chunk 141 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 65 optimal weight: 0.0470 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.159423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124814 restraints weight = 18321.695| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.24 r_work: 0.3195 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13433 Z= 0.089 Angle : 0.517 7.815 18322 Z= 0.260 Chirality : 0.044 0.240 1979 Planarity : 0.004 0.036 2384 Dihedral : 7.377 88.981 2042 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.37 % Allowed : 15.94 % Favored : 81.70 % 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: -0.53 (0.21), residues: 1629 helix: 0.63 (0.45), residues: 141 sheet: -0.16 (0.28), residues: 356 loop : -0.53 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 108 TYR 0.013 0.001 TYR C 131 PHE 0.008 0.001 PHE C 19 TRP 0.014 0.001 TRP D1325 HIS 0.003 0.000 HIS C 482 Details of bonding type rmsd covalent geometry : bond 0.00203 (13376) covalent geometry : angle 0.50723 (18202) SS BOND : bond 0.00176 ( 42) SS BOND : angle 1.01839 ( 84) hydrogen bonds : bond 0.02775 ( 292) hydrogen bonds : angle 4.90030 ( 801) metal coordination : bond 0.00116 ( 3) link_BETA1-4 : bond 0.00219 ( 1) link_BETA1-4 : angle 1.23409 ( 3) link_NAG-ASN : bond 0.00608 ( 11) link_NAG-ASN : angle 1.90359 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.45 seconds wall clock time: 48 minutes 24.84 seconds (2904.84 seconds total)