Starting phenix.real_space_refine on Fri Jul 3 07:25:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gz2_34388/07_2026/8gz2_34388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz2_34388/07_2026/8gz2_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2026/8gz2_34388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2026/8gz2_34388.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2026/8gz2_34388.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2026/8gz2_34388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2026/8gz2_34388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz2_34388/07_2026/8gz2_34388.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} 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: {'ARG:plan': 1, 'PHE: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: {'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 2.78, per 1000 atoms: 0.23 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: 1.02 Conformation dependent library (CDL) restraints added in 556.7 milliseconds 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: 0.35 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: 2.16 Time building geometry restraints manager: 1.30 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 - 17.54: 6319 17.54 - 35.08: 645 35.08 - 52.63: 125 52.63 - 70.17: 20 70.17 - 87.71: 15 Dihedral angle restraints: 7124 sinusoidal: 2828 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 7121 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.160 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 14.585 87.709 4316 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.75 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (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 ARG 0.007 0.001 ARG B1299 TYR 0.026 0.002 TYR B1488 PHE 0.029 0.002 PHE B1337 TRP 0.065 0.002 TRP B1415 HIS 0.004 0.001 HIS B 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.28 (12278) covalent geometry : angle 0.88044 / 0.47 (16662) SS BOND : bond 0.01552 / 0.97 ( 10) SS BOND : angle 3.23560 / 1.96 ( 20) hydrogen bonds : bond 0.12983 / 8.65 ( 735) hydrogen bonds : angle 6.03672 / 4.11 ( 2076) link_BETA1-4 : bond 0.00692 / 0.52 ( 10) link_BETA1-4 : angle 2.72865 / 1.34 ( 30) link_NAG-ASN : bond 0.00376 / 0.28 ( 7) link_NAG-ASN : angle 3.47546 / 2.14 ( 21) *********************** 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 : 0.449 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: 0.1019 time to fit residues: 42.7850 Evaluate side-chains 234 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4253 r_free = 0.4253 target = 0.179255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122251 restraints weight = 17321.533| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.47 r_work: 0.3433 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12305 Z= 0.179 Angle : 0.683 8.516 16733 Z= 0.348 Chirality : 0.044 0.216 1954 Planarity : 0.004 0.041 2031 Dihedral : 5.407 59.495 1638 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.05 % Allowed : 10.17 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.22), residues: 1457 helix: 0.99 (0.18), residues: 837 sheet: -0.88 (0.48), residues: 117 loop : -1.72 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1617 TYR 0.025 0.002 TYR B1488 PHE 0.025 0.002 PHE B 726 TRP 0.039 0.002 TRP B1185 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (12278) covalent geometry : angle 0.66953 / 0.35 (16662) SS BOND : bond 0.00432 / 0.31 ( 10) SS BOND : angle 1.50776 / 1.02 ( 20) hydrogen bonds : bond 0.04322 / 2.83 ( 735) hydrogen bonds : angle 4.89354 / 3.34 ( 2076) link_BETA1-4 : bond 0.00570 / 0.39 ( 10) link_BETA1-4 : angle 2.39095 / 1.27 ( 30) link_NAG-ASN : bond 0.00207 / 0.14 ( 7) link_NAG-ASN : angle 2.32818 / 1.41 ( 21) *********************** 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: 26 poor density : 248 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 917 TRP cc_start: 0.7785 (m-10) cc_final: 0.6955 (m-10) REVERT: B 1185 TRP cc_start: 0.6205 (t60) cc_final: 0.5695 (t60) REVERT: B 1207 MET cc_start: 0.9226 (tpp) cc_final: 0.8819 (tpp) REVERT: B 1529 MET cc_start: 0.9043 (mmp) cc_final: 0.8830 (mmt) REVERT: B 1540 MET cc_start: 0.8887 (ptp) cc_final: 0.8636 (ptp) REVERT: B 1645 MET cc_start: 0.8400 (tpt) cc_final: 0.8070 (tpt) REVERT: C 104 ASN cc_start: 0.7702 (t0) cc_final: 0.7444 (t0) outliers start: 26 outliers final: 17 residues processed: 258 average time/residue: 0.0972 time to fit residues: 37.7768 Evaluate side-chains 248 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 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 115 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 0.0370 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 87 optimal weight: 0.0470 chunk 85 optimal weight: 10.0000 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1586 ASN ** B1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.184476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.126915 restraints weight = 17729.035| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.52 r_work: 0.3494 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1728 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= 0.120 Angle : 0.607 10.295 16733 Z= 0.307 Chirality : 0.041 0.289 1954 Planarity : 0.004 0.043 2031 Dihedral : 5.006 50.185 1638 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.44 % Allowed : 12.61 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1457 helix: 1.24 (0.18), residues: 841 sheet: -0.46 (0.49), residues: 104 loop : -1.65 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1626 TYR 0.026 0.001 TYR D 32 PHE 0.021 0.001 PHE B 171 TRP 0.029 0.001 TRP B1185 HIS 0.003 0.001 HIS B 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (12278) covalent geometry : angle 0.59442 / 0.30 (16662) SS BOND : bond 0.00553 / 0.36 ( 10) SS BOND : angle 1.08548 / 0.76 ( 20) hydrogen bonds : bond 0.03852 / 2.51 ( 735) hydrogen bonds : angle 4.56190 / 3.12 ( 2076) link_BETA1-4 : bond 0.00535 / 0.37 ( 10) link_BETA1-4 : angle 2.19015 / 1.18 ( 30) link_NAG-ASN : bond 0.00303 / 0.22 ( 7) link_NAG-ASN : angle 2.20087 / 1.30 ( 21) *********************** 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 290 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: B 258 THR cc_start: 0.8073 (m) cc_final: 0.7765 (p) REVERT: B 827 LEU cc_start: 0.9031 (mp) cc_final: 0.8751 (mt) REVERT: B 917 TRP cc_start: 0.7547 (m-10) cc_final: 0.6880 (m100) REVERT: B 1207 MET cc_start: 0.9198 (tpp) cc_final: 0.8797 (tpp) REVERT: B 1645 MET cc_start: 0.8440 (tpt) cc_final: 0.8135 (tpt) REVERT: C 104 ASN cc_start: 0.7626 (t0) cc_final: 0.7380 (t0) outliers start: 31 outliers final: 15 residues processed: 273 average time/residue: 0.0951 time to fit residues: 39.1019 Evaluate side-chains 250 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU 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 858 TRP Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1249 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 1534 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS B1768 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.177146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123709 restraints weight = 17860.525| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.25 r_work: 0.3303 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 12305 Z= 0.300 Angle : 0.752 7.927 16733 Z= 0.382 Chirality : 0.047 0.279 1954 Planarity : 0.004 0.052 2031 Dihedral : 5.239 43.187 1638 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.23 % Allowed : 15.84 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1457 helix: 0.99 (0.18), residues: 835 sheet: -0.24 (0.50), residues: 102 loop : -1.70 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 365 TYR 0.030 0.002 TYR B 371 PHE 0.022 0.002 PHE B1746 TRP 0.047 0.002 TRP B1185 HIS 0.005 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.30 (12278) covalent geometry : angle 0.73966 / 0.38 (16662) SS BOND : bond 0.00640 / 0.46 ( 10) SS BOND : angle 1.64984 / 1.10 ( 20) hydrogen bonds : bond 0.04414 / 2.90 ( 735) hydrogen bonds : angle 4.81926 / 3.30 ( 2076) link_BETA1-4 : bond 0.00665 / 0.49 ( 10) link_BETA1-4 : angle 2.44472 / 1.33 ( 30) link_NAG-ASN : bond 0.00237 / 0.17 ( 7) link_NAG-ASN : angle 2.28713 / 1.43 ( 21) *********************** 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 271 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 754 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7721 (t80) REVERT: B 1265 CYS cc_start: 0.8468 (m) cc_final: 0.7998 (m) REVERT: B 1406 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8217 (mp) REVERT: B 1529 MET cc_start: 0.8582 (mmt) cc_final: 0.7945 (ptm) REVERT: C 104 ASN cc_start: 0.7880 (t0) cc_final: 0.7649 (t0) outliers start: 41 outliers final: 31 residues processed: 254 average time/residue: 0.0919 time to fit residues: 35.6404 Evaluate side-chains 259 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER 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 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 772 MET Chi-restraints excluded: chain B residue 780 GLN 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 1227 THR Chi-restraints excluded: chain B residue 1321 VAL Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1363 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 1708 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.181147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122787 restraints weight = 17691.372| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.50 r_work: 0.3414 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12305 Z= 0.137 Angle : 0.643 8.197 16733 Z= 0.324 Chirality : 0.042 0.296 1954 Planarity : 0.004 0.049 2031 Dihedral : 4.715 25.362 1635 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.92 % Allowed : 17.73 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1457 helix: 1.20 (0.18), residues: 846 sheet: -0.32 (0.50), residues: 102 loop : -1.60 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1629 TYR 0.026 0.002 TYR B1488 PHE 0.015 0.001 PHE B 189 TRP 0.032 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (12278) covalent geometry : angle 0.62842 / 0.32 (16662) SS BOND : bond 0.00251 / 0.19 ( 10) SS BOND : angle 1.95146 / 1.05 ( 20) hydrogen bonds : bond 0.03904 / 2.56 ( 735) hydrogen bonds : angle 4.55878 / 3.12 ( 2076) link_BETA1-4 : bond 0.00579 / 0.41 ( 10) link_BETA1-4 : angle 2.27700 / 1.21 ( 30) link_NAG-ASN : bond 0.00220 / 0.16 ( 7) link_NAG-ASN : angle 2.19197 / 1.29 ( 21) *********************** 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 276 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: D 130 GLU cc_start: 0.7475 (mp0) cc_final: 0.7167 (mp0) REVERT: B 396 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.6963 (m-10) REVERT: B 412 MET cc_start: 0.8621 (mtm) cc_final: 0.8276 (mtp) REVERT: B 751 MET cc_start: 0.6132 (tpp) cc_final: 0.5310 (mtp) REVERT: B 1207 MET cc_start: 0.9185 (tpp) cc_final: 0.8754 (tpp) REVERT: B 1265 CYS cc_start: 0.8503 (m) cc_final: 0.8044 (m) REVERT: B 1529 MET cc_start: 0.8604 (mmt) cc_final: 0.7969 (ptm) REVERT: B 1555 TYR cc_start: 0.7798 (t80) cc_final: 0.7411 (t80) REVERT: B 1578 HIS cc_start: 0.7342 (p-80) cc_final: 0.6950 (p-80) REVERT: C 104 ASN cc_start: 0.7822 (t0) cc_final: 0.7589 (t0) outliers start: 37 outliers final: 25 residues processed: 263 average time/residue: 0.0923 time to fit residues: 37.2098 Evaluate side-chains 251 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 396 PHE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1198 ASN Chi-restraints excluded: chain B residue 1227 THR 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 1708 ASP Chi-restraints excluded: chain B residue 1748 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1535 ASN 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 = 0.4229 r_free = 0.4229 target = 0.176870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119381 restraints weight = 17519.831| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.42 r_work: 0.3370 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12305 Z= 0.241 Angle : 0.704 8.235 16733 Z= 0.355 Chirality : 0.044 0.236 1954 Planarity : 0.004 0.049 2031 Dihedral : 4.802 28.199 1634 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.86 % Allowed : 18.36 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1457 helix: 1.08 (0.18), residues: 846 sheet: -0.32 (0.51), residues: 102 loop : -1.64 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1426 TYR 0.027 0.002 TYR B 376 PHE 0.020 0.002 PHE B1746 TRP 0.027 0.002 TRP B1185 HIS 0.004 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (12278) covalent geometry : angle 0.69197 / 0.35 (16662) SS BOND : bond 0.00469 / 0.35 ( 10) SS BOND : angle 1.71479 / 1.06 ( 20) hydrogen bonds : bond 0.04085 / 2.69 ( 735) hydrogen bonds : angle 4.65175 / 3.19 ( 2076) link_BETA1-4 : bond 0.00654 / 0.48 ( 10) link_BETA1-4 : angle 2.33769 / 1.27 ( 30) link_NAG-ASN : bond 0.00133 / 0.09 ( 7) link_NAG-ASN : angle 2.19243 / 1.34 ( 21) *********************** 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 285 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: D 23 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7346 (mt-10) REVERT: D 130 GLU cc_start: 0.7552 (mp0) cc_final: 0.7253 (mp0) REVERT: B 396 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7043 (m-10) REVERT: B 412 MET cc_start: 0.8613 (mtm) cc_final: 0.8268 (mtp) REVERT: B 751 MET cc_start: 0.6370 (tpp) cc_final: 0.5461 (mtp) REVERT: B 1207 MET cc_start: 0.9266 (tpp) cc_final: 0.8815 (tpp) REVERT: B 1265 CYS cc_start: 0.8516 (m) cc_final: 0.8079 (m) REVERT: B 1406 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8048 (mp) REVERT: B 1573 MET cc_start: 0.8160 (mmm) cc_final: 0.7862 (ppp) REVERT: B 1578 HIS cc_start: 0.7290 (p-80) cc_final: 0.6873 (p-80) REVERT: B 1588 PHE cc_start: 0.8681 (t80) cc_final: 0.8221 (t80) REVERT: C 104 ASN cc_start: 0.7949 (t0) cc_final: 0.7741 (t0) outliers start: 49 outliers final: 36 residues processed: 268 average time/residue: 0.0923 time to fit residues: 37.6539 Evaluate side-chains 264 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 129 LEU 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 780 GLN 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 878 LEU 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 1198 ASN 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 1363 ILE 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 1656 LEU Chi-restraints excluded: chain B residue 1698 LEU Chi-restraints excluded: chain B residue 1708 ASP Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 66 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 HIS B 271 GLN B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1653 ASN ** 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 = 0.4264 r_free = 0.4264 target = 0.180366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123934 restraints weight = 17374.004| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.44 r_work: 0.3438 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12305 Z= 0.132 Angle : 0.637 8.556 16733 Z= 0.318 Chirality : 0.042 0.207 1954 Planarity : 0.003 0.052 2031 Dihedral : 4.577 27.548 1634 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.07 % Allowed : 19.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1457 helix: 1.30 (0.18), residues: 845 sheet: -0.29 (0.51), residues: 102 loop : -1.52 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1299 TYR 0.021 0.001 TYR B1488 PHE 0.015 0.001 PHE B 189 TRP 0.026 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12278) covalent geometry : angle 0.62249 / 0.31 (16662) SS BOND : bond 0.00219 / 0.17 ( 10) SS BOND : angle 1.99246 / 1.05 ( 20) hydrogen bonds : bond 0.03732 / 2.44 ( 735) hydrogen bonds : angle 4.46897 / 3.07 ( 2076) link_BETA1-4 : bond 0.00538 / 0.38 ( 10) link_BETA1-4 : angle 2.23100 / 1.18 ( 30) link_NAG-ASN : bond 0.00200 / 0.14 ( 7) link_NAG-ASN : angle 2.11884 / 1.24 ( 21) *********************** 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 286 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: D 130 GLU cc_start: 0.7394 (mp0) cc_final: 0.7012 (mp0) REVERT: B 169 TYR cc_start: 0.8401 (m-80) cc_final: 0.8129 (m-80) REVERT: B 206 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6700 (m-10) REVERT: B 396 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.6859 (m-10) REVERT: B 412 MET cc_start: 0.8612 (mtm) cc_final: 0.8261 (mtp) REVERT: B 1207 MET cc_start: 0.9239 (tpp) cc_final: 0.8810 (tpp) REVERT: B 1429 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7628 (t0) REVERT: B 1529 MET cc_start: 0.8929 (mmp) cc_final: 0.8115 (ptm) REVERT: B 1573 MET cc_start: 0.8095 (mmm) cc_final: 0.7810 (ppp) REVERT: B 1578 HIS cc_start: 0.7280 (p-80) cc_final: 0.6865 (p-80) REVERT: B 1588 PHE cc_start: 0.8637 (t80) cc_final: 0.8216 (t80) REVERT: C 104 ASN cc_start: 0.7774 (t0) cc_final: 0.7540 (t0) outliers start: 39 outliers final: 26 residues processed: 269 average time/residue: 0.0834 time to fit residues: 34.5787 Evaluate side-chains 261 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 780 GLN 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 1198 ASN 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 1656 LEU Chi-restraints excluded: chain B residue 1708 ASP Chi-restraints excluded: chain B residue 1722 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 57 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1653 ASN ** 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 = 0.4270 r_free = 0.4270 target = 0.180831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125747 restraints weight = 17477.145| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.78 r_work: 0.3422 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2490 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= 0.138 Angle : 0.658 14.165 16733 Z= 0.326 Chirality : 0.042 0.336 1954 Planarity : 0.004 0.052 2031 Dihedral : 4.492 27.247 1634 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.07 % Allowed : 20.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1457 helix: 1.30 (0.18), residues: 846 sheet: -0.25 (0.51), residues: 102 loop : -1.49 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1299 TYR 0.024 0.001 TYR B1488 PHE 0.037 0.001 PHE B1447 TRP 0.027 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12278) covalent geometry : angle 0.64595 / 0.32 (16662) SS BOND : bond 0.00252 / 0.18 ( 10) SS BOND : angle 1.63361 / 0.93 ( 20) hydrogen bonds : bond 0.03728 / 2.45 ( 735) hydrogen bonds : angle 4.43846 / 3.05 ( 2076) link_BETA1-4 : bond 0.00546 / 0.40 ( 10) link_BETA1-4 : angle 2.19599 / 1.16 ( 30) link_NAG-ASN : bond 0.00132 / 0.08 ( 7) link_NAG-ASN : angle 2.06910 / 1.21 ( 21) *********************** 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 278 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: D 130 GLU cc_start: 0.7449 (mp0) cc_final: 0.7146 (mp0) REVERT: B 206 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6698 (m-10) REVERT: B 396 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.6901 (m-10) REVERT: B 412 MET cc_start: 0.8634 (mtm) cc_final: 0.8281 (mtp) REVERT: B 1207 MET cc_start: 0.9260 (tpp) cc_final: 0.8812 (tpp) REVERT: B 1429 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7669 (t0) REVERT: B 1430 GLU cc_start: 0.8463 (mp0) cc_final: 0.8201 (mp0) REVERT: B 1529 MET cc_start: 0.8880 (mmp) cc_final: 0.7971 (ptm) REVERT: B 1530 MET cc_start: 0.7307 (mmt) cc_final: 0.6724 (mmm) REVERT: B 1555 TYR cc_start: 0.7826 (t80) cc_final: 0.7474 (t80) REVERT: B 1578 HIS cc_start: 0.7297 (p-80) cc_final: 0.6862 (p-80) REVERT: B 1588 PHE cc_start: 0.8642 (t80) cc_final: 0.8257 (t80) REVERT: C 104 ASN cc_start: 0.7797 (t0) cc_final: 0.7564 (t0) outliers start: 39 outliers final: 30 residues processed: 262 average time/residue: 0.0900 time to fit residues: 36.1104 Evaluate side-chains 269 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 780 GLN 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 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1198 ASN 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 1656 LEU Chi-restraints excluded: chain B residue 1708 ASP Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 15 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1653 ASN ** 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 = 0.4278 r_free = 0.4278 target = 0.182107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125469 restraints weight = 17533.542| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.45 r_work: 0.3430 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12305 Z= 0.143 Angle : 0.655 11.876 16733 Z= 0.326 Chirality : 0.042 0.336 1954 Planarity : 0.004 0.052 2031 Dihedral : 4.444 25.947 1634 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.07 % Allowed : 20.72 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1457 helix: 1.34 (0.18), residues: 841 sheet: -0.15 (0.52), residues: 102 loop : -1.50 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1299 TYR 0.025 0.001 TYR B1488 PHE 0.029 0.001 PHE B1447 TRP 0.027 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (12278) covalent geometry : angle 0.64412 / 0.32 (16662) SS BOND : bond 0.00288 / 0.20 ( 10) SS BOND : angle 1.42930 / 0.85 ( 20) hydrogen bonds : bond 0.03721 / 2.45 ( 735) hydrogen bonds : angle 4.43674 / 3.06 ( 2076) link_BETA1-4 : bond 0.00548 / 0.39 ( 10) link_BETA1-4 : angle 2.18673 / 1.15 ( 30) link_NAG-ASN : bond 0.00122 / 0.07 ( 7) link_NAG-ASN : angle 2.06633 / 1.21 ( 21) *********************** 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 281 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: D 128 PHE cc_start: 0.8655 (m-80) cc_final: 0.8445 (m-10) REVERT: D 130 GLU cc_start: 0.7465 (mp0) cc_final: 0.7167 (mp0) REVERT: B 169 TYR cc_start: 0.8447 (m-80) cc_final: 0.8196 (m-80) REVERT: B 206 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6701 (m-10) REVERT: B 396 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: B 412 MET cc_start: 0.8607 (mtm) cc_final: 0.8254 (mtp) REVERT: B 1207 MET cc_start: 0.9246 (tpp) cc_final: 0.8805 (tpp) REVERT: B 1429 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7697 (t0) REVERT: B 1430 GLU cc_start: 0.8430 (mp0) cc_final: 0.8188 (mp0) REVERT: B 1529 MET cc_start: 0.8882 (mmp) cc_final: 0.7959 (ptm) REVERT: B 1530 MET cc_start: 0.7286 (mmt) cc_final: 0.6729 (mmm) REVERT: B 1555 TYR cc_start: 0.7841 (t80) cc_final: 0.7475 (t80) REVERT: B 1573 MET cc_start: 0.8130 (mmm) cc_final: 0.7825 (ppp) REVERT: B 1578 HIS cc_start: 0.7235 (p-80) cc_final: 0.6813 (p-80) REVERT: B 1588 PHE cc_start: 0.8622 (t80) cc_final: 0.8247 (t80) REVERT: C 104 ASN cc_start: 0.7818 (t0) cc_final: 0.7577 (t0) outliers start: 39 outliers final: 34 residues processed: 267 average time/residue: 0.0849 time to fit residues: 34.9456 Evaluate side-chains 274 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 142 ILE 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 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 780 GLN 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 878 LEU 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 1198 ASN 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 1656 LEU Chi-restraints excluded: chain B residue 1708 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 95 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 27 optimal weight: 0.0170 chunk 144 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN B 728 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.181349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125296 restraints weight = 17384.915| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.42 r_work: 0.3446 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2652 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= 0.134 Angle : 0.656 12.034 16733 Z= 0.326 Chirality : 0.042 0.318 1954 Planarity : 0.004 0.052 2031 Dihedral : 4.399 26.672 1634 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.07 % Allowed : 20.72 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1457 helix: 1.35 (0.18), residues: 844 sheet: -0.19 (0.52), residues: 103 loop : -1.48 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1299 TYR 0.026 0.001 TYR B1488 PHE 0.021 0.001 PHE B1616 TRP 0.028 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12278) covalent geometry : angle 0.64509 / 0.32 (16662) SS BOND : bond 0.00225 / 0.17 ( 10) SS BOND : angle 1.30754 / 0.80 ( 20) hydrogen bonds : bond 0.03676 / 2.41 ( 735) hydrogen bonds : angle 4.40929 / 3.04 ( 2076) link_BETA1-4 : bond 0.00540 / 0.38 ( 10) link_BETA1-4 : angle 2.15470 / 1.14 ( 30) link_NAG-ASN : bond 0.00135 / 0.09 ( 7) link_NAG-ASN : angle 2.02093 / 1.18 ( 21) ********************** 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 290 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.453 Fit side-chains REVERT: D 130 GLU cc_start: 0.7453 (mp0) cc_final: 0.7142 (mp0) REVERT: B 169 TYR cc_start: 0.8414 (m-80) cc_final: 0.8172 (m-80) REVERT: B 206 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6653 (m-10) REVERT: B 396 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: B 412 MET cc_start: 0.8591 (mtm) cc_final: 0.8246 (mtp) REVERT: B 724 TYR cc_start: 0.6726 (m-80) cc_final: 0.6495 (m-80) REVERT: B 1207 MET cc_start: 0.9232 (tpp) cc_final: 0.8792 (tpp) REVERT: B 1429 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7710 (t0) REVERT: B 1430 GLU cc_start: 0.8393 (mp0) cc_final: 0.8174 (mp0) REVERT: B 1529 MET cc_start: 0.8856 (mmp) cc_final: 0.7962 (ptm) REVERT: B 1530 MET cc_start: 0.7196 (mmt) cc_final: 0.6746 (mmm) REVERT: B 1573 MET cc_start: 0.8146 (mmm) cc_final: 0.7839 (ppp) REVERT: B 1578 HIS cc_start: 0.7184 (p-80) cc_final: 0.6758 (p-80) REVERT: B 1588 PHE cc_start: 0.8602 (t80) cc_final: 0.8238 (t80) REVERT: C 104 ASN cc_start: 0.7785 (t0) cc_final: 0.7567 (t0) outliers start: 39 outliers final: 33 residues processed: 276 average time/residue: 0.0845 time to fit residues: 35.4483 Evaluate side-chains 278 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 142 ILE 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 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 780 GLN 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 878 LEU 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 1198 ASN 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 1656 LEU Chi-restraints excluded: chain B residue 1708 ASP Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 20 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 HIS B 271 GLN B 287 ASN B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.181192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124138 restraints weight = 17687.643| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.50 r_work: 0.3406 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12305 Z= 0.172 Angle : 0.677 13.943 16733 Z= 0.338 Chirality : 0.043 0.297 1954 Planarity : 0.004 0.051 2031 Dihedral : 4.453 25.323 1634 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.07 % Allowed : 21.20 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1457 helix: 1.33 (0.18), residues: 841 sheet: -0.11 (0.52), residues: 102 loop : -1.57 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1299 TYR 0.024 0.002 TYR B1488 PHE 0.022 0.001 PHE B1447 TRP 0.028 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (12278) covalent geometry : angle 0.66585 / 0.34 (16662) SS BOND : bond 0.00343 / 0.25 ( 10) SS BOND : angle 1.42411 / 0.89 ( 20) hydrogen bonds : bond 0.03816 / 2.51 ( 735) hydrogen bonds : angle 4.48862 / 3.09 ( 2076) link_BETA1-4 : bond 0.00576 / 0.42 ( 10) link_BETA1-4 : angle 2.19033 / 1.15 ( 30) link_NAG-ASN : bond 0.00163 / 0.10 ( 7) link_NAG-ASN : angle 2.10918 / 1.31 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3930.61 seconds wall clock time: 67 minutes 50.17 seconds (4070.17 seconds total)