Starting phenix.real_space_refine on Fri Jul 3 12:39:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ync_33958/07_2026/7ync_33958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ync_33958/07_2026/7ync_33958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ync_33958/07_2026/7ync_33958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ync_33958/07_2026/7ync_33958.map" model { file = "/net/cci-nas-00/data/ceres_data/7ync_33958/07_2026/7ync_33958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ync_33958/07_2026/7ync_33958.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ync_33958/07_2026/7ync_33958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ync_33958/07_2026/7ync_33958.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 57 5.16 5 C 8497 2.51 5 N 2467 2.21 5 O 2761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13848 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1536, 12447 Classifications: {'peptide': 1536} Link IDs: {'PTRANS': 84, 'TRANS': 1451} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 5, 'rna3p_pur': 7, 'rna3p_pyr': 12} Link IDs: {'rna2p': 19, 'rna3p': 18} Chain: "C" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 591 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 14} Link IDs: {'rna2p': 3, 'rna3p': 24} Time building chain proxies: 2.46, per 1000 atoms: 0.18 Number of scatterers: 13848 At special positions: 0 Unit cell: (94.16, 169.06, 133.75, 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 57 16.00 P 66 15.00 O 2761 8.00 N 2467 7.00 C 8497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.81 Conformation dependent library (CDL) restraints added in 525.9 milliseconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 19 sheets defined 21.4% alpha, 19.6% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 57 through 74 removed outlier: 4.187A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.537A pdb=" N ASN A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 291 through 294 removed outlier: 4.078A pdb=" N ARG A 294 " --> pdb=" O SER A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.983A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 302' Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.125A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.573A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.114A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.570A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.755A pdb=" N GLU A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 784' Processing helix chain 'A' and resid 787 through 801 removed outlier: 3.727A pdb=" N ALA A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.582A pdb=" N ILE A 812 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 813' Processing helix chain 'A' and resid 946 through 962 removed outlier: 4.205A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1105 removed outlier: 3.552A pdb=" N ASP A1104 " --> pdb=" O ASP A1101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A1105 " --> pdb=" O ASN A1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1105' Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.901A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 removed outlier: 3.526A pdb=" N GLU A1264 " --> pdb=" O ARG A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.608A pdb=" N LYS A1303 " --> pdb=" O MET A1300 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A1304 " --> pdb=" O ILE A1301 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1300 through 1305' Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 4.192A pdb=" N LEU A1347 " --> pdb=" O PRO A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.856A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1476 Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 removed outlier: 3.713A pdb=" N GLY A1524 " --> pdb=" O PRO A1520 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A1534 " --> pdb=" O LEU A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1548 Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 3.572A pdb=" N LYS A1580 " --> pdb=" O TYR A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1595 removed outlier: 3.528A pdb=" N THR A1595 " --> pdb=" O LYS A1591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.746A pdb=" N PHE A 187 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 191 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 169 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.705A pdb=" N GLU A 403 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 576 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.770A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 723 through 724 removed outlier: 6.803A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 659 through 663 Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.646A pdb=" N PHE A 757 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 743 " --> pdb=" O LYS A 755 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB1, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.463A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AB3, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.459A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB5, first strand: chain 'A' and resid 1001 through 1012 removed outlier: 41.983A pdb=" N VAL A1121 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 35.885A pdb=" N LYS A1004 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 29.703A pdb=" N ASP A1123 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 23.731A pdb=" N SER A1006 " --> pdb=" O ASP A1123 " (cutoff:3.500A) removed outlier: 17.731A pdb=" N ARG A1125 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 14.195A pdb=" N THR A1008 " --> pdb=" O ARG A1125 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN A1127 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A1010 " --> pdb=" O GLN A1127 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1129 " --> pdb=" O ARG A1010 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP A1120 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1047 " --> pdb=" O TRP A1120 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A1122 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A1041 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS A1128 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A1039 " --> pdb=" O LYS A1128 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A1130 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N MET A1037 " --> pdb=" O PHE A1130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A1037 " --> pdb=" O LYS A1144 " (cutoff:3.500A) removed outlier: 19.244A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.148A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A1275 " --> pdb=" O GLY A 993 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A1283 " --> pdb=" O ASN A1280 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL A1284 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU A1229 " --> pdb=" O VAL A1284 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASP A1286 " --> pdb=" O GLU A1229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1086 removed outlier: 3.623A pdb=" N PHE A1083 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1096 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A1085 " --> pdb=" O PHE A1094 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A1094 " --> pdb=" O VAL A1085 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1187 through 1188 Processing sheet with id=AB9, first strand: chain 'A' and resid 1200 through 1202 removed outlier: 3.519A pdb=" N TYR A1209 " --> pdb=" O CYS A1201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1385 through 1387 302 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4227 1.34 - 1.45: 2635 1.45 - 1.57: 7235 1.57 - 1.69: 130 1.69 - 1.81: 82 Bond restraints: 14309 Sorted by residual: bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.79e+00 bond pdb=" N CYS A 86 " pdb=" CA CYS A 86 " ideal model delta sigma weight residual 1.452 1.491 -0.038 1.41e-02 5.03e+03 7.42e+00 bond pdb=" N CYS A1342 " pdb=" CA CYS A1342 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.98e+00 bond pdb=" N CYS A 711 " pdb=" CA CYS A 711 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.31e-02 5.83e+03 6.08e+00 bond pdb=" N CYS A 708 " pdb=" CA CYS A 708 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.37e-02 5.33e+03 5.87e+00 ... (remaining 14304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 18830 1.48 - 2.95: 637 2.95 - 4.43: 98 4.43 - 5.90: 22 5.90 - 7.38: 9 Bond angle restraints: 19596 Sorted by residual: angle pdb=" N ARG A1346 " pdb=" CA ARG A1346 " pdb=" C ARG A1346 " ideal model delta sigma weight residual 114.04 108.63 5.41 1.24e+00 6.50e-01 1.91e+01 angle pdb=" N TYR A 866 " pdb=" CA TYR A 866 " pdb=" C TYR A 866 " ideal model delta sigma weight residual 111.02 115.93 -4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" N CYS A 123 " pdb=" CA CYS A 123 " pdb=" C CYS A 123 " ideal model delta sigma weight residual 110.39 105.74 4.65 1.30e+00 5.92e-01 1.28e+01 angle pdb=" CA CYS A1312 " pdb=" C CYS A1312 " pdb=" O CYS A1312 " ideal model delta sigma weight residual 122.64 118.52 4.12 1.25e+00 6.40e-01 1.09e+01 angle pdb=" C ALA A 919 " pdb=" N ASP A 920 " pdb=" CA ASP A 920 " ideal model delta sigma weight residual 122.46 126.98 -4.52 1.41e+00 5.03e-01 1.03e+01 ... (remaining 19591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.39: 8158 31.39 - 62.79: 343 62.79 - 94.18: 31 94.18 - 125.58: 4 125.58 - 156.97: 1 Dihedral angle restraints: 8537 sinusoidal: 4106 harmonic: 4431 Sorted by residual: dihedral pdb=" CA GLY A1411 " pdb=" C GLY A1411 " pdb=" N ARG A1412 " pdb=" CA ARG A1412 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA HIS A 383 " pdb=" C HIS A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" C4' U B -14 " pdb=" C3' U B -14 " pdb=" O3' U B -14 " pdb=" P G B -13 " ideal model delta sinusoidal sigma weight residual 220.00 63.03 156.97 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 8534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1535 0.042 - 0.084: 429 0.084 - 0.126: 108 0.126 - 0.168: 25 0.168 - 0.210: 2 Chirality restraints: 2099 Sorted by residual: chirality pdb=" CA CYS A 123 " pdb=" N CYS A 123 " pdb=" C CYS A 123 " pdb=" CB CYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1' A C 6 " pdb=" O4' A C 6 " pdb=" C2' A C 6 " pdb=" N9 A C 6 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA ASN A1061 " pdb=" N ASN A1061 " pdb=" C ASN A1061 " pdb=" CB ASN A1061 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 2096 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 435 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO A 436 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO A 864 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 636 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 637 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 637 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 637 " -0.033 5.00e-02 4.00e+02 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 408 2.68 - 3.24: 11818 3.24 - 3.79: 20054 3.79 - 4.35: 27001 4.35 - 4.90: 45936 Nonbonded interactions: 105217 Sorted by model distance: nonbonded pdb=" O2' A B 11 " pdb=" O4' C B 12 " model vdw 2.130 3.040 nonbonded pdb=" OE1 GLU A 70 " pdb=" NH2 ARG A 104 " model vdw 2.246 3.120 nonbonded pdb=" O ARG A 330 " pdb=" OG1 THR A 334 " model vdw 2.262 3.040 nonbonded pdb=" O SER A 180 " pdb=" OG SER A 180 " model vdw 2.305 3.040 nonbonded pdb=" NH2 ARG A 917 " pdb=" O GLU A 922 " model vdw 2.308 3.120 ... (remaining 105212 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: 2.430 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.003 0.040 14309 Z= 0.159 Angle : 0.651 7.377 19596 Z= 0.383 Chirality : 0.043 0.210 2099 Planarity : 0.006 0.077 2318 Dihedral : 16.477 156.972 5679 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.55 % Favored : 89.38 % Rotamer: Outliers : 1.04 % Allowed : 10.94 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.17), residues: 1526 helix: -2.16 (0.24), residues: 293 sheet: -1.75 (0.29), residues: 267 loop : -3.90 (0.14), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 967 TYR 0.010 0.001 TYR A 313 PHE 0.012 0.001 PHE A 416 TRP 0.035 0.001 TRP A1600 HIS 0.004 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (14309) covalent geometry : angle 0.65056 / 0.38 (19596) hydrogen bonds : bond 0.19880 / 12.45 ( 335) hydrogen bonds : angle 7.10924 / 4.99 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.373 Fit side-chains REVERT: A 393 ARG cc_start: 0.7549 (mpp80) cc_final: 0.7202 (ptt-90) REVERT: A 437 ASP cc_start: 0.7376 (p0) cc_final: 0.7173 (t0) REVERT: A 577 TYR cc_start: 0.8005 (p90) cc_final: 0.7725 (p90) REVERT: A 621 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7647 (mmt-90) REVERT: A 634 MET cc_start: 0.8421 (mtt) cc_final: 0.8206 (mtm) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.1421 time to fit residues: 27.9590 Evaluate side-chains 98 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 965 CYS Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1590 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 306 HIS A 456 GLN A 464 ASN A 531 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN A1098 HIS A1113 ASN A1127 GLN A1313 HIS A1483 HIS A1590 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097186 restraints weight = 19434.945| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.35 r_work: 0.3022 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14309 Z= 0.141 Angle : 0.619 9.973 19596 Z= 0.325 Chirality : 0.043 0.192 2099 Planarity : 0.006 0.070 2318 Dihedral : 12.068 161.470 2485 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 1.93 % Allowed : 13.47 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.18), residues: 1526 helix: -0.43 (0.30), residues: 296 sheet: -1.30 (0.31), residues: 262 loop : -3.53 (0.15), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 470 TYR 0.009 0.001 TYR A1276 PHE 0.012 0.001 PHE A 187 TRP 0.026 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (14309) covalent geometry : angle 0.61850 / 0.32 (19596) hydrogen bonds : bond 0.04542 / 2.99 ( 335) hydrogen bonds : angle 4.70525 / 3.29 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.318 Fit side-chains REVERT: A 314 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8519 (pt) REVERT: A 393 ARG cc_start: 0.7819 (mpp80) cc_final: 0.7058 (ptt-90) REVERT: A 437 ASP cc_start: 0.7611 (p0) cc_final: 0.7361 (t0) REVERT: A 634 MET cc_start: 0.8715 (mtt) cc_final: 0.8456 (mtt) REVERT: A 1211 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.6578 (tmm) outliers start: 26 outliers final: 15 residues processed: 113 average time/residue: 0.1069 time to fit residues: 17.7364 Evaluate side-chains 107 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1594 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 106 optimal weight: 0.0370 overall best weight: 1.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1113 ASN A1313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095760 restraints weight = 19528.156| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.51 r_work: 0.2991 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14309 Z= 0.147 Angle : 0.608 9.904 19596 Z= 0.319 Chirality : 0.043 0.191 2099 Planarity : 0.005 0.068 2318 Dihedral : 11.828 159.735 2472 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 2.38 % Allowed : 14.58 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.19), residues: 1526 helix: 0.42 (0.32), residues: 303 sheet: -0.97 (0.31), residues: 263 loop : -3.36 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 470 TYR 0.010 0.001 TYR A1276 PHE 0.012 0.001 PHE A 416 TRP 0.024 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (14309) covalent geometry : angle 0.60754 / 0.32 (19596) hydrogen bonds : bond 0.04329 / 2.85 ( 335) hydrogen bonds : angle 4.35996 / 3.05 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.382 Fit side-chains REVERT: A 314 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8557 (pt) REVERT: A 393 ARG cc_start: 0.7862 (mpp80) cc_final: 0.7022 (ptt-90) REVERT: A 634 MET cc_start: 0.8721 (mtt) cc_final: 0.8480 (mtp) REVERT: A 1082 TYR cc_start: 0.7246 (t80) cc_final: 0.6829 (m-80) REVERT: A 1211 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6677 (tmm) outliers start: 32 outliers final: 22 residues processed: 115 average time/residue: 0.0990 time to fit residues: 17.1189 Evaluate side-chains 108 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1594 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 112 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1113 ASN A1428 ASN A1452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094876 restraints weight = 19568.349| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.47 r_work: 0.2977 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14309 Z= 0.155 Angle : 0.617 15.945 19596 Z= 0.320 Chirality : 0.044 0.192 2099 Planarity : 0.005 0.070 2318 Dihedral : 11.810 158.867 2472 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 2.83 % Allowed : 15.77 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.20), residues: 1526 helix: 0.89 (0.32), residues: 303 sheet: -0.91 (0.31), residues: 273 loop : -3.20 (0.16), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 470 TYR 0.010 0.001 TYR A1276 PHE 0.013 0.001 PHE A 416 TRP 0.023 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (14309) covalent geometry : angle 0.61675 / 0.32 (19596) hydrogen bonds : bond 0.04217 / 2.78 ( 335) hydrogen bonds : angle 4.24611 / 2.97 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.854 Fit side-chains REVERT: A 314 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8617 (pt) REVERT: A 393 ARG cc_start: 0.7813 (mpp80) cc_final: 0.7027 (ptt-90) REVERT: A 634 MET cc_start: 0.8718 (mtt) cc_final: 0.8478 (mtp) REVERT: A 1211 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6673 (tmm) outliers start: 38 outliers final: 27 residues processed: 113 average time/residue: 0.1027 time to fit residues: 17.3689 Evaluate side-chains 111 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1594 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 97 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 33 optimal weight: 0.0060 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1113 ASN A1452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092634 restraints weight = 19686.835| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.42 r_work: 0.2949 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14309 Z= 0.177 Angle : 0.631 15.146 19596 Z= 0.329 Chirality : 0.045 0.190 2099 Planarity : 0.005 0.069 2318 Dihedral : 11.827 157.895 2472 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 3.12 % Allowed : 15.77 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.20), residues: 1526 helix: 1.00 (0.32), residues: 305 sheet: -0.65 (0.32), residues: 266 loop : -3.18 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 470 TYR 0.011 0.001 TYR A1276 PHE 0.014 0.002 PHE A1218 TRP 0.023 0.001 TRP A1600 HIS 0.007 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (14309) covalent geometry : angle 0.63114 / 0.33 (19596) hydrogen bonds : bond 0.04503 / 2.96 ( 335) hydrogen bonds : angle 4.24304 / 2.97 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 86 time to evaluate : 0.474 Fit side-chains REVERT: A 314 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8708 (pt) REVERT: A 393 ARG cc_start: 0.7799 (mpp80) cc_final: 0.7026 (ptt-90) REVERT: A 634 MET cc_start: 0.8740 (mtt) cc_final: 0.8487 (mtp) REVERT: A 1211 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.6740 (tmm) REVERT: A 1268 LYS cc_start: 0.7990 (mttm) cc_final: 0.7582 (mtmm) REVERT: A 1300 MET cc_start: 0.8671 (mtm) cc_final: 0.8415 (mtp) outliers start: 42 outliers final: 32 residues processed: 119 average time/residue: 0.1031 time to fit residues: 18.1639 Evaluate side-chains 114 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1594 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1113 ASN A1452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.093043 restraints weight = 19594.926| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.18 r_work: 0.2929 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14309 Z= 0.193 Angle : 0.641 14.510 19596 Z= 0.334 Chirality : 0.046 0.189 2099 Planarity : 0.005 0.071 2318 Dihedral : 11.852 157.429 2472 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 3.12 % Allowed : 16.44 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.20), residues: 1526 helix: 1.12 (0.32), residues: 299 sheet: -0.53 (0.32), residues: 269 loop : -3.12 (0.17), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.012 0.001 TYR A1276 PHE 0.014 0.002 PHE A 416 TRP 0.024 0.001 TRP A1600 HIS 0.009 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (14309) covalent geometry : angle 0.64070 / 0.33 (19596) hydrogen bonds : bond 0.04636 / 3.05 ( 335) hydrogen bonds : angle 4.26273 / 2.98 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 0.447 Fit side-chains REVERT: A 314 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8712 (pt) REVERT: A 393 ARG cc_start: 0.7801 (mpp80) cc_final: 0.7034 (ptt-90) REVERT: A 600 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7034 (tp30) REVERT: A 634 MET cc_start: 0.8755 (mtt) cc_final: 0.8506 (mtp) REVERT: A 1113 ASN cc_start: 0.6200 (OUTLIER) cc_final: 0.5881 (t0) REVERT: A 1211 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.6813 (tmm) REVERT: A 1268 LYS cc_start: 0.8010 (mttm) cc_final: 0.7584 (mtmm) REVERT: A 1300 MET cc_start: 0.8708 (mtm) cc_final: 0.8447 (mtp) outliers start: 42 outliers final: 34 residues processed: 117 average time/residue: 0.1108 time to fit residues: 18.8896 Evaluate side-chains 114 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1113 ASN Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1594 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094290 restraints weight = 19585.446| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.47 r_work: 0.2967 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14309 Z= 0.146 Angle : 0.606 13.887 19596 Z= 0.316 Chirality : 0.044 0.191 2099 Planarity : 0.005 0.071 2318 Dihedral : 11.833 158.403 2472 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 2.90 % Allowed : 17.19 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.35 (0.21), residues: 1526 helix: 1.27 (0.33), residues: 299 sheet: -0.51 (0.32), residues: 266 loop : -3.04 (0.17), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1260 TYR 0.010 0.001 TYR A1276 PHE 0.013 0.001 PHE A 747 TRP 0.023 0.001 TRP A1600 HIS 0.007 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14309) covalent geometry : angle 0.60596 / 0.32 (19596) hydrogen bonds : bond 0.04013 / 2.65 ( 335) hydrogen bonds : angle 4.15637 / 2.90 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 0.384 Fit side-chains REVERT: A 314 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8679 (pt) REVERT: A 393 ARG cc_start: 0.7799 (mpp80) cc_final: 0.7028 (ptt-90) REVERT: A 600 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7012 (tp30) REVERT: A 634 MET cc_start: 0.8705 (mtt) cc_final: 0.8458 (mtp) REVERT: A 1211 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6661 (tmm) REVERT: A 1268 LYS cc_start: 0.7979 (mttm) cc_final: 0.7569 (mtmm) REVERT: A 1282 LYS cc_start: 0.8187 (pttt) cc_final: 0.7944 (pttm) REVERT: A 1300 MET cc_start: 0.8664 (mtm) cc_final: 0.8418 (mtp) outliers start: 39 outliers final: 30 residues processed: 116 average time/residue: 0.0976 time to fit residues: 16.8075 Evaluate side-chains 112 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094634 restraints weight = 19545.872| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.51 r_work: 0.2971 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14309 Z= 0.146 Angle : 0.601 13.629 19596 Z= 0.312 Chirality : 0.044 0.191 2099 Planarity : 0.005 0.073 2318 Dihedral : 11.798 158.473 2472 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 2.75 % Allowed : 17.63 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.21), residues: 1526 helix: 1.30 (0.32), residues: 300 sheet: -0.45 (0.32), residues: 274 loop : -2.99 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 470 TYR 0.009 0.001 TYR A1276 PHE 0.013 0.001 PHE A 776 TRP 0.023 0.001 TRP A1600 HIS 0.006 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (14309) covalent geometry : angle 0.60101 / 0.31 (19596) hydrogen bonds : bond 0.03970 / 2.62 ( 335) hydrogen bonds : angle 4.10741 / 2.87 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.496 Fit side-chains REVERT: A 314 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8699 (pt) REVERT: A 393 ARG cc_start: 0.7802 (mpp80) cc_final: 0.7046 (ptt-90) REVERT: A 600 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7042 (tp30) REVERT: A 634 MET cc_start: 0.8702 (mtt) cc_final: 0.8445 (mtp) REVERT: A 1211 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6627 (tmm) REVERT: A 1268 LYS cc_start: 0.7984 (mttm) cc_final: 0.7582 (mtmm) REVERT: A 1282 LYS cc_start: 0.8125 (pttt) cc_final: 0.7884 (pttm) REVERT: A 1300 MET cc_start: 0.8684 (mtm) cc_final: 0.8446 (mtp) outliers start: 37 outliers final: 31 residues processed: 119 average time/residue: 0.1092 time to fit residues: 19.3008 Evaluate side-chains 116 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 HIS A1452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.127957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095124 restraints weight = 19537.877| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.17 r_work: 0.2961 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14309 Z= 0.143 Angle : 0.605 13.474 19596 Z= 0.314 Chirality : 0.043 0.190 2099 Planarity : 0.005 0.075 2318 Dihedral : 11.782 158.601 2472 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 2.83 % Allowed : 17.86 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.21), residues: 1526 helix: 1.34 (0.32), residues: 300 sheet: -0.38 (0.32), residues: 273 loop : -2.97 (0.17), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 470 TYR 0.009 0.001 TYR A1276 PHE 0.013 0.001 PHE A 776 TRP 0.023 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (14309) covalent geometry : angle 0.60480 / 0.31 (19596) hydrogen bonds : bond 0.03889 / 2.56 ( 335) hydrogen bonds : angle 4.08059 / 2.85 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.426 Fit side-chains REVERT: A 314 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8708 (pt) REVERT: A 393 ARG cc_start: 0.7826 (mpp80) cc_final: 0.7063 (ptt-90) REVERT: A 600 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7062 (tp30) REVERT: A 634 MET cc_start: 0.8697 (mtt) cc_final: 0.8434 (mtp) REVERT: A 1211 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6623 (tmm) REVERT: A 1268 LYS cc_start: 0.7989 (mttm) cc_final: 0.7591 (mtmm) REVERT: A 1282 LYS cc_start: 0.8143 (pttt) cc_final: 0.7898 (pttm) REVERT: A 1300 MET cc_start: 0.8702 (mtm) cc_final: 0.8461 (mtp) outliers start: 38 outliers final: 35 residues processed: 118 average time/residue: 0.1055 time to fit residues: 18.3644 Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.129318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097706 restraints weight = 19521.912| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.30 r_work: 0.3016 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14309 Z= 0.163 Angle : 0.615 13.320 19596 Z= 0.321 Chirality : 0.044 0.187 2099 Planarity : 0.005 0.076 2318 Dihedral : 11.789 157.830 2472 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 2.98 % Allowed : 17.71 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.21), residues: 1526 helix: 1.22 (0.32), residues: 306 sheet: -0.24 (0.32), residues: 268 loop : -3.02 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 470 TYR 0.010 0.001 TYR A1276 PHE 0.013 0.001 PHE A 776 TRP 0.023 0.001 TRP A1600 HIS 0.006 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (14309) covalent geometry : angle 0.61510 / 0.32 (19596) hydrogen bonds : bond 0.04211 / 2.77 ( 335) hydrogen bonds : angle 4.11399 / 2.88 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.378 Fit side-chains REVERT: A 314 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8851 (pt) REVERT: A 393 ARG cc_start: 0.7826 (mpp80) cc_final: 0.7246 (ptt-90) REVERT: A 600 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7116 (tp30) REVERT: A 634 MET cc_start: 0.8677 (mtt) cc_final: 0.8406 (mtp) REVERT: A 1120 TRP cc_start: 0.7189 (m100) cc_final: 0.6479 (m100) REVERT: A 1211 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.6608 (tmm) REVERT: A 1260 ARG cc_start: 0.8516 (ttp-170) cc_final: 0.8107 (ttt-90) REVERT: A 1268 LYS cc_start: 0.8014 (mttm) cc_final: 0.7613 (mtmm) REVERT: A 1282 LYS cc_start: 0.8103 (pttt) cc_final: 0.7889 (pttm) REVERT: A 1300 MET cc_start: 0.8715 (mtm) cc_final: 0.8503 (mtp) outliers start: 40 outliers final: 36 residues processed: 115 average time/residue: 0.1096 time to fit residues: 18.6588 Evaluate side-chains 119 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 691 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094635 restraints weight = 19576.299| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.09 r_work: 0.2964 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14309 Z= 0.226 Angle : 0.679 13.401 19596 Z= 0.355 Chirality : 0.047 0.210 2099 Planarity : 0.005 0.077 2318 Dihedral : 11.887 155.875 2472 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 3.05 % Allowed : 17.78 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.21), residues: 1526 helix: 1.17 (0.32), residues: 300 sheet: -0.22 (0.33), residues: 272 loop : -3.00 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.012 0.001 TYR A1276 PHE 0.015 0.002 PHE A 528 TRP 0.023 0.002 TRP A1600 HIS 0.007 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (14309) covalent geometry : angle 0.67895 / 0.36 (19596) hydrogen bonds : bond 0.05043 / 3.30 ( 335) hydrogen bonds : angle 4.25890 / 2.99 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.93 seconds wall clock time: 53 minutes 48.70 seconds (3228.70 seconds total)