Starting phenix.real_space_refine on Wed Jul 30 23:02:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz2_34388/07_2025/8gz2_34388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz2_34388/07_2025/8gz2_34388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2025/8gz2_34388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2025/8gz2_34388.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2025/8gz2_34388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2025/8gz2_34388.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 872 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 7874 2.51 5 N 1870 2.21 5 O 2141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11984 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 172} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 9474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9474 Classifications: {'peptide': 1174} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 1139} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 885 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'WMK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 11.64, per 1000 atoms: 0.97 Number of scatterers: 11984 At special positions: 0 Unit cell: (132.08, 138.32, 115.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2141 8.00 N 1870 7.00 C 7874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 43 " distance=2.08 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 121 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 904 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 906 " - pdb=" SG CYS B 912 " distance=2.03 Simple disulfide: pdb=" SG CYS B 944 " - pdb=" SG CYS B 953 " distance=2.03 Simple disulfide: pdb=" SG CYS B1356 " - pdb=" SG CYS B1376 " distance=2.04 Simple disulfide: pdb=" SG CYS B1721 " - pdb=" SG CYS B1736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 1 " - " ASN B 295 " " NAG B2001 " - " ASN B 289 " " NAG D 301 " - " ASN D 135 " " NAG E 1 " - " ASN B 308 " " NAG F 1 " - " ASN B 326 " " NAG G 1 " - " ASN B1358 " " NAG H 1 " - " ASN B1372 " Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 6 sheets defined 65.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'D' and resid 153 through 190 removed outlier: 3.679A pdb=" N ILE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 131 Processing helix chain 'B' and resid 131 through 151 removed outlier: 3.781A pdb=" N SER B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 158 through 179 Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.820A pdb=" N TRP B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 223 through 234 removed outlier: 4.128A pdb=" N ALA B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 251 Processing helix chain 'B' and resid 251 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.710A pdb=" N PHE B 312 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 355 through 369 Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.047A pdb=" N LEU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.706A pdb=" N PHE B 391 " --> pdb=" O TYR B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 424 Processing helix chain 'B' and resid 722 through 731 removed outlier: 3.836A pdb=" N PHE B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 750 Processing helix chain 'B' and resid 751 through 772 removed outlier: 3.865A pdb=" N ASP B 756 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 757 " --> pdb=" O PRO B 753 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 758 " --> pdb=" O PHE B 754 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET B 772 " --> pdb=" O LEU B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 807 Processing helix chain 'B' and resid 808 through 814 Processing helix chain 'B' and resid 815 through 834 removed outlier: 3.646A pdb=" N GLU B 831 " --> pdb=" O LEU B 827 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 832 " --> pdb=" O SER B 828 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 833 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 857 removed outlier: 3.766A pdb=" N ARG B 847 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 856 " --> pdb=" O LYS B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 873 removed outlier: 3.573A pdb=" N VAL B 872 " --> pdb=" O ILE B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 897 Processing helix chain 'B' and resid 899 through 904 Processing helix chain 'B' and resid 904 through 909 removed outlier: 3.989A pdb=" N ILE B 908 " --> pdb=" O CYS B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 Processing helix chain 'B' and resid 937 through 949 removed outlier: 4.416A pdb=" N ASP B 943 " --> pdb=" O GLU B 939 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 949 " --> pdb=" O MET B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 981 removed outlier: 3.674A pdb=" N CYS B 953 " --> pdb=" O GLY B 949 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1183 through 1196 Processing helix chain 'B' and resid 1197 through 1214 Processing helix chain 'B' and resid 1225 through 1255 removed outlier: 3.726A pdb=" N LYS B1237 " --> pdb=" O GLU B1233 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B1238 " --> pdb=" O TYR B1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1261 Processing helix chain 'B' and resid 1262 through 1284 Processing helix chain 'B' and resid 1291 through 1297 removed outlier: 3.646A pdb=" N THR B1297 " --> pdb=" O LYS B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1298 through 1302 Processing helix chain 'B' and resid 1303 through 1310 removed outlier: 3.890A pdb=" N LEU B1307 " --> pdb=" O PRO B1303 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B1308 " --> pdb=" O LEU B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1324 Processing helix chain 'B' and resid 1324 through 1350 removed outlier: 4.263A pdb=" N ASN B1329 " --> pdb=" O PRO B1325 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B1330 " --> pdb=" O SER B1326 " (cutoff:3.500A) Processing helix chain 'B' and resid 1372 through 1383 removed outlier: 3.603A pdb=" N CYS B1376 " --> pdb=" O ASN B1372 " (cutoff:3.500A) Processing helix chain 'B' and resid 1398 through 1412 Processing helix chain 'B' and resid 1414 through 1424 removed outlier: 4.020A pdb=" N ILE B1418 " --> pdb=" O GLY B1414 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1439 No H-bonds generated for 'chain 'B' and resid 1437 through 1439' Processing helix chain 'B' and resid 1440 through 1451 removed outlier: 3.750A pdb=" N PHE B1444 " --> pdb=" O MET B1440 " (cutoff:3.500A) Processing helix chain 'B' and resid 1453 through 1474 removed outlier: 3.712A pdb=" N PHE B1474 " --> pdb=" O GLN B1470 " (cutoff:3.500A) Processing helix chain 'B' and resid 1482 through 1496 Processing helix chain 'B' and resid 1509 through 1521 Processing helix chain 'B' and resid 1521 through 1541 removed outlier: 3.684A pdb=" N ASP B1525 " --> pdb=" O GLN B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1547 through 1581 removed outlier: 8.050A pdb=" N HIS B1578 " --> pdb=" O PHE B1574 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR B1579 " --> pdb=" O ALA B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1583 through 1605 Processing helix chain 'B' and resid 1612 through 1622 Processing helix chain 'B' and resid 1623 through 1634 removed outlier: 3.525A pdb=" N ILE B1631 " --> pdb=" O LEU B1628 " (cutoff:3.500A) Processing helix chain 'B' and resid 1635 through 1673 Proline residue: B1649 - end of helix Processing helix chain 'B' and resid 1690 through 1703 removed outlier: 4.066A pdb=" N THR B1703 " --> pdb=" O PHE B1699 " (cutoff:3.500A) Processing helix chain 'B' and resid 1706 through 1712 removed outlier: 3.526A pdb=" N LEU B1710 " --> pdb=" O GLY B1706 " (cutoff:3.500A) Processing helix chain 'B' and resid 1717 through 1721 Processing helix chain 'B' and resid 1738 through 1772 removed outlier: 3.534A pdb=" N ASN B1759 " --> pdb=" O LEU B1755 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B1767 " --> pdb=" O ALA B1763 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B1772 " --> pdb=" O ASN B1768 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 31 removed outlier: 5.925A pdb=" N ALA D 30 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN D 50 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR D 55 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG D 72 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP D 57 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 36 through 40 Processing sheet with id=AA3, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.342A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 64 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 65 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN C 82 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TRP C 67 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 48 735 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1870 1.32 - 1.45: 3507 1.45 - 1.58: 6741 1.58 - 1.71: 0 1.71 - 1.84: 160 Bond restraints: 12278 Sorted by residual: bond pdb=" CA ARG D 46 " pdb=" C ARG D 46 " ideal model delta sigma weight residual 1.520 1.446 0.074 1.16e-02 7.43e+03 4.09e+01 bond pdb=" CA SER D 42 " pdb=" CB SER D 42 " ideal model delta sigma weight residual 1.528 1.464 0.065 1.35e-02 5.49e+03 2.29e+01 bond pdb=" CA SER D 47 " pdb=" CB SER D 47 " ideal model delta sigma weight residual 1.530 1.455 0.075 1.68e-02 3.54e+03 2.01e+01 bond pdb=" CA ARG D 46 " pdb=" CB ARG D 46 " ideal model delta sigma weight residual 1.532 1.471 0.061 1.62e-02 3.81e+03 1.42e+01 bond pdb=" N ILE B1387 " pdb=" CA ILE B1387 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.28e-02 6.10e+03 1.39e+01 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 16529 3.95 - 7.90: 123 7.90 - 11.84: 6 11.84 - 15.79: 2 15.79 - 19.74: 2 Bond angle restraints: 16662 Sorted by residual: angle pdb=" N SER D 47 " pdb=" CA SER D 47 " pdb=" C SER D 47 " ideal model delta sigma weight residual 112.89 121.06 -8.17 1.24e+00 6.50e-01 4.34e+01 angle pdb=" C04 WMK B2002 " pdb=" C05 WMK B2002 " pdb=" O21 WMK B2002 " ideal model delta sigma weight residual 110.56 90.82 19.74 3.00e+00 1.11e-01 4.33e+01 angle pdb=" N PRO C 133 " pdb=" CA PRO C 133 " pdb=" CB PRO C 133 " ideal model delta sigma weight residual 103.52 97.67 5.85 1.06e+00 8.90e-01 3.05e+01 angle pdb=" C06 WMK B2002 " pdb=" C05 WMK B2002 " pdb=" O21 WMK B2002 " ideal model delta sigma weight residual 106.97 90.67 16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" C08 WMK B2002 " pdb=" C05 WMK B2002 " pdb=" O21 WMK B2002 " ideal model delta sigma weight residual 112.07 96.82 15.25 3.00e+00 1.11e-01 2.58e+01 ... (remaining 16657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 6909 23.75 - 47.50: 443 47.50 - 71.25: 61 71.25 - 95.00: 38 95.00 - 118.75: 20 Dihedral angle restraints: 7471 sinusoidal: 3175 harmonic: 4296 Sorted by residual: dihedral pdb=" CB CYS C 72 " pdb=" SG CYS C 72 " pdb=" SG CYS C 75 " pdb=" CB CYS C 75 " ideal model delta sinusoidal sigma weight residual 93.00 179.76 -86.76 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS B 944 " pdb=" SG CYS B 944 " pdb=" SG CYS B 953 " pdb=" CB CYS B 953 " ideal model delta sinusoidal sigma weight residual -86.00 -162.57 76.57 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS B1356 " pdb=" SG CYS B1356 " pdb=" SG CYS B1376 " pdb=" CB CYS B1376 " ideal model delta sinusoidal sigma weight residual -86.00 -145.22 59.22 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 7468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.488: 1953 0.488 - 0.976: 0 0.976 - 1.464: 0 1.464 - 1.952: 0 1.952 - 2.439: 1 Chirality restraints: 1954 Sorted by residual: chirality pdb=" C05 WMK B2002 " pdb=" C04 WMK B2002 " pdb=" C06 WMK B2002 " pdb=" C08 WMK B2002 " both_signs ideal model delta sigma weight residual False -2.84 -0.40 -2.44 2.00e-01 2.50e+01 1.49e+02 chirality pdb=" CA PHE B1396 " pdb=" N PHE B1396 " pdb=" C PHE B1396 " pdb=" CB PHE B1396 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B1358 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1951 not shown) Planarity restraints: 2038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1415 " -0.030 2.00e-02 2.50e+03 2.38e-02 1.41e+01 pdb=" CG TRP B1415 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP B1415 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B1415 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B1415 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B1415 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1415 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1415 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1415 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B1415 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1390 " -0.011 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C LYS B1390 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS B1390 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B1391 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1386 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C GLU B1386 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU B1386 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE B1387 " -0.013 2.00e-02 2.50e+03 ... (remaining 2035 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1193 2.74 - 3.28: 12899 3.28 - 3.82: 19604 3.82 - 4.36: 22662 4.36 - 4.90: 38925 Nonbonded interactions: 95283 Sorted by model distance: nonbonded pdb=" O VAL B 283 " pdb=" OH TYR B 305 " model vdw 2.202 3.040 nonbonded pdb=" O ALA B 890 " pdb=" OG SER B 925 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU B 939 " pdb=" O20 WMK B2002 " model vdw 2.272 3.040 nonbonded pdb=" O PRO B 346 " pdb=" OG1 THR B 351 " model vdw 2.274 3.040 nonbonded pdb=" N SER D 47 " pdb=" OG SER D 47 " model vdw 2.278 2.496 ... (remaining 95278 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.41 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: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.340 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 0.075 12305 Z= 0.278 Angle : 0.902 19.739 16733 Z= 0.475 Chirality : 0.076 2.439 1954 Planarity : 0.004 0.050 2031 Dihedral : 17.394 118.753 4663 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.16 % Allowed : 0.95 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1457 helix: 0.67 (0.17), residues: 836 sheet: -0.44 (0.51), residues: 106 loop : -1.85 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B1415 HIS 0.004 0.001 HIS B 775 PHE 0.029 0.002 PHE B1337 TYR 0.026 0.002 TYR B1488 ARG 0.007 0.001 ARG B1299 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 7) link_NAG-ASN : angle 3.47546 ( 21) link_BETA1-4 : bond 0.00692 ( 10) link_BETA1-4 : angle 2.72865 ( 30) hydrogen bonds : bond 0.12983 ( 735) hydrogen bonds : angle 6.03672 ( 2076) SS BOND : bond 0.01552 ( 10) SS BOND : angle 3.23560 ( 20) covalent geometry : bond 0.00527 (12278) covalent geometry : angle 0.88044 (16662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: D 48 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: B 222 PHE cc_start: 0.6549 (m-10) cc_final: 0.6339 (m-10) REVERT: B 807 MET cc_start: 0.7586 (ptm) cc_final: 0.7102 (ptm) REVERT: B 1207 MET cc_start: 0.8780 (tpp) cc_final: 0.8523 (tpp) REVERT: B 1416 MET cc_start: 0.8019 (mmm) cc_final: 0.7701 (mmm) REVERT: C 104 ASN cc_start: 0.7403 (t0) cc_final: 0.7099 (t0) outliers start: 2 outliers final: 1 residues processed: 283 average time/residue: 0.2446 time to fit residues: 102.1777 Evaluate side-chains 235 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS B 332 GLN B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1653 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 = 0.4249 r_free = 0.4249 target = 0.178842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121742 restraints weight = 17274.381| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.45 r_work: 0.3395 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12305 Z= 0.189 Angle : 0.701 8.498 16733 Z= 0.354 Chirality : 0.045 0.238 1954 Planarity : 0.004 0.040 2031 Dihedral : 11.993 85.886 1985 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.21 % Allowed : 9.93 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1457 helix: 0.97 (0.18), residues: 837 sheet: -0.90 (0.48), residues: 117 loop : -1.74 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B1415 HIS 0.005 0.001 HIS D 143 PHE 0.024 0.002 PHE B 726 TYR 0.025 0.002 TYR B1488 ARG 0.005 0.001 ARG B1617 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 7) link_NAG-ASN : angle 2.41661 ( 21) link_BETA1-4 : bond 0.00760 ( 10) link_BETA1-4 : angle 2.90519 ( 30) hydrogen bonds : bond 0.04452 ( 735) hydrogen bonds : angle 4.92775 ( 2076) SS BOND : bond 0.00493 ( 10) SS BOND : angle 1.54009 ( 20) covalent geometry : bond 0.00434 (12278) covalent geometry : angle 0.68380 (16662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: B 829 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8048 (mm) REVERT: B 917 TRP cc_start: 0.7858 (m-10) cc_final: 0.7062 (m-10) REVERT: B 1185 TRP cc_start: 0.6212 (t60) cc_final: 0.5689 (t60) REVERT: B 1207 MET cc_start: 0.9257 (tpp) cc_final: 0.8846 (tpp) REVERT: B 1529 MET cc_start: 0.9073 (mmp) cc_final: 0.8864 (mmt) REVERT: B 1645 MET cc_start: 0.8273 (tpt) cc_final: 0.7936 (tpt) REVERT: C 104 ASN cc_start: 0.7721 (t0) cc_final: 0.7455 (t0) outliers start: 28 outliers final: 18 residues processed: 258 average time/residue: 0.2946 time to fit residues: 112.7342 Evaluate side-chains 246 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1202 THR Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Chi-restraints excluded: chain B residue 1768 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1586 ASN B1768 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.178344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124566 restraints weight = 17608.822| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.84 r_work: 0.3358 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12305 Z= 0.199 Angle : 0.679 8.264 16733 Z= 0.341 Chirality : 0.044 0.225 1954 Planarity : 0.004 0.040 2031 Dihedral : 9.763 79.731 1985 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.84 % Allowed : 13.32 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1457 helix: 1.07 (0.18), residues: 838 sheet: -0.37 (0.50), residues: 102 loop : -1.76 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1415 HIS 0.004 0.001 HIS B 131 PHE 0.021 0.002 PHE B 171 TYR 0.025 0.002 TYR D 32 ARG 0.004 0.000 ARG B1626 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 7) link_NAG-ASN : angle 2.30761 ( 21) link_BETA1-4 : bond 0.00703 ( 10) link_BETA1-4 : angle 2.85983 ( 30) hydrogen bonds : bond 0.04166 ( 735) hydrogen bonds : angle 4.74081 ( 2076) SS BOND : bond 0.00482 ( 10) SS BOND : angle 1.31412 ( 20) covalent geometry : bond 0.00465 (12278) covalent geometry : angle 0.66278 (16662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: B 1207 MET cc_start: 0.9140 (tpp) cc_final: 0.8736 (tpp) REVERT: B 1265 CYS cc_start: 0.8355 (m) cc_final: 0.7997 (m) REVERT: B 1645 MET cc_start: 0.8328 (tpt) cc_final: 0.7961 (tpt) REVERT: C 104 ASN cc_start: 0.7795 (t0) cc_final: 0.7553 (t0) outliers start: 36 outliers final: 23 residues processed: 255 average time/residue: 0.2125 time to fit residues: 81.7745 Evaluate side-chains 249 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1202 THR Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1244 ILE Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Chi-restraints excluded: chain B residue 1768 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN B 404 ASN ** B1431 GLN ** 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 = 0.4262 r_free = 0.4262 target = 0.180591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123286 restraints weight = 17540.551| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.45 r_work: 0.3405 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12305 Z= 0.162 Angle : 0.654 9.932 16733 Z= 0.327 Chirality : 0.043 0.275 1954 Planarity : 0.004 0.046 2031 Dihedral : 8.327 70.571 1985 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.84 % Allowed : 15.60 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1457 helix: 1.18 (0.18), residues: 839 sheet: -0.32 (0.50), residues: 102 loop : -1.69 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 PHE 0.020 0.001 PHE B1616 TYR 0.024 0.002 TYR B1488 ARG 0.003 0.000 ARG B1626 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 7) link_NAG-ASN : angle 2.29410 ( 21) link_BETA1-4 : bond 0.00711 ( 10) link_BETA1-4 : angle 2.76628 ( 30) hydrogen bonds : bond 0.03934 ( 735) hydrogen bonds : angle 4.62694 ( 2076) SS BOND : bond 0.00345 ( 10) SS BOND : angle 1.61146 ( 20) covalent geometry : bond 0.00367 (12278) covalent geometry : angle 0.63671 (16662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: D 130 GLU cc_start: 0.7457 (mp0) cc_final: 0.7017 (mp0) REVERT: B 754 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7674 (t80) REVERT: B 827 LEU cc_start: 0.9133 (mp) cc_final: 0.8827 (mt) REVERT: B 1207 MET cc_start: 0.9236 (tpp) cc_final: 0.8839 (tpp) REVERT: B 1265 CYS cc_start: 0.8474 (m) cc_final: 0.8127 (m) REVERT: B 1529 MET cc_start: 0.8632 (mmt) cc_final: 0.8066 (ptm) REVERT: C 104 ASN cc_start: 0.7829 (t0) cc_final: 0.7594 (t0) outliers start: 36 outliers final: 27 residues processed: 257 average time/residue: 0.2085 time to fit residues: 81.1253 Evaluate side-chains 253 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1698 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 94 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.178932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125169 restraints weight = 17592.748| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.28 r_work: 0.3343 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12305 Z= 0.209 Angle : 0.674 8.067 16733 Z= 0.340 Chirality : 0.044 0.245 1954 Planarity : 0.004 0.048 2031 Dihedral : 7.843 70.794 1985 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.10 % Allowed : 16.00 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1457 helix: 1.14 (0.18), residues: 844 sheet: -0.33 (0.51), residues: 102 loop : -1.68 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B1185 HIS 0.003 0.001 HIS D 134 PHE 0.018 0.002 PHE B1746 TYR 0.023 0.002 TYR B1488 ARG 0.003 0.000 ARG B1626 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 7) link_NAG-ASN : angle 2.27964 ( 21) link_BETA1-4 : bond 0.00632 ( 10) link_BETA1-4 : angle 2.66016 ( 30) hydrogen bonds : bond 0.04010 ( 735) hydrogen bonds : angle 4.63506 ( 2076) SS BOND : bond 0.00411 ( 10) SS BOND : angle 2.13039 ( 20) covalent geometry : bond 0.00488 (12278) covalent geometry : angle 0.65637 (16662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: D 130 GLU cc_start: 0.7433 (mp0) cc_final: 0.7148 (mp0) REVERT: B 396 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.6697 (m-10) REVERT: B 777 MET cc_start: 0.7363 (mmm) cc_final: 0.6799 (mtt) REVERT: B 827 LEU cc_start: 0.9154 (mp) cc_final: 0.8911 (mt) REVERT: B 1265 CYS cc_start: 0.8463 (m) cc_final: 0.7967 (m) REVERT: B 1406 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8252 (mp) REVERT: B 1529 MET cc_start: 0.8581 (mmt) cc_final: 0.7975 (ptm) REVERT: B 1555 TYR cc_start: 0.7735 (t80) cc_final: 0.7345 (t80) REVERT: B 1573 MET cc_start: 0.7711 (mmm) cc_final: 0.7483 (ppp) REVERT: C 104 ASN cc_start: 0.7874 (t0) cc_final: 0.7641 (t0) outliers start: 52 outliers final: 31 residues processed: 268 average time/residue: 0.2023 time to fit residues: 81.8792 Evaluate side-chains 258 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1202 THR Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1387 ILE Chi-restraints excluded: chain B residue 1406 LEU Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1698 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Chi-restraints excluded: chain B residue 1758 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 13 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 95 optimal weight: 0.0870 chunk 6 optimal weight: 0.0870 chunk 81 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS B1768 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.181742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125261 restraints weight = 17517.806| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.48 r_work: 0.3446 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12305 Z= 0.118 Angle : 0.628 14.295 16733 Z= 0.312 Chirality : 0.042 0.238 1954 Planarity : 0.003 0.051 2031 Dihedral : 6.446 53.502 1981 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.52 % Allowed : 18.52 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1457 helix: 1.35 (0.18), residues: 843 sheet: -0.52 (0.50), residues: 104 loop : -1.51 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 PHE 0.025 0.001 PHE B1200 TYR 0.024 0.001 TYR B1488 ARG 0.006 0.000 ARG B1299 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 7) link_NAG-ASN : angle 2.25034 ( 21) link_BETA1-4 : bond 0.00594 ( 10) link_BETA1-4 : angle 2.47066 ( 30) hydrogen bonds : bond 0.03644 ( 735) hydrogen bonds : angle 4.44926 ( 2076) SS BOND : bond 0.00201 ( 10) SS BOND : angle 1.50498 ( 20) covalent geometry : bond 0.00246 (12278) covalent geometry : angle 0.61316 (16662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: B 169 TYR cc_start: 0.8401 (m-80) cc_final: 0.8093 (m-80) REVERT: B 258 THR cc_start: 0.8045 (m) cc_final: 0.7675 (p) REVERT: B 751 MET cc_start: 0.6215 (tpp) cc_final: 0.5405 (mtp) REVERT: B 777 MET cc_start: 0.7378 (mmm) cc_final: 0.6849 (mtt) REVERT: B 1207 MET cc_start: 0.9171 (tpp) cc_final: 0.8734 (tpp) REVERT: B 1265 CYS cc_start: 0.8481 (m) cc_final: 0.8262 (m) REVERT: B 1406 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8345 (mp) REVERT: B 1429 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7634 (t0) REVERT: B 1529 MET cc_start: 0.8588 (mmt) cc_final: 0.8055 (ptm) REVERT: B 1573 MET cc_start: 0.7929 (mmm) cc_final: 0.7677 (ppp) REVERT: B 1588 PHE cc_start: 0.8611 (t80) cc_final: 0.8136 (t80) outliers start: 32 outliers final: 20 residues processed: 270 average time/residue: 0.2103 time to fit residues: 84.9102 Evaluate side-chains 255 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1406 LEU Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1758 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 142 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.181309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124013 restraints weight = 17611.841| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.47 r_work: 0.3407 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12305 Z= 0.163 Angle : 0.661 8.810 16733 Z= 0.328 Chirality : 0.043 0.252 1954 Planarity : 0.004 0.051 2031 Dihedral : 6.069 54.140 1981 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.99 % Allowed : 19.78 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1457 helix: 1.32 (0.18), residues: 842 sheet: -0.48 (0.50), residues: 104 loop : -1.54 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 PHE 0.021 0.001 PHE B1616 TYR 0.022 0.001 TYR B 376 ARG 0.005 0.000 ARG B1629 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 7) link_NAG-ASN : angle 2.20331 ( 21) link_BETA1-4 : bond 0.00615 ( 10) link_BETA1-4 : angle 2.44715 ( 30) hydrogen bonds : bond 0.03755 ( 735) hydrogen bonds : angle 4.45604 ( 2076) SS BOND : bond 0.00325 ( 10) SS BOND : angle 1.36602 ( 20) covalent geometry : bond 0.00378 (12278) covalent geometry : angle 0.64759 (16662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: D 128 PHE cc_start: 0.8657 (m-80) cc_final: 0.8420 (m-10) REVERT: B 206 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6687 (m-10) REVERT: B 396 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.6881 (m-10) REVERT: B 777 MET cc_start: 0.7336 (mmm) cc_final: 0.6754 (mtt) REVERT: B 827 LEU cc_start: 0.9167 (mp) cc_final: 0.8851 (mt) REVERT: B 1207 MET cc_start: 0.9249 (tpp) cc_final: 0.8803 (tpp) REVERT: B 1406 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7988 (mp) REVERT: B 1529 MET cc_start: 0.8594 (mmt) cc_final: 0.8080 (ptm) REVERT: B 1555 TYR cc_start: 0.7814 (t80) cc_final: 0.7431 (t80) REVERT: B 1588 PHE cc_start: 0.8635 (t80) cc_final: 0.8123 (t80) outliers start: 38 outliers final: 25 residues processed: 257 average time/residue: 0.2096 time to fit residues: 80.9139 Evaluate side-chains 258 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 TRP Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1406 LEU Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1698 LEU Chi-restraints excluded: chain B residue 1758 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 22 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 71 optimal weight: 0.5980 chunk 130 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 145 optimal weight: 50.0000 chunk 114 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.182676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125893 restraints weight = 17660.766| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.48 r_work: 0.3443 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12305 Z= 0.135 Angle : 0.638 9.422 16733 Z= 0.318 Chirality : 0.042 0.229 1954 Planarity : 0.004 0.052 2031 Dihedral : 5.558 54.008 1981 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.15 % Allowed : 19.70 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1457 helix: 1.37 (0.18), residues: 842 sheet: -0.55 (0.51), residues: 102 loop : -1.46 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B1185 HIS 0.005 0.001 HIS B 131 PHE 0.015 0.001 PHE B1447 TYR 0.025 0.001 TYR B1488 ARG 0.003 0.000 ARG B1299 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 7) link_NAG-ASN : angle 2.18352 ( 21) link_BETA1-4 : bond 0.00582 ( 10) link_BETA1-4 : angle 2.34384 ( 30) hydrogen bonds : bond 0.03642 ( 735) hydrogen bonds : angle 4.40085 ( 2076) SS BOND : bond 0.00251 ( 10) SS BOND : angle 1.29740 ( 20) covalent geometry : bond 0.00302 (12278) covalent geometry : angle 0.62482 (16662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 128 PHE cc_start: 0.8663 (m-80) cc_final: 0.8446 (m-10) REVERT: B 169 TYR cc_start: 0.8398 (m-80) cc_final: 0.8145 (m-80) REVERT: B 206 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6700 (m-10) REVERT: B 396 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: B 777 MET cc_start: 0.7279 (mmm) cc_final: 0.6731 (mtt) REVERT: B 827 LEU cc_start: 0.9141 (mp) cc_final: 0.8891 (mt) REVERT: B 1207 MET cc_start: 0.9255 (tpp) cc_final: 0.8803 (tpp) REVERT: B 1406 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 1430 GLU cc_start: 0.8430 (mp0) cc_final: 0.8186 (mp0) REVERT: B 1479 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8731 (tp) REVERT: B 1529 MET cc_start: 0.8577 (mmt) cc_final: 0.7941 (ptm) REVERT: B 1530 MET cc_start: 0.7211 (mmt) cc_final: 0.6634 (mmm) REVERT: B 1555 TYR cc_start: 0.7761 (t80) cc_final: 0.7435 (t80) REVERT: B 1573 MET cc_start: 0.8177 (mmm) cc_final: 0.7794 (ppp) REVERT: B 1588 PHE cc_start: 0.8638 (t80) cc_final: 0.8126 (t80) REVERT: B 1623 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7755 (mtm180) outliers start: 40 outliers final: 26 residues processed: 266 average time/residue: 0.2094 time to fit residues: 83.3184 Evaluate side-chains 264 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 TRP Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1406 LEU Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1479 ILE Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1748 SER Chi-restraints excluded: chain B residue 1758 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 19 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 404 ASN B 728 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS B1768 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.179026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121345 restraints weight = 17681.271| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.48 r_work: 0.3372 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12305 Z= 0.215 Angle : 0.699 13.093 16733 Z= 0.350 Chirality : 0.044 0.278 1954 Planarity : 0.004 0.050 2031 Dihedral : 5.678 54.610 1981 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.31 % Allowed : 20.02 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1457 helix: 1.22 (0.18), residues: 838 sheet: -0.41 (0.51), residues: 104 loop : -1.54 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B1185 HIS 0.005 0.001 HIS B 131 PHE 0.027 0.002 PHE B1447 TYR 0.026 0.002 TYR B1488 ARG 0.003 0.000 ARG B 931 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 7) link_NAG-ASN : angle 2.20292 ( 21) link_BETA1-4 : bond 0.00610 ( 10) link_BETA1-4 : angle 2.35681 ( 30) hydrogen bonds : bond 0.03952 ( 735) hydrogen bonds : angle 4.55424 ( 2076) SS BOND : bond 0.00460 ( 10) SS BOND : angle 1.47610 ( 20) covalent geometry : bond 0.00506 (12278) covalent geometry : angle 0.68694 (16662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: B 396 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: B 412 MET cc_start: 0.8627 (mtm) cc_final: 0.8287 (mtp) REVERT: B 777 MET cc_start: 0.7332 (mmm) cc_final: 0.6842 (mtt) REVERT: B 827 LEU cc_start: 0.9157 (mp) cc_final: 0.8853 (mt) REVERT: B 1207 MET cc_start: 0.9281 (tpp) cc_final: 0.8832 (tpp) REVERT: B 1479 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8731 (tp) REVERT: B 1529 MET cc_start: 0.8571 (mmt) cc_final: 0.7845 (ptm) REVERT: B 1530 MET cc_start: 0.7261 (mmt) cc_final: 0.6796 (mmm) REVERT: B 1573 MET cc_start: 0.8171 (mmm) cc_final: 0.7901 (ppp) REVERT: B 1578 HIS cc_start: 0.7297 (p-80) cc_final: 0.6856 (p-80) REVERT: B 1588 PHE cc_start: 0.8640 (t80) cc_final: 0.8102 (t80) outliers start: 42 outliers final: 33 residues processed: 262 average time/residue: 0.2286 time to fit residues: 90.9118 Evaluate side-chains 264 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 TRP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1387 ILE Chi-restraints excluded: chain B residue 1406 LEU Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1479 ILE Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1698 LEU Chi-restraints excluded: chain B residue 1748 SER Chi-restraints excluded: chain B residue 1758 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 145 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 0.0170 chunk 134 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 overall best weight: 2.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.178905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121374 restraints weight = 17540.296| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.46 r_work: 0.3371 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 12305 Z= 0.222 Angle : 0.710 11.445 16733 Z= 0.357 Chirality : 0.045 0.323 1954 Planarity : 0.004 0.051 2031 Dihedral : 5.713 54.457 1981 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.23 % Allowed : 20.09 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1457 helix: 1.13 (0.18), residues: 837 sheet: -0.41 (0.52), residues: 101 loop : -1.54 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1185 HIS 0.009 0.001 HIS B 131 PHE 0.028 0.002 PHE B1447 TYR 0.030 0.002 TYR B1488 ARG 0.006 0.001 ARG D 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 7) link_NAG-ASN : angle 2.28952 ( 21) link_BETA1-4 : bond 0.00600 ( 10) link_BETA1-4 : angle 2.31052 ( 30) hydrogen bonds : bond 0.04016 ( 735) hydrogen bonds : angle 4.60997 ( 2076) SS BOND : bond 0.00464 ( 10) SS BOND : angle 1.47802 ( 20) covalent geometry : bond 0.00526 (12278) covalent geometry : angle 0.69797 (16662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: B 169 TYR cc_start: 0.8423 (m-80) cc_final: 0.8180 (m-80) REVERT: B 396 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.6959 (m-10) REVERT: B 412 MET cc_start: 0.8675 (mtm) cc_final: 0.8342 (mtp) REVERT: B 777 MET cc_start: 0.7386 (mmm) cc_final: 0.6815 (mtt) REVERT: B 827 LEU cc_start: 0.9157 (mp) cc_final: 0.8847 (mt) REVERT: B 1207 MET cc_start: 0.9266 (tpp) cc_final: 0.8840 (tpp) REVERT: B 1479 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8707 (tp) REVERT: B 1529 MET cc_start: 0.8532 (mmt) cc_final: 0.7897 (ptm) REVERT: B 1530 MET cc_start: 0.7261 (mmt) cc_final: 0.6791 (mmm) REVERT: B 1573 MET cc_start: 0.8183 (mmm) cc_final: 0.7912 (ppp) REVERT: B 1578 HIS cc_start: 0.7127 (p-80) cc_final: 0.6682 (p-80) outliers start: 41 outliers final: 35 residues processed: 255 average time/residue: 0.1941 time to fit residues: 75.1445 Evaluate side-chains 263 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 TRP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1298 LEU Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1387 ILE Chi-restraints excluded: chain B residue 1406 LEU Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1479 ILE Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1698 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Chi-restraints excluded: chain B residue 1758 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS B1768 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.180912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124506 restraints weight = 17439.028| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.47 r_work: 0.3441 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12305 Z= 0.133 Angle : 0.653 12.568 16733 Z= 0.325 Chirality : 0.043 0.330 1954 Planarity : 0.004 0.053 2031 Dihedral : 5.353 53.810 1981 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.52 % Allowed : 20.88 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1457 helix: 1.35 (0.18), residues: 835 sheet: -0.40 (0.52), residues: 102 loop : -1.44 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1185 HIS 0.002 0.001 HIS B 131 PHE 0.027 0.001 PHE B1447 TYR 0.035 0.001 TYR B1488 ARG 0.004 0.000 ARG B1388 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 7) link_NAG-ASN : angle 2.22176 ( 21) link_BETA1-4 : bond 0.00556 ( 10) link_BETA1-4 : angle 2.16355 ( 30) hydrogen bonds : bond 0.03697 ( 735) hydrogen bonds : angle 4.44976 ( 2076) SS BOND : bond 0.00225 ( 10) SS BOND : angle 1.10783 ( 20) covalent geometry : bond 0.00297 (12278) covalent geometry : angle 0.64225 (16662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8503.78 seconds wall clock time: 146 minutes 51.63 seconds (8811.63 seconds total)