Starting phenix.real_space_refine on Mon Dec 30 22:49:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ync_33958/12_2024/7ync_33958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ync_33958/12_2024/7ync_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_33958/12_2024/7ync_33958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ync_33958/12_2024/7ync_33958.map" model { file = "/net/cci-nas-00/data/ceres_data/7ync_33958/12_2024/7ync_33958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ync_33958/12_2024/7ync_33958.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.42, per 1000 atoms: 0.61 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: 3.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.99 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: 6.86 Time building geometry restraints manager: 4.29 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: 8253 31.39 - 62.79: 415 62.79 - 94.18: 70 94.18 - 125.58: 4 125.58 - 156.97: 1 Dihedral angle restraints: 8743 sinusoidal: 4312 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 8740 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: 1.890 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.740 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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= 0.207 Angle : 0.651 7.377 19596 Z= 0.383 Chirality : 0.043 0.210 2099 Planarity : 0.006 0.077 2318 Dihedral : 18.049 156.972 5885 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.001 TRP A1600 HIS 0.004 0.001 HIS A 691 PHE 0.012 0.001 PHE A 416 TYR 0.010 0.001 TYR A 313 ARG 0.003 0.000 ARG A 967 *********************** 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 : 1.478 Fit side-chains REVERT: A 393 ARG cc_start: 0.7549 (mpp80) cc_final: 0.7202 (ptt-90) REVERT: A 437 ASP cc_start: 0.7377 (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: 0.3797 time to fit residues: 74.2886 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 : 1.717 ------------------------------------------------------------------------------- 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 133 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14309 Z= 0.291 Angle : 0.671 9.707 19596 Z= 0.354 Chirality : 0.046 0.189 2099 Planarity : 0.006 0.072 2318 Dihedral : 16.320 159.923 2691 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 2.31 % Allowed : 13.39 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.19), residues: 1526 helix: -0.57 (0.30), residues: 308 sheet: -1.48 (0.30), residues: 281 loop : -3.55 (0.15), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1600 HIS 0.006 0.001 HIS A1149 PHE 0.014 0.002 PHE A 200 TYR 0.011 0.001 TYR A1276 ARG 0.004 0.000 ARG A 444 *********************** 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 124 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.425 Fit side-chains REVERT: A 314 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8569 (pt) REVERT: A 634 MET cc_start: 0.8492 (mtt) cc_final: 0.8261 (mtp) REVERT: A 1113 ASN cc_start: 0.6091 (OUTLIER) cc_final: 0.5890 (t0) REVERT: A 1211 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.6586 (tmm) outliers start: 31 outliers final: 17 residues processed: 117 average time/residue: 0.3035 time to fit residues: 51.9314 Evaluate side-chains 105 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 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 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 1113 ASN 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 79 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1313 HIS A1428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14309 Z= 0.296 Angle : 0.652 9.264 19596 Z= 0.344 Chirality : 0.045 0.189 2099 Planarity : 0.005 0.074 2318 Dihedral : 16.212 158.646 2678 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 2.68 % Allowed : 14.66 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.19), residues: 1526 helix: 0.36 (0.32), residues: 303 sheet: -0.97 (0.31), residues: 265 loop : -3.40 (0.16), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1600 HIS 0.005 0.001 HIS A 184 PHE 0.014 0.002 PHE A 416 TYR 0.011 0.001 TYR A1276 ARG 0.004 0.000 ARG A 470 *********************** 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: 36 poor density : 87 time to evaluate : 1.516 Fit side-chains REVERT: A 314 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8618 (pt) REVERT: A 634 MET cc_start: 0.8484 (mtt) cc_final: 0.8227 (mtp) REVERT: A 1211 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6642 (tmm) outliers start: 36 outliers final: 25 residues processed: 114 average time/residue: 0.2982 time to fit residues: 49.8844 Evaluate side-chains 109 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 659 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14309 Z= 0.197 Angle : 0.585 9.410 19596 Z= 0.305 Chirality : 0.043 0.197 2099 Planarity : 0.005 0.065 2318 Dihedral : 16.112 160.245 2678 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.75 % Allowed : 15.40 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1526 helix: 0.86 (0.32), residues: 303 sheet: -0.93 (0.31), residues: 279 loop : -3.18 (0.16), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1600 HIS 0.004 0.001 HIS A1149 PHE 0.012 0.001 PHE A 416 TYR 0.009 0.001 TYR A1276 ARG 0.004 0.000 ARG A 470 *********************** 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 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 1.515 Fit side-chains REVERT: A 314 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8603 (pt) REVERT: A 634 MET cc_start: 0.8424 (mtt) cc_final: 0.8171 (mtp) REVERT: A 1211 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6449 (tmm) REVERT: A 1260 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7687 (ttt-90) outliers start: 37 outliers final: 27 residues processed: 115 average time/residue: 0.2861 time to fit residues: 49.0437 Evaluate side-chains 110 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 314 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 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 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 1271 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 105 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14309 Z= 0.297 Angle : 0.638 9.453 19596 Z= 0.335 Chirality : 0.045 0.189 2099 Planarity : 0.005 0.069 2318 Dihedral : 16.100 157.941 2678 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 3.42 % Allowed : 15.92 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.20), residues: 1526 helix: 0.97 (0.32), residues: 304 sheet: -0.71 (0.32), residues: 275 loop : -3.14 (0.17), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1600 HIS 0.006 0.001 HIS A 184 PHE 0.014 0.002 PHE A 776 TYR 0.010 0.001 TYR A1276 ARG 0.004 0.000 ARG A 470 *********************** 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 130 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 1.642 Fit side-chains REVERT: A 314 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8683 (pt) REVERT: A 634 MET cc_start: 0.8504 (mtt) cc_final: 0.8254 (mtp) REVERT: A 1211 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6627 (tmm) REVERT: A 1260 ARG cc_start: 0.8013 (ttp-170) cc_final: 0.7682 (ttt-90) REVERT: A 1268 LYS cc_start: 0.7731 (mttm) cc_final: 0.7394 (mtmm) REVERT: A 1282 LYS cc_start: 0.8111 (pttt) cc_final: 0.7867 (pttm) outliers start: 46 outliers final: 35 residues processed: 119 average time/residue: 0.2869 time to fit residues: 50.7353 Evaluate side-chains 119 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 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 1082 TYR Chi-restraints excluded: chain A residue 1096 LEU 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 1271 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.0030 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14309 Z= 0.197 Angle : 0.580 8.634 19596 Z= 0.303 Chirality : 0.043 0.193 2099 Planarity : 0.005 0.065 2318 Dihedral : 16.080 159.502 2678 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 2.68 % Allowed : 17.04 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.21), residues: 1526 helix: 1.27 (0.33), residues: 299 sheet: -0.70 (0.31), residues: 279 loop : -3.01 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1600 HIS 0.010 0.001 HIS A1149 PHE 0.012 0.001 PHE A 776 TYR 0.010 0.001 TYR A1276 ARG 0.004 0.000 ARG A 470 *********************** 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: 36 poor density : 88 time to evaluate : 1.450 Fit side-chains REVERT: A 314 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8646 (pt) REVERT: A 634 MET cc_start: 0.8428 (mtt) cc_final: 0.8170 (mtp) REVERT: A 1211 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6404 (tmm) REVERT: A 1260 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7654 (ttt-90) REVERT: A 1268 LYS cc_start: 0.7672 (mttm) cc_final: 0.7338 (mtmm) REVERT: A 1282 LYS cc_start: 0.8041 (pttt) cc_final: 0.7794 (pttm) outliers start: 36 outliers final: 29 residues processed: 114 average time/residue: 0.3014 time to fit residues: 50.8076 Evaluate side-chains 112 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 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 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 1399 SER Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 0.0050 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 0.0370 chunk 85 optimal weight: 0.0570 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 587 GLN A1452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14309 Z= 0.164 Angle : 0.559 9.462 19596 Z= 0.291 Chirality : 0.041 0.199 2099 Planarity : 0.005 0.069 2318 Dihedral : 15.959 160.955 2678 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.21), residues: 1526 helix: 1.33 (0.32), residues: 307 sheet: -0.50 (0.31), residues: 271 loop : -2.97 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1600 HIS 0.007 0.001 HIS A1149 PHE 0.011 0.001 PHE A 776 TYR 0.009 0.001 TYR A1126 ARG 0.010 0.000 ARG A 108 *********************** 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 133 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 1.521 Fit side-chains REVERT: A 314 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8631 (pt) REVERT: A 634 MET cc_start: 0.8388 (mtt) cc_final: 0.8138 (mtp) REVERT: A 692 MET cc_start: 0.8310 (tpp) cc_final: 0.7885 (tpt) REVERT: A 1211 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6120 (tmm) REVERT: A 1268 LYS cc_start: 0.7611 (mttm) cc_final: 0.7291 (mtmm) outliers start: 39 outliers final: 28 residues processed: 123 average time/residue: 0.2953 time to fit residues: 53.8803 Evaluate side-chains 116 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 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 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 1252 VAL Chi-restraints excluded: chain A residue 1271 SER 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 94 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14309 Z= 0.312 Angle : 0.640 15.035 19596 Z= 0.333 Chirality : 0.046 0.189 2099 Planarity : 0.005 0.073 2318 Dihedral : 16.012 157.591 2678 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 3.27 % Allowed : 17.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.21), residues: 1526 helix: 1.24 (0.32), residues: 306 sheet: -0.36 (0.32), residues: 274 loop : -2.99 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1600 HIS 0.008 0.001 HIS A1149 PHE 0.015 0.002 PHE A 528 TYR 0.011 0.001 TYR A1276 ARG 0.007 0.000 ARG A 108 *********************** 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 129 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 1.476 Fit side-chains REVERT: A 314 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8674 (pt) REVERT: A 634 MET cc_start: 0.8491 (mtt) cc_final: 0.8213 (mtp) REVERT: A 1211 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6441 (tmm) REVERT: A 1260 ARG cc_start: 0.7923 (ttp-170) cc_final: 0.7602 (ttt-90) REVERT: A 1268 LYS cc_start: 0.7743 (mttm) cc_final: 0.7415 (mtmm) outliers start: 44 outliers final: 39 residues processed: 120 average time/residue: 0.2805 time to fit residues: 49.9996 Evaluate side-chains 123 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 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 933 SER 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 1074 ILE 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 1271 SER 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 Chi-restraints excluded: chain A residue 1594 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.1980 chunk 133 optimal weight: 0.0060 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 61 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A1020 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14309 Z= 0.144 Angle : 0.556 11.628 19596 Z= 0.287 Chirality : 0.041 0.197 2099 Planarity : 0.005 0.073 2318 Dihedral : 15.943 161.493 2678 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.71 % Allowed : 18.90 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1526 helix: 1.52 (0.32), residues: 306 sheet: -0.44 (0.32), residues: 279 loop : -2.86 (0.17), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 PHE 0.011 0.001 PHE A1407 TYR 0.008 0.001 TYR A1126 ARG 0.007 0.000 ARG A 108 *********************** 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 115 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.194 Fit side-chains REVERT: A 314 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8594 (pt) REVERT: A 634 MET cc_start: 0.8361 (mtt) cc_final: 0.8103 (mtp) REVERT: A 692 MET cc_start: 0.8297 (tpp) cc_final: 0.7868 (tpt) REVERT: A 1120 TRP cc_start: 0.7272 (m100) cc_final: 0.6705 (m100) REVERT: A 1211 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.5970 (tmm) REVERT: A 1268 LYS cc_start: 0.7621 (mttm) cc_final: 0.7317 (mtmm) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.2955 time to fit residues: 48.8679 Evaluate side-chains 104 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 314 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 466 GLU 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 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1008 THR 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 1211 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 691 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14309 Z= 0.358 Angle : 0.666 14.300 19596 Z= 0.346 Chirality : 0.047 0.210 2099 Planarity : 0.005 0.071 2318 Dihedral : 15.993 156.490 2676 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 1.86 % Allowed : 18.75 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.21), residues: 1526 helix: 1.16 (0.32), residues: 311 sheet: -0.15 (0.32), residues: 268 loop : -2.95 (0.17), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1600 HIS 0.009 0.001 HIS A1149 PHE 0.016 0.002 PHE A 528 TYR 0.013 0.001 TYR A 930 ARG 0.007 0.000 ARG A 108 ********************** 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 105 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 1.479 Fit side-chains REVERT: A 314 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8702 (pt) REVERT: A 634 MET cc_start: 0.8517 (mtt) cc_final: 0.8241 (mtp) REVERT: A 1211 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6527 (tmm) REVERT: A 1268 LYS cc_start: 0.7801 (mttm) cc_final: 0.7463 (mtmm) outliers start: 25 outliers final: 20 residues processed: 100 average time/residue: 0.3124 time to fit residues: 45.4764 Evaluate side-chains 100 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 587 GLN 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 930 TYR Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1082 TYR Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1284 VAL 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 38 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.127668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096023 restraints weight = 19454.867| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.21 r_work: 0.2983 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14309 Z= 0.333 Angle : 0.666 13.874 19596 Z= 0.347 Chirality : 0.046 0.200 2099 Planarity : 0.005 0.070 2318 Dihedral : 16.035 156.854 2676 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 2.31 % Allowed : 18.23 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.21), residues: 1526 helix: 1.17 (0.32), residues: 306 sheet: -0.13 (0.33), residues: 267 loop : -2.90 (0.17), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1600 HIS 0.008 0.001 HIS A1149 PHE 0.015 0.002 PHE A 528 TYR 0.013 0.001 TYR A 930 ARG 0.006 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.28 seconds wall clock time: 51 minutes 28.72 seconds (3088.72 seconds total)