Starting phenix.real_space_refine on Wed Mar 4 00:58:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xsu_33435/03_2026/7xsu_33435.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsu_33435/03_2026/7xsu_33435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xsu_33435/03_2026/7xsu_33435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsu_33435/03_2026/7xsu_33435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xsu_33435/03_2026/7xsu_33435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsu_33435/03_2026/7xsu_33435.map" } resolution = 3.4 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= 0.005 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 68 5.16 5 C 5929 2.51 5 N 1394 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8969 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8247 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 1058} Chain breaks: 6 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 628 Unresolved non-hydrogen dihedrals: 439 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 16, 'PHE:plan': 7, 'TRP:plan': 3, 'GLU:plan': 14, 'HIS:plan': 1, 'TYR:plan': 8, 'ASP:plan': 7, 'ASN:plan1': 7, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 324 Chain: "B" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 463 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 62} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'6OU': 6, '9Z9': 1, 'BMA': 1, 'NAG': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'6OU:plan-1': 6, '6OU:plan-3': 1, '6OU:plan-2': 2} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 8969 At special positions: 0 Unit cell: (135.168, 127.776, 104.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 2 15.00 O 1576 8.00 N 1394 7.00 C 5929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 336 " distance=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.04 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.01 Simple disulfide: pdb=" SG CYS A1730 " - pdb=" SG CYS A1744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 12 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 49 " distance=2.04 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 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 469.3 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 3 sheets defined 76.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.085A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.557A pdb=" N TYR A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 181 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 192 through 210 removed outlier: 3.535A pdb=" N TRP A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.538A pdb=" N ARG A 223 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 224 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.211A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 Processing helix chain 'A' and resid 251 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.610A pdb=" N ASP A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 315 Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 374 through 387 removed outlier: 4.114A pdb=" N LEU A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 423 removed outlier: 3.760A pdb=" N PHE A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 717 removed outlier: 3.580A pdb=" N LYS A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 737 Processing helix chain 'A' and resid 743 through 772 Processing helix chain 'A' and resid 776 through 779 Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 807 through 821 removed outlier: 3.935A pdb=" N PHE A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 812 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 814 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 819 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 821 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 838 removed outlier: 3.659A pdb=" N VAL A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 869 removed outlier: 4.941A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 3.722A pdb=" N ILE A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 900 Processing helix chain 'A' and resid 901 through 914 removed outlier: 4.492A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 945 removed outlier: 3.666A pdb=" N CYS A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 920 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1206 Processing helix chain 'A' and resid 1206 through 1226 removed outlier: 3.756A pdb=" N LEU A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1225 " --> pdb=" O SER A1221 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A1226 " --> pdb=" O GLY A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1271 removed outlier: 3.554A pdb=" N LEU A1240 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE A1265 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N LYS A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A1270 " --> pdb=" O LYS A1266 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1294 Processing helix chain 'A' and resid 1300 through 1307 Processing helix chain 'A' and resid 1310 through 1319 removed outlier: 4.103A pdb=" N ARG A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA A1315 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1332 Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 3.597A pdb=" N ASN A1338 " --> pdb=" O PRO A1334 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A1339 " --> pdb=" O SER A1335 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A1350 " --> pdb=" O PHE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 Processing helix chain 'A' and resid 1406 through 1420 Processing helix chain 'A' and resid 1422 through 1432 removed outlier: 3.653A pdb=" N ILE A1426 " --> pdb=" O GLY A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1447 No H-bonds generated for 'chain 'A' and resid 1445 through 1447' Processing helix chain 'A' and resid 1448 through 1460 removed outlier: 3.625A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1482 Processing helix chain 'A' and resid 1518 through 1528 removed outlier: 4.531A pdb=" N THR A1528 " --> pdb=" O PHE A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1549 removed outlier: 4.218A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A1536 " --> pdb=" O PHE A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1582 removed outlier: 3.883A pdb=" N ASN A1560 " --> pdb=" O PRO A1556 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A1582 " --> pdb=" O ILE A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1591 removed outlier: 3.890A pdb=" N ASN A1591 " --> pdb=" O TYR A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1610 removed outlier: 3.613A pdb=" N ILE A1595 " --> pdb=" O ASN A1591 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1599 " --> pdb=" O ILE A1595 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A1609 " --> pdb=" O ILE A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1618 removed outlier: 3.766A pdb=" N GLN A1615 " --> pdb=" O SER A1611 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1621 through 1625 Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.970A pdb=" N ALA A1630 " --> pdb=" O VAL A1626 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A1631 " --> pdb=" O ILE A1627 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1626 through 1631' Processing helix chain 'A' and resid 1632 through 1639 removed outlier: 3.787A pdb=" N LEU A1636 " --> pdb=" O ILE A1632 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A1637 " --> pdb=" O GLY A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1655 Processing helix chain 'A' and resid 1655 through 1682 removed outlier: 3.685A pdb=" N PHE A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1711 removed outlier: 3.722A pdb=" N LEU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 Proline residue: A1721 - end of helix Processing helix chain 'A' and resid 1746 through 1777 Processing helix chain 'B' and resid 23 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 40 602 hydrogen bonds defined for protein. 1749 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: 1.42 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1375 1.30 - 1.43: 2468 1.43 - 1.56: 5200 1.56 - 1.69: 18 1.69 - 1.82: 106 Bond restraints: 9167 Sorted by residual: bond pdb=" C13 9Z9 A3013 " pdb=" C14 9Z9 A3013 " ideal model delta sigma weight residual 1.332 1.670 -0.338 2.00e-02 2.50e+03 2.85e+02 bond pdb=" C07 6OU A3012 " pdb=" C08 6OU A3012 " ideal model delta sigma weight residual 1.524 1.311 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C07 6OU A3011 " pdb=" C08 6OU A3011 " ideal model delta sigma weight residual 1.524 1.312 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C73 9Z9 A3013 " pdb=" O72 9Z9 A3013 " ideal model delta sigma weight residual 1.406 1.568 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C04 9Z9 A3013 " pdb=" O72 9Z9 A3013 " ideal model delta sigma weight residual 1.420 1.261 0.159 2.00e-02 2.50e+03 6.35e+01 ... (remaining 9162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 12389 7.28 - 14.56: 59 14.56 - 21.84: 5 21.84 - 29.12: 0 29.12 - 36.40: 3 Bond angle restraints: 12456 Sorted by residual: angle pdb=" N PRO A 349 " pdb=" CA PRO A 349 " pdb=" C PRO A 349 " ideal model delta sigma weight residual 112.47 148.87 -36.40 2.06e+00 2.36e-01 3.12e+02 angle pdb=" N THR A1378 " pdb=" CA THR A1378 " pdb=" C THR A1378 " ideal model delta sigma weight residual 112.93 132.06 -19.13 1.33e+00 5.65e-01 2.07e+02 angle pdb=" N ILE A1379 " pdb=" CA ILE A1379 " pdb=" C ILE A1379 " ideal model delta sigma weight residual 111.90 100.95 10.95 8.10e-01 1.52e+00 1.83e+02 angle pdb=" N ASP A 350 " pdb=" CA ASP A 350 " pdb=" C ASP A 350 " ideal model delta sigma weight residual 112.12 95.77 16.35 1.34e+00 5.57e-01 1.49e+02 angle pdb=" C LEU A1373 " pdb=" N PRO A1374 " pdb=" CA PRO A1374 " ideal model delta sigma weight residual 120.52 132.29 -11.77 9.90e-01 1.02e+00 1.41e+02 ... (remaining 12451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 5264 35.03 - 70.05: 185 70.05 - 105.08: 23 105.08 - 140.11: 18 140.11 - 175.13: 1 Dihedral angle restraints: 5491 sinusoidal: 2158 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 918 " pdb=" CB CYS A 918 " ideal model delta sinusoidal sigma weight residual -86.00 -170.42 84.42 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A1730 " pdb=" SG CYS A1730 " pdb=" SG CYS A1744 " pdb=" CB CYS A1744 " ideal model delta sinusoidal sigma weight residual -86.00 -148.90 62.90 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" C PHE A 285 " pdb=" N PHE A 285 " pdb=" CA PHE A 285 " pdb=" CB PHE A 285 " ideal model delta harmonic sigma weight residual -122.60 -105.71 -16.89 0 2.50e+00 1.60e-01 4.56e+01 ... (remaining 5488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 1440 0.237 - 0.474: 46 0.474 - 0.710: 3 0.710 - 0.947: 1 0.947 - 1.184: 1 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CA PRO A 349 " pdb=" N PRO A 349 " pdb=" C PRO A 349 " pdb=" CB PRO A 349 " both_signs ideal model delta sigma weight residual False 2.72 1.53 1.18 2.00e-01 2.50e+01 3.50e+01 chirality pdb=" C02 9Z9 A3013 " pdb=" C03 9Z9 A3013 " pdb=" C06 9Z9 A3013 " pdb=" C10 9Z9 A3013 " both_signs ideal model delta sigma weight residual False 2.92 2.18 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA CYS A1365 " pdb=" N CYS A1365 " pdb=" C CYS A1365 " pdb=" CB CYS A1365 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 1488 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3003 " 0.324 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG A3003 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A3003 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG A3003 " -0.505 2.00e-02 2.50e+03 pdb=" O7 NAG A3003 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3004 " -0.237 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C7 NAG A3004 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A3004 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG A3004 " 0.327 2.00e-02 2.50e+03 pdb=" O7 NAG A3004 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3001 " 0.239 2.00e-02 2.50e+03 1.97e-01 4.84e+02 pdb=" C7 NAG A3001 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A3001 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A3001 " -0.322 2.00e-02 2.50e+03 pdb=" O7 NAG A3001 " -0.020 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 4 2.13 - 2.82: 3010 2.82 - 3.52: 13237 3.52 - 4.21: 18933 4.21 - 4.90: 34962 Nonbonded interactions: 70146 Sorted by model distance: nonbonded pdb=" OD1 ASN A1445 " pdb=" CE MET A1448 " model vdw 1.440 3.460 nonbonded pdb=" CG ASN A1445 " pdb=" CE MET A1448 " model vdw 1.598 3.690 nonbonded pdb=" ND2 ASN A1445 " pdb=" CE MET A1448 " model vdw 1.748 3.540 nonbonded pdb=" O3 NAG A3001 " pdb=" O6 NAG A3001 " model vdw 1.809 3.040 nonbonded pdb=" N PHE A 285 " pdb=" O PHE A 285 " model vdw 2.255 2.496 ... (remaining 70141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.011 0.338 9174 Z= 0.675 Angle : 1.611 36.397 12470 Z= 1.013 Chirality : 0.106 1.184 1491 Planarity : 0.013 0.282 1510 Dihedral : 19.266 175.133 3314 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.46 % Favored : 94.10 % Rotamer: Outliers : 5.06 % Allowed : 18.09 % Favored : 76.85 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.25), residues: 1136 helix: 2.38 (0.18), residues: 731 sheet: -0.35 (2.23), residues: 12 loop : -1.44 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 881 TYR 0.025 0.002 TYR A 379 PHE 0.020 0.002 PHE A 887 TRP 0.024 0.002 TRP A1715 HIS 0.008 0.002 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.01109 ( 9167) covalent geometry : angle 1.61071 (12456) SS BOND : bond 0.00843 ( 7) SS BOND : angle 1.85747 ( 14) hydrogen bonds : bond 0.24239 ( 602) hydrogen bonds : angle 7.18576 ( 1749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.5939 (tpp) cc_final: 0.5328 (tmm) REVERT: A 137 LEU cc_start: 0.8841 (tt) cc_final: 0.8600 (tp) REVERT: A 249 LYS cc_start: 0.6300 (mptt) cc_final: 0.6004 (tttp) REVERT: A 260 PHE cc_start: 0.8580 (t80) cc_final: 0.8277 (t80) REVERT: A 351 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6090 (t-90) REVERT: A 379 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8035 (t80) REVERT: A 778 PHE cc_start: 0.5588 (t80) cc_final: 0.4781 (t80) REVERT: A 835 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8472 (t0) REVERT: A 1197 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7480 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7356 (mtp-110) REVERT: A 1209 PHE cc_start: 0.8539 (t80) cc_final: 0.8145 (t80) REVERT: A 1233 GLU cc_start: 0.6449 (tt0) cc_final: 0.6204 (tt0) REVERT: A 1302 LYS cc_start: 0.7936 (pttt) cc_final: 0.7734 (mptt) REVERT: A 1424 MET cc_start: 0.7862 (mmp) cc_final: 0.7588 (mmm) REVERT: A 1538 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7324 (t80) REVERT: A 1581 MET cc_start: 0.4007 (ppp) cc_final: 0.3189 (tpp) REVERT: A 1619 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5787 (p90) REVERT: A 1664 LEU cc_start: 0.7985 (tp) cc_final: 0.7748 (mt) REVERT: A 1762 PHE cc_start: 0.8989 (t80) cc_final: 0.8611 (t80) outliers start: 45 outliers final: 19 residues processed: 276 average time/residue: 0.0830 time to fit residues: 33.2615 Evaluate side-chains 213 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1345 ILE Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1404 PHE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1619 PHE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain B residue 29 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 827 ASN A 865 ASN A 889 HIS A1271 ASN A1441 GLN B 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.199956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.154792 restraints weight = 11323.301| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.36 r_work: 0.3571 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9174 Z= 0.160 Angle : 0.698 9.465 12470 Z= 0.361 Chirality : 0.041 0.251 1491 Planarity : 0.004 0.050 1510 Dihedral : 13.206 147.940 1582 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 3.71 % Allowed : 20.11 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1136 helix: 1.92 (0.18), residues: 761 sheet: -0.53 (1.96), residues: 12 loop : -1.50 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1305 TYR 0.019 0.001 TYR A 379 PHE 0.019 0.001 PHE A1215 TRP 0.022 0.001 TRP A1715 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9167) covalent geometry : angle 0.68942 (12456) SS BOND : bond 0.00727 ( 7) SS BOND : angle 3.36906 ( 14) hydrogen bonds : bond 0.04997 ( 602) hydrogen bonds : angle 5.05833 ( 1749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8366 (t-90) cc_final: 0.7956 (t-90) REVERT: A 136 MET cc_start: 0.6048 (tpp) cc_final: 0.5376 (tmm) REVERT: A 137 LEU cc_start: 0.8718 (tt) cc_final: 0.8424 (tp) REVERT: A 229 LYS cc_start: 0.7233 (mtpt) cc_final: 0.6989 (ttpp) REVERT: A 260 PHE cc_start: 0.8769 (t80) cc_final: 0.8474 (t80) REVERT: A 341 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.5436 (mpt180) REVERT: A 415 MET cc_start: 0.7740 (mmm) cc_final: 0.7193 (mmm) REVERT: A 938 LEU cc_start: 0.8532 (tp) cc_final: 0.8213 (mm) REVERT: A 1197 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7316 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7533 (ttm170) cc_final: 0.7149 (mtp-110) REVERT: A 1206 HIS cc_start: 0.5857 (t-90) cc_final: 0.5639 (t-170) REVERT: A 1209 PHE cc_start: 0.8421 (t80) cc_final: 0.8062 (t80) REVERT: A 1216 MET cc_start: 0.9069 (mmm) cc_final: 0.8840 (tpt) REVERT: A 1298 MET cc_start: 0.3448 (ptm) cc_final: 0.3242 (ptm) REVERT: A 1302 LYS cc_start: 0.7416 (pttt) cc_final: 0.7037 (tttm) REVERT: A 1364 ARG cc_start: 0.6628 (ptt180) cc_final: 0.6332 (ptm160) REVERT: A 1406 ASN cc_start: 0.7817 (m110) cc_final: 0.7607 (m-40) REVERT: A 1448 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7537 (mpp) REVERT: A 1538 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 1547 MET cc_start: 0.6780 (mtm) cc_final: 0.6529 (mtm) REVERT: A 1664 LEU cc_start: 0.7995 (tp) cc_final: 0.7784 (tp) outliers start: 33 outliers final: 12 residues processed: 249 average time/residue: 0.0814 time to fit residues: 29.1873 Evaluate side-chains 208 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1448 MET Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain B residue 3 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 0.0170 chunk 96 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 47 optimal weight: 0.6980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.205381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159301 restraints weight = 10906.148| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.91 r_work: 0.3704 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 9174 Z= 0.152 Angle : 0.616 10.033 12470 Z= 0.323 Chirality : 0.038 0.166 1491 Planarity : 0.004 0.045 1510 Dihedral : 10.017 139.514 1550 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 4.72 % Allowed : 22.02 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1136 helix: 1.66 (0.18), residues: 776 sheet: -0.96 (1.80), residues: 12 loop : -1.46 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.019 0.001 TYR A 379 PHE 0.019 0.001 PHE A 778 TRP 0.021 0.001 TRP A1715 HIS 0.002 0.000 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9167) covalent geometry : angle 0.60610 (12456) SS BOND : bond 0.00783 ( 7) SS BOND : angle 3.34025 ( 14) hydrogen bonds : bond 0.04282 ( 602) hydrogen bonds : angle 4.77186 ( 1749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8467 (t-90) cc_final: 0.8203 (t-90) REVERT: A 136 MET cc_start: 0.6565 (tpp) cc_final: 0.5756 (tmm) REVERT: A 137 LEU cc_start: 0.8641 (tt) cc_final: 0.8333 (tp) REVERT: A 238 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7342 (pttm) REVERT: A 260 PHE cc_start: 0.8827 (t80) cc_final: 0.8518 (t80) REVERT: A 341 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.4646 (mpt180) REVERT: A 1195 ARG cc_start: 0.8769 (ptp90) cc_final: 0.8545 (ptp-170) REVERT: A 1197 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7194 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7416 (ttm170) cc_final: 0.7145 (mtp-110) REVERT: A 1206 HIS cc_start: 0.6026 (t-90) cc_final: 0.5536 (t70) REVERT: A 1209 PHE cc_start: 0.8570 (t80) cc_final: 0.8173 (t80) REVERT: A 1263 TYR cc_start: 0.7894 (m-80) cc_final: 0.7629 (m-80) REVERT: A 1302 LYS cc_start: 0.7577 (pttt) cc_final: 0.7236 (tttp) REVERT: A 1562 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8391 (mm) REVERT: A 1568 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8456 (pp) REVERT: A 1653 MET cc_start: 0.7420 (mmt) cc_final: 0.6791 (mmm) REVERT: B 3 ASP cc_start: 0.4581 (OUTLIER) cc_final: 0.4259 (t70) outliers start: 42 outliers final: 19 residues processed: 237 average time/residue: 0.0818 time to fit residues: 28.3958 Evaluate side-chains 209 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.205748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.161150 restraints weight = 11002.653| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.00 r_work: 0.3700 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9174 Z= 0.139 Angle : 0.573 7.955 12470 Z= 0.302 Chirality : 0.037 0.166 1491 Planarity : 0.003 0.042 1510 Dihedral : 9.360 134.307 1548 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 5.06 % Allowed : 23.15 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.91 (0.25), residues: 1136 helix: 1.55 (0.18), residues: 786 sheet: -1.52 (1.71), residues: 12 loop : -1.61 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.019 0.001 TYR A 379 PHE 0.028 0.001 PHE A 778 TRP 0.023 0.001 TRP A1715 HIS 0.005 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9167) covalent geometry : angle 0.56868 (12456) SS BOND : bond 0.00292 ( 7) SS BOND : angle 2.28522 ( 14) hydrogen bonds : bond 0.03977 ( 602) hydrogen bonds : angle 4.58280 ( 1749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6583 (tpp) cc_final: 0.5772 (tmm) REVERT: A 137 LEU cc_start: 0.8626 (tt) cc_final: 0.8342 (tp) REVERT: A 260 PHE cc_start: 0.8795 (t80) cc_final: 0.8498 (t80) REVERT: A 904 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: A 1209 PHE cc_start: 0.8575 (t80) cc_final: 0.8224 (t80) REVERT: A 1263 TYR cc_start: 0.7844 (m-80) cc_final: 0.7635 (m-10) REVERT: A 1302 LYS cc_start: 0.7508 (pttt) cc_final: 0.7145 (tttp) REVERT: A 1477 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8493 (mm-40) REVERT: A 1562 LEU cc_start: 0.8607 (mm) cc_final: 0.8320 (mm) REVERT: A 1664 LEU cc_start: 0.8055 (tp) cc_final: 0.7747 (tp) REVERT: A 1680 ASN cc_start: 0.7735 (m-40) cc_final: 0.7449 (m110) REVERT: A 1693 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8138 (ttp) REVERT: B 3 ASP cc_start: 0.5055 (OUTLIER) cc_final: 0.4778 (t70) outliers start: 45 outliers final: 33 residues processed: 228 average time/residue: 0.0792 time to fit residues: 27.1859 Evaluate side-chains 222 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.201306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156302 restraints weight = 11214.851| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.59 r_work: 0.3556 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9174 Z= 0.126 Angle : 0.556 8.713 12470 Z= 0.290 Chirality : 0.036 0.180 1491 Planarity : 0.003 0.041 1510 Dihedral : 8.922 128.505 1548 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 6.18 % Allowed : 22.25 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.93 (0.25), residues: 1136 helix: 1.56 (0.18), residues: 787 sheet: -1.50 (1.65), residues: 12 loop : -1.59 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 341 TYR 0.018 0.001 TYR A 163 PHE 0.028 0.001 PHE A 778 TRP 0.024 0.001 TRP A1715 HIS 0.003 0.000 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9167) covalent geometry : angle 0.55108 (12456) SS BOND : bond 0.00256 ( 7) SS BOND : angle 2.19907 ( 14) hydrogen bonds : bond 0.03791 ( 602) hydrogen bonds : angle 4.47622 ( 1749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6467 (tpp) cc_final: 0.5694 (tmm) REVERT: A 137 LEU cc_start: 0.8727 (tt) cc_final: 0.8428 (tp) REVERT: A 260 PHE cc_start: 0.8783 (t80) cc_final: 0.8520 (t80) REVERT: A 379 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8097 (t80) REVERT: A 415 MET cc_start: 0.7749 (mmm) cc_final: 0.7298 (mmm) REVERT: A 904 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: A 1197 ARG cc_start: 0.7518 (ptt90) cc_final: 0.7257 (ptt-90) REVERT: A 1209 PHE cc_start: 0.8458 (t80) cc_final: 0.8066 (t80) REVERT: A 1302 LYS cc_start: 0.7440 (pttt) cc_final: 0.7115 (tttp) REVERT: A 1477 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8545 (mm-40) REVERT: A 1562 LEU cc_start: 0.8604 (mm) cc_final: 0.8371 (mm) REVERT: A 1693 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8100 (ttp) REVERT: B 3 ASP cc_start: 0.5088 (OUTLIER) cc_final: 0.4880 (t70) outliers start: 55 outliers final: 31 residues processed: 235 average time/residue: 0.0743 time to fit residues: 26.5165 Evaluate side-chains 222 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1547 MET Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.0470 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 0.0020 chunk 90 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 103 optimal weight: 0.0060 overall best weight: 0.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1680 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.205118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.146706 restraints weight = 11202.146| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.44 r_work: 0.3641 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9174 Z= 0.107 Angle : 0.537 7.999 12470 Z= 0.278 Chirality : 0.035 0.184 1491 Planarity : 0.003 0.036 1510 Dihedral : 8.251 118.459 1546 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.21 % Rotamer: Outliers : 4.49 % Allowed : 24.38 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1136 helix: 1.66 (0.18), residues: 788 sheet: -1.41 (1.60), residues: 12 loop : -1.53 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.016 0.001 TYR A1201 PHE 0.028 0.001 PHE A 778 TRP 0.019 0.001 TRP A1715 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9167) covalent geometry : angle 0.53363 (12456) SS BOND : bond 0.00257 ( 7) SS BOND : angle 1.92069 ( 14) hydrogen bonds : bond 0.03574 ( 602) hydrogen bonds : angle 4.32258 ( 1749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6603 (tpp) cc_final: 0.5796 (tmm) REVERT: A 137 LEU cc_start: 0.8695 (tt) cc_final: 0.8400 (tp) REVERT: A 196 TRP cc_start: 0.7585 (m-10) cc_final: 0.7384 (m-10) REVERT: A 229 LYS cc_start: 0.6937 (ttpp) cc_final: 0.6687 (ttpp) REVERT: A 415 MET cc_start: 0.7737 (mmm) cc_final: 0.7334 (mmm) REVERT: A 904 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 1197 ARG cc_start: 0.7538 (ptt90) cc_final: 0.7303 (ptt-90) REVERT: A 1209 PHE cc_start: 0.8418 (t80) cc_final: 0.8049 (t80) REVERT: A 1263 TYR cc_start: 0.8065 (m-80) cc_final: 0.7708 (m-80) REVERT: A 1277 ASP cc_start: 0.8362 (m-30) cc_final: 0.8103 (m-30) REVERT: A 1302 LYS cc_start: 0.7444 (pttt) cc_final: 0.7139 (tttp) REVERT: A 1448 MET cc_start: 0.8468 (mmt) cc_final: 0.8008 (mmm) REVERT: A 1477 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8606 (mm-40) REVERT: A 1653 MET cc_start: 0.5855 (mmt) cc_final: 0.5650 (mmm) REVERT: A 1664 LEU cc_start: 0.8000 (tp) cc_final: 0.7711 (tp) REVERT: A 1693 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7928 (ttp) outliers start: 40 outliers final: 25 residues processed: 237 average time/residue: 0.0724 time to fit residues: 26.1354 Evaluate side-chains 224 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1547 MET Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.202031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143219 restraints weight = 11177.565| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.47 r_work: 0.3584 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9174 Z= 0.134 Angle : 0.586 8.133 12470 Z= 0.303 Chirality : 0.036 0.180 1491 Planarity : 0.003 0.037 1510 Dihedral : 8.202 114.710 1546 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 4.38 % Allowed : 25.06 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.97 (0.26), residues: 1136 helix: 1.61 (0.19), residues: 786 sheet: -1.56 (1.50), residues: 12 loop : -1.61 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.021 0.001 TYR A 379 PHE 0.029 0.001 PHE A 778 TRP 0.023 0.001 TRP A 375 HIS 0.002 0.000 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9167) covalent geometry : angle 0.57872 (12456) SS BOND : bond 0.00485 ( 7) SS BOND : angle 2.87501 ( 14) hydrogen bonds : bond 0.03779 ( 602) hydrogen bonds : angle 4.45944 ( 1749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6729 (tpp) cc_final: 0.5891 (tmm) REVERT: A 137 LEU cc_start: 0.8700 (tt) cc_final: 0.8406 (tp) REVERT: A 149 MET cc_start: 0.7811 (ptm) cc_final: 0.7433 (ptt) REVERT: A 379 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8149 (t80) REVERT: A 415 MET cc_start: 0.7709 (mmm) cc_final: 0.7341 (mmm) REVERT: A 901 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: A 904 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: A 1194 TRP cc_start: 0.6793 (m-10) cc_final: 0.6546 (m-90) REVERT: A 1197 ARG cc_start: 0.7557 (ptt90) cc_final: 0.7351 (ptt-90) REVERT: A 1209 PHE cc_start: 0.8411 (t80) cc_final: 0.8045 (t80) REVERT: A 1227 GLU cc_start: 0.8041 (tp30) cc_final: 0.7814 (mm-30) REVERT: A 1263 TYR cc_start: 0.8008 (m-80) cc_final: 0.7685 (m-80) REVERT: A 1302 LYS cc_start: 0.7362 (pttt) cc_final: 0.7049 (tttp) REVERT: A 1448 MET cc_start: 0.8546 (mmt) cc_final: 0.8002 (mmm) REVERT: A 1477 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8588 (mm-40) REVERT: A 1653 MET cc_start: 0.6112 (mmt) cc_final: 0.5845 (mmm) REVERT: A 1693 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8142 (ttp) outliers start: 39 outliers final: 28 residues processed: 221 average time/residue: 0.0708 time to fit residues: 23.8181 Evaluate side-chains 221 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1547 MET Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 30 optimal weight: 0.0470 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.203398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.143981 restraints weight = 11143.171| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.09 r_work: 0.3635 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9174 Z= 0.121 Angle : 0.586 9.195 12470 Z= 0.301 Chirality : 0.036 0.197 1491 Planarity : 0.003 0.038 1510 Dihedral : 7.958 113.544 1546 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.13 % Rotamer: Outliers : 4.27 % Allowed : 25.96 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.83 (0.26), residues: 1136 helix: 1.53 (0.19), residues: 797 sheet: -1.61 (1.50), residues: 12 loop : -1.87 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.019 0.001 TYR A 379 PHE 0.034 0.001 PHE A 260 TRP 0.026 0.001 TRP A 375 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9167) covalent geometry : angle 0.57990 (12456) SS BOND : bond 0.00399 ( 7) SS BOND : angle 2.61415 ( 14) hydrogen bonds : bond 0.03644 ( 602) hydrogen bonds : angle 4.44397 ( 1749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 136 MET cc_start: 0.6634 (tpp) cc_final: 0.5808 (tmm) REVERT: A 137 LEU cc_start: 0.8674 (tt) cc_final: 0.8390 (tp) REVERT: A 149 MET cc_start: 0.7884 (ptm) cc_final: 0.7591 (ptt) REVERT: A 379 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8264 (t80) REVERT: A 395 MET cc_start: 0.8123 (tmm) cc_final: 0.7921 (ttp) REVERT: A 415 MET cc_start: 0.7966 (mmm) cc_final: 0.7586 (mmm) REVERT: A 901 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: A 904 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: A 926 MET cc_start: 0.8294 (ttt) cc_final: 0.8093 (mtp) REVERT: A 1197 ARG cc_start: 0.7536 (ptt90) cc_final: 0.7330 (ptt-90) REVERT: A 1209 PHE cc_start: 0.8399 (t80) cc_final: 0.8025 (t80) REVERT: A 1227 GLU cc_start: 0.8116 (tp30) cc_final: 0.7898 (mm-30) REVERT: A 1255 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: A 1263 TYR cc_start: 0.8137 (m-80) cc_final: 0.7876 (m-80) REVERT: A 1277 ASP cc_start: 0.8553 (m-30) cc_final: 0.8204 (m-30) REVERT: A 1302 LYS cc_start: 0.7329 (pttt) cc_final: 0.6995 (tttp) REVERT: A 1448 MET cc_start: 0.8494 (mmt) cc_final: 0.8024 (mmm) REVERT: A 1477 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8583 (mm-40) REVERT: A 1653 MET cc_start: 0.5716 (mmt) cc_final: 0.5424 (mmm) REVERT: A 1664 LEU cc_start: 0.7804 (tp) cc_final: 0.7586 (mt) REVERT: A 1693 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8188 (ttp) outliers start: 38 outliers final: 23 residues processed: 227 average time/residue: 0.0727 time to fit residues: 25.1075 Evaluate side-chains 217 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1547 MET Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.0010 chunk 84 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.0030 chunk 74 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.204833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146574 restraints weight = 11083.110| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.53 r_work: 0.3626 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9174 Z= 0.118 Angle : 0.597 9.951 12470 Z= 0.305 Chirality : 0.036 0.199 1491 Planarity : 0.003 0.037 1510 Dihedral : 7.723 111.925 1546 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 3.60 % Allowed : 26.85 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.88 (0.25), residues: 1136 helix: 1.54 (0.18), residues: 793 sheet: -1.78 (1.44), residues: 12 loop : -1.71 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1305 TYR 0.018 0.001 TYR A1201 PHE 0.031 0.001 PHE A 260 TRP 0.029 0.001 TRP A 375 HIS 0.010 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9167) covalent geometry : angle 0.59165 (12456) SS BOND : bond 0.00404 ( 7) SS BOND : angle 2.42922 ( 14) hydrogen bonds : bond 0.03604 ( 602) hydrogen bonds : angle 4.42480 ( 1749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 136 MET cc_start: 0.6732 (tpp) cc_final: 0.5895 (tmm) REVERT: A 137 LEU cc_start: 0.8653 (tt) cc_final: 0.8364 (tp) REVERT: A 149 MET cc_start: 0.7795 (ptm) cc_final: 0.7483 (ptt) REVERT: A 395 MET cc_start: 0.7942 (tmm) cc_final: 0.7742 (ttp) REVERT: A 415 MET cc_start: 0.7727 (mmm) cc_final: 0.7411 (mmm) REVERT: A 705 MET cc_start: 0.5925 (tpt) cc_final: 0.5550 (ptp) REVERT: A 749 MET cc_start: 0.9154 (tmm) cc_final: 0.8952 (tmm) REVERT: A 901 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: A 904 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 1194 TRP cc_start: 0.6785 (m-10) cc_final: 0.6549 (m-90) REVERT: A 1209 PHE cc_start: 0.8408 (t80) cc_final: 0.8045 (t80) REVERT: A 1242 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: A 1263 TYR cc_start: 0.7893 (m-80) cc_final: 0.7602 (m-80) REVERT: A 1277 ASP cc_start: 0.8461 (m-30) cc_final: 0.8148 (m-30) REVERT: A 1302 LYS cc_start: 0.7352 (pttt) cc_final: 0.7027 (tttp) REVERT: A 1448 MET cc_start: 0.8505 (mmt) cc_final: 0.8065 (mmm) REVERT: A 1477 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8562 (mm-40) REVERT: A 1653 MET cc_start: 0.5754 (mmt) cc_final: 0.5430 (mmm) REVERT: A 1670 MET cc_start: 0.9030 (mtp) cc_final: 0.8539 (mtp) REVERT: A 1693 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8028 (ttp) outliers start: 32 outliers final: 22 residues processed: 230 average time/residue: 0.0735 time to fit residues: 25.4932 Evaluate side-chains 223 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1547 MET Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1441 GLN ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.202364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144663 restraints weight = 11177.983| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.40 r_work: 0.3588 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9174 Z= 0.137 Angle : 0.618 9.712 12470 Z= 0.316 Chirality : 0.037 0.196 1491 Planarity : 0.004 0.038 1510 Dihedral : 7.841 111.418 1544 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.04 % Rotamer: Outliers : 3.82 % Allowed : 26.63 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.26), residues: 1136 helix: 1.46 (0.19), residues: 798 sheet: -0.86 (1.55), residues: 10 loop : -1.68 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1305 TYR 0.022 0.001 TYR A 379 PHE 0.030 0.001 PHE A 260 TRP 0.033 0.001 TRP A 375 HIS 0.022 0.002 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9167) covalent geometry : angle 0.61319 (12456) SS BOND : bond 0.00385 ( 7) SS BOND : angle 2.45306 ( 14) hydrogen bonds : bond 0.03794 ( 602) hydrogen bonds : angle 4.49443 ( 1749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 136 MET cc_start: 0.6579 (tpp) cc_final: 0.5808 (tmm) REVERT: A 137 LEU cc_start: 0.8690 (tt) cc_final: 0.8393 (tp) REVERT: A 149 MET cc_start: 0.7833 (ptm) cc_final: 0.7414 (ptt) REVERT: A 379 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8251 (t80) REVERT: A 395 MET cc_start: 0.7918 (tmm) cc_final: 0.7711 (ttp) REVERT: A 415 MET cc_start: 0.7788 (mmm) cc_final: 0.7468 (mmm) REVERT: A 901 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: A 904 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: A 1194 TRP cc_start: 0.6803 (m-10) cc_final: 0.6545 (m-90) REVERT: A 1209 PHE cc_start: 0.8415 (t80) cc_final: 0.7833 (t80) REVERT: A 1242 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: A 1277 ASP cc_start: 0.8464 (m-30) cc_final: 0.8114 (m-30) REVERT: A 1302 LYS cc_start: 0.7269 (pttt) cc_final: 0.6918 (tttp) REVERT: A 1318 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7642 (mtp85) REVERT: A 1477 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8582 (mm-40) REVERT: A 1693 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8105 (ttp) outliers start: 34 outliers final: 24 residues processed: 221 average time/residue: 0.0743 time to fit residues: 24.8316 Evaluate side-chains 217 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1547 MET Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1693 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.203213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145732 restraints weight = 11039.145| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.77 r_work: 0.3579 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9174 Z= 0.135 Angle : 0.645 9.876 12470 Z= 0.326 Chirality : 0.038 0.202 1491 Planarity : 0.004 0.038 1510 Dihedral : 7.845 110.412 1544 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 3.37 % Allowed : 28.20 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.93 (0.26), residues: 1136 helix: 1.48 (0.19), residues: 785 sheet: -1.96 (1.42), residues: 12 loop : -1.34 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1305 TYR 0.021 0.001 TYR A 379 PHE 0.030 0.001 PHE A 778 TRP 0.034 0.001 TRP A 375 HIS 0.021 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9167) covalent geometry : angle 0.63662 (12456) SS BOND : bond 0.00407 ( 7) SS BOND : angle 3.20342 ( 14) hydrogen bonds : bond 0.03808 ( 602) hydrogen bonds : angle 4.53636 ( 1749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.33 seconds wall clock time: 45 minutes 50.42 seconds (2750.42 seconds total)