Starting phenix.real_space_refine on Fri May 16 21:41:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g8r_51137/05_2025/9g8r_51137.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g8r_51137/05_2025/9g8r_51137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g8r_51137/05_2025/9g8r_51137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g8r_51137/05_2025/9g8r_51137.map" model { file = "/net/cci-nas-00/data/ceres_data/9g8r_51137/05_2025/9g8r_51137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g8r_51137/05_2025/9g8r_51137.cif" } resolution = 3.4 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= 0.001 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 9426 2.51 5 N 2524 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14837 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 8718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8718 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 24, 'TRANS': 1088} Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "D" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 105 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1268 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 20, 'TRANS': 142} Chain breaks: 1 Time building chain proxies: 15.93, per 1000 atoms: 1.07 Number of scatterers: 14837 At special positions: 0 Unit cell: (93.632, 173.645, 144.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 2820 8.00 N 2524 7.00 C 9426 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: 3.21 Conformation dependent library (CDL) restraints added in 6.5 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 51.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'B' and resid 453 through 468 removed outlier: 4.156A pdb=" N GLY B 468 " --> pdb=" O TYR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 492 through 506 removed outlier: 3.664A pdb=" N PHE B 496 " --> pdb=" O MET B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 527 through 541 Processing helix chain 'B' and resid 543 through 558 Processing helix chain 'B' and resid 563 through 577 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 597 through 612 removed outlier: 3.745A pdb=" N TRP B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 603 " --> pdb=" O ASN B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.539A pdb=" N ALA B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.522A pdb=" N LEU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 3.936A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 727 removed outlier: 4.394A pdb=" N LEU B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 754 through 773 Processing helix chain 'B' and resid 775 through 796 removed outlier: 3.617A pdb=" N THR B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 Processing helix chain 'B' and resid 842 through 857 removed outlier: 3.531A pdb=" N GLU B 857 " --> pdb=" O SER B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 874 Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 909 removed outlier: 3.951A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 925 removed outlier: 3.620A pdb=" N ASN B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 943 Processing helix chain 'B' and resid 950 through 958 removed outlier: 3.659A pdb=" N TYR B 954 " --> pdb=" O GLU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.828A pdb=" N ALA B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 993 Processing helix chain 'B' and resid 995 through 1011 Processing helix chain 'B' and resid 1017 through 1033 Processing helix chain 'B' and resid 1035 through 1045 Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1066 through 1081 Processing helix chain 'B' and resid 1083 through 1101 removed outlier: 3.719A pdb=" N LYS B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1117 removed outlier: 3.770A pdb=" N ALA B1107 " --> pdb=" O LYS B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1135 Processing helix chain 'B' and resid 1139 through 1152 removed outlier: 3.690A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1172 removed outlier: 3.744A pdb=" N ARG B1161 " --> pdb=" O SER B1157 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 removed outlier: 3.655A pdb=" N LYS B1180 " --> pdb=" O VAL B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1206 removed outlier: 3.839A pdb=" N TRP B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1225 removed outlier: 3.812A pdb=" N ASP B1225 " --> pdb=" O ALA B1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 1228 through 1244 Processing helix chain 'B' and resid 1254 through 1266 Processing helix chain 'B' and resid 1269 through 1291 removed outlier: 4.151A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1312 Processing helix chain 'B' and resid 1317 through 1340 Processing helix chain 'B' and resid 1341 through 1356 removed outlier: 3.554A pdb=" N ASN B1356 " --> pdb=" O ASN B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1371 Processing helix chain 'B' and resid 1382 through 1396 removed outlier: 3.712A pdb=" N ASN B1396 " --> pdb=" O THR B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.606A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1433 Processing helix chain 'B' and resid 1436 through 1456 Processing helix chain 'B' and resid 1462 through 1478 Processing helix chain 'B' and resid 1480 through 1495 Processing helix chain 'B' and resid 1498 through 1511 removed outlier: 3.995A pdb=" N ARG B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1534 Processing helix chain 'B' and resid 1535 through 1549 Processing helix chain 'B' and resid 1552 through 1563 Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.388A pdb=" N TRP A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.715A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.629A pdb=" N SER A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 91 " --> pdb=" O TRP A 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 737 through 740 Processing sheet with id=AA2, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.669A pdb=" N GLY C 6 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 8 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE C 300 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LYS C 10 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE C 298 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 25 removed outlier: 6.509A pdb=" N VAL C 46 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.814A pdb=" N SER C 81 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 89 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER C 83 " --> pdb=" O HIS C 87 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N HIS C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 124 removed outlier: 3.623A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 140 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.560A pdb=" N GLY C 166 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE C 154 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 164 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 174 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 196 through 197 removed outlier: 3.572A pdb=" N THR C 197 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE C 216 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 240 removed outlier: 3.614A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 11 removed outlier: 5.996A pdb=" N ILE D 7 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 302 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE D 9 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 298 " --> pdb=" O GLN D 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.678A pdb=" N LYS D 48 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU D 56 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.723A pdb=" N SER D 81 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D 89 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER D 83 " --> pdb=" O HIS D 87 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 112 through 113 removed outlier: 3.799A pdb=" N TYR D 142 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY D 134 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS D 140 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.548A pdb=" N GLY D 166 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE D 154 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA D 164 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 174 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS D 184 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 196 through 197 removed outlier: 3.630A pdb=" N THR D 197 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE D 214 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR D 227 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 216 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 235 through 240 removed outlier: 3.613A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 20 through 23 817 hydrogen bonds defined for protein. 2379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3422 1.33 - 1.45: 3229 1.45 - 1.58: 8401 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 15152 Sorted by residual: bond pdb=" N ASP B1015 " pdb=" CA ASP B1015 " ideal model delta sigma weight residual 1.459 1.478 -0.019 1.32e-02 5.74e+03 2.14e+00 bond pdb=" CG ARG B 512 " pdb=" CD ARG B 512 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" N ASP D 169 " pdb=" CA ASP D 169 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.77e-02 3.19e+03 2.02e+00 bond pdb=" N ASP C 169 " pdb=" CA ASP C 169 " ideal model delta sigma weight residual 1.458 1.483 -0.024 1.77e-02 3.19e+03 1.90e+00 bond pdb=" CG GLN B 588 " pdb=" CD GLN B 588 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 20337 3.29 - 6.59: 199 6.59 - 9.88: 18 9.88 - 13.17: 7 13.17 - 16.47: 3 Bond angle restraints: 20564 Sorted by residual: angle pdb=" C PRO A 12 " pdb=" N ASP A 13 " pdb=" CA ASP A 13 " ideal model delta sigma weight residual 121.80 133.84 -12.04 2.44e+00 1.68e-01 2.44e+01 angle pdb=" CB ARG B 512 " pdb=" CG ARG B 512 " pdb=" CD ARG B 512 " ideal model delta sigma weight residual 111.30 100.12 11.18 2.30e+00 1.89e-01 2.36e+01 angle pdb=" C GLU B1014 " pdb=" N ASP B1015 " pdb=" CA ASP B1015 " ideal model delta sigma weight residual 124.31 132.41 -8.10 1.67e+00 3.59e-01 2.35e+01 angle pdb=" C ILE D 168 " pdb=" N ASP D 169 " pdb=" CA ASP D 169 " ideal model delta sigma weight residual 125.66 134.47 -8.81 1.85e+00 2.92e-01 2.27e+01 angle pdb=" N GLN B 588 " pdb=" CA GLN B 588 " pdb=" CB GLN B 588 " ideal model delta sigma weight residual 110.12 117.10 -6.98 1.47e+00 4.63e-01 2.25e+01 ... (remaining 20559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8070 17.77 - 35.54: 802 35.54 - 53.31: 125 53.31 - 71.07: 30 71.07 - 88.84: 15 Dihedral angle restraints: 9042 sinusoidal: 3513 harmonic: 5529 Sorted by residual: dihedral pdb=" CA ASN A 34 " pdb=" C ASN A 34 " pdb=" N LEU A 35 " pdb=" CA LEU A 35 " ideal model delta harmonic sigma weight residual 180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASP C 201 " pdb=" C ASP C 201 " pdb=" N SER C 202 " pdb=" CA SER C 202 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 9039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1834 0.052 - 0.104: 377 0.104 - 0.156: 98 0.156 - 0.208: 9 0.208 - 0.260: 4 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CA ASP B1015 " pdb=" N ASP B1015 " pdb=" C ASP B1015 " pdb=" CB ASP B1015 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASN B1356 " pdb=" N ASN B1356 " pdb=" C ASN B1356 " pdb=" CB ASN B1356 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE D 78 " pdb=" N ILE D 78 " pdb=" C ILE D 78 " pdb=" CB ILE D 78 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2319 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 69 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO A 70 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1381 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B1382 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO B1382 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1382 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1014 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLU B1014 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU B1014 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP B1015 " -0.021 2.00e-02 2.50e+03 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 313 2.68 - 3.24: 14446 3.24 - 3.79: 22426 3.79 - 4.35: 28963 4.35 - 4.90: 49690 Nonbonded interactions: 115838 Sorted by model distance: nonbonded pdb=" OD1 ASP B 722 " pdb=" OH TYR B 766 " model vdw 2.127 3.040 nonbonded pdb=" OG SER C 251 " pdb=" OD1 ASP C 253 " model vdw 2.140 3.040 nonbonded pdb=" OG SER D 251 " pdb=" OD1 ASP D 253 " model vdw 2.156 3.040 nonbonded pdb=" O VAL C 107 " pdb=" OG1 THR C 125 " model vdw 2.174 3.040 nonbonded pdb=" O VAL D 107 " pdb=" OG1 THR D 125 " model vdw 2.178 3.040 ... (remaining 115833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 67.980 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.730 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.049 15152 Z= 0.155 Angle : 0.838 16.468 20564 Z= 0.446 Chirality : 0.046 0.260 2322 Planarity : 0.006 0.113 2616 Dihedral : 14.720 88.843 5482 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1888 helix: 2.41 (0.16), residues: 953 sheet: -1.13 (0.34), residues: 218 loop : -2.88 (0.19), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 601 HIS 0.011 0.001 HIS D 126 PHE 0.022 0.002 PHE C 114 TYR 0.042 0.002 TYR B1525 ARG 0.024 0.001 ARG B 512 Details of bonding type rmsd hydrogen bonds : bond 0.11346 ( 817) hydrogen bonds : angle 4.63177 ( 2379) covalent geometry : bond 0.00316 (15152) covalent geometry : angle 0.83792 (20564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 567 TRP cc_start: 0.8182 (m100) cc_final: 0.7807 (m100) REVERT: B 598 PHE cc_start: 0.8330 (p90) cc_final: 0.8056 (p90) REVERT: B 1063 MET cc_start: 0.9044 (mmt) cc_final: 0.8827 (mmm) REVERT: E 456 GLU cc_start: 0.7466 (mp0) cc_final: 0.7186 (mp0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2683 time to fit residues: 65.3952 Evaluate side-chains 129 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 147 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS B 791 GLN C 98 GLN D 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.067074 restraints weight = 31940.096| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.24 r_work: 0.2697 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15152 Z= 0.194 Angle : 0.711 11.693 20564 Z= 0.369 Chirality : 0.045 0.181 2322 Planarity : 0.005 0.067 2616 Dihedral : 4.895 32.513 2029 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.00 % Favored : 90.84 % Rotamer: Outliers : 1.00 % Allowed : 9.72 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1888 helix: 2.59 (0.17), residues: 953 sheet: -1.66 (0.31), residues: 250 loop : -2.68 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 47 HIS 0.011 0.001 HIS D 126 PHE 0.013 0.002 PHE D 150 TYR 0.015 0.002 TYR B1531 ARG 0.010 0.001 ARG B 512 Details of bonding type rmsd hydrogen bonds : bond 0.05740 ( 817) hydrogen bonds : angle 3.94092 ( 2379) covalent geometry : bond 0.00453 (15152) covalent geometry : angle 0.71100 (20564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.578 Fit side-chains REVERT: B 546 MET cc_start: 0.8347 (mpp) cc_final: 0.7867 (ttm) REVERT: B 567 TRP cc_start: 0.8134 (m100) cc_final: 0.7611 (m100) REVERT: B 598 PHE cc_start: 0.8400 (p90) cc_final: 0.8114 (p90) REVERT: B 679 MET cc_start: 0.9442 (mtp) cc_final: 0.9234 (mtp) REVERT: B 1063 MET cc_start: 0.9386 (mmt) cc_final: 0.9171 (mmm) REVERT: C 50 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7364 (ptp-110) REVERT: C 61 GLU cc_start: 0.8411 (pm20) cc_final: 0.7957 (pm20) REVERT: E 456 GLU cc_start: 0.7575 (mp0) cc_final: 0.7298 (mp0) outliers start: 16 outliers final: 8 residues processed: 139 average time/residue: 0.2804 time to fit residues: 58.1022 Evaluate side-chains 121 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain E residue 455 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 chunk 67 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS D 126 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.066543 restraints weight = 31884.760| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.12 r_work: 0.2679 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15152 Z= 0.174 Angle : 0.667 11.118 20564 Z= 0.347 Chirality : 0.043 0.269 2322 Planarity : 0.005 0.054 2616 Dihedral : 4.959 33.196 2029 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.69 % Favored : 91.15 % Rotamer: Outliers : 2.70 % Allowed : 11.23 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1888 helix: 2.59 (0.17), residues: 958 sheet: -1.33 (0.31), residues: 238 loop : -2.70 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1524 HIS 0.009 0.001 HIS D 126 PHE 0.013 0.002 PHE D 150 TYR 0.019 0.001 TYR B1525 ARG 0.008 0.001 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 817) hydrogen bonds : angle 3.80353 ( 2379) covalent geometry : bond 0.00406 (15152) covalent geometry : angle 0.66726 (20564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 1.778 Fit side-chains REVERT: B 527 ASP cc_start: 0.7270 (t0) cc_final: 0.6812 (p0) REVERT: B 567 TRP cc_start: 0.8145 (m100) cc_final: 0.7655 (m100) REVERT: B 598 PHE cc_start: 0.8451 (p90) cc_final: 0.8165 (p90) REVERT: B 1489 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8414 (mm) REVERT: C 50 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7312 (ptp-110) REVERT: C 61 GLU cc_start: 0.8466 (pm20) cc_final: 0.8002 (pm20) REVERT: C 184 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.7743 (p-80) REVERT: D 297 GLU cc_start: 0.8317 (tt0) cc_final: 0.8084 (tt0) REVERT: E 456 GLU cc_start: 0.7610 (mp0) cc_final: 0.7356 (mp0) outliers start: 43 outliers final: 20 residues processed: 153 average time/residue: 0.2565 time to fit residues: 59.6824 Evaluate side-chains 131 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1502 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 207 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 125 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS B 791 GLN ** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 GLN D 11 GLN D 126 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.094413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.063276 restraints weight = 31928.271| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.20 r_work: 0.2609 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15152 Z= 0.248 Angle : 0.726 15.461 20564 Z= 0.380 Chirality : 0.046 0.187 2322 Planarity : 0.005 0.054 2616 Dihedral : 5.221 35.819 2029 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.06 % Favored : 89.78 % Rotamer: Outliers : 2.95 % Allowed : 14.05 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1888 helix: 2.51 (0.16), residues: 951 sheet: -1.38 (0.31), residues: 246 loop : -2.86 (0.19), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1524 HIS 0.020 0.002 HIS D 126 PHE 0.015 0.002 PHE D 150 TYR 0.016 0.002 TYR B1525 ARG 0.008 0.001 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.06490 ( 817) hydrogen bonds : angle 3.92168 ( 2379) covalent geometry : bond 0.00591 (15152) covalent geometry : angle 0.72599 (20564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.590 Fit side-chains REVERT: B 527 ASP cc_start: 0.7169 (t0) cc_final: 0.6787 (p0) REVERT: B 567 TRP cc_start: 0.8092 (m100) cc_final: 0.7613 (m100) REVERT: B 598 PHE cc_start: 0.8475 (p90) cc_final: 0.8214 (p90) REVERT: B 1415 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7922 (mpp) REVERT: B 1489 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8596 (mm) REVERT: C 50 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7550 (ptp-110) REVERT: C 61 GLU cc_start: 0.8596 (pm20) cc_final: 0.8113 (pm20) REVERT: C 184 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.7832 (p-80) REVERT: C 240 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8849 (t80) REVERT: D 221 HIS cc_start: 0.7588 (m-70) cc_final: 0.7330 (m-70) REVERT: E 456 GLU cc_start: 0.7570 (mp0) cc_final: 0.7336 (mp0) outliers start: 47 outliers final: 32 residues processed: 154 average time/residue: 0.2613 time to fit residues: 60.6112 Evaluate side-chains 147 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1415 MET Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1502 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 453 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 81 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.3980 chunk 158 optimal weight: 0.4980 chunk 100 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 HIS B 860 ASN D 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.064331 restraints weight = 32099.883| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.15 r_work: 0.2642 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15152 Z= 0.173 Angle : 0.654 12.958 20564 Z= 0.342 Chirality : 0.043 0.183 2322 Planarity : 0.004 0.049 2616 Dihedral : 5.099 35.285 2029 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.27 % Favored : 90.57 % Rotamer: Outliers : 2.82 % Allowed : 15.37 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1888 helix: 2.60 (0.16), residues: 952 sheet: -1.12 (0.31), residues: 238 loop : -2.83 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1524 HIS 0.013 0.001 HIS D 126 PHE 0.012 0.001 PHE B 598 TYR 0.016 0.001 TYR B1525 ARG 0.008 0.001 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 817) hydrogen bonds : angle 3.73455 ( 2379) covalent geometry : bond 0.00404 (15152) covalent geometry : angle 0.65425 (20564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: B 527 ASP cc_start: 0.7056 (t0) cc_final: 0.6687 (p0) REVERT: B 567 TRP cc_start: 0.8129 (m100) cc_final: 0.7593 (m100) REVERT: B 598 PHE cc_start: 0.8419 (p90) cc_final: 0.8179 (p90) REVERT: B 1489 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8677 (mm) REVERT: C 50 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7498 (ptp-110) REVERT: C 184 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.7839 (p-80) REVERT: C 240 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8740 (t80) REVERT: D 33 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8176 (mm-30) REVERT: D 221 HIS cc_start: 0.7614 (m-70) cc_final: 0.7328 (m-70) REVERT: E 456 GLU cc_start: 0.7623 (mp0) cc_final: 0.7393 (mp0) outliers start: 45 outliers final: 32 residues processed: 157 average time/residue: 0.2623 time to fit residues: 62.5161 Evaluate side-chains 145 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1502 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain A residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 166 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 149 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.065628 restraints weight = 32273.610| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.79 r_work: 0.2693 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15152 Z= 0.135 Angle : 0.615 11.688 20564 Z= 0.320 Chirality : 0.041 0.174 2322 Planarity : 0.004 0.045 2616 Dihedral : 4.869 33.579 2029 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.22 % Favored : 90.62 % Rotamer: Outliers : 2.38 % Allowed : 16.69 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1888 helix: 2.77 (0.16), residues: 952 sheet: -0.98 (0.32), residues: 236 loop : -2.76 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.010 0.001 HIS D 126 PHE 0.011 0.001 PHE C 247 TYR 0.017 0.001 TYR B1525 ARG 0.011 0.001 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 817) hydrogen bonds : angle 3.54300 ( 2379) covalent geometry : bond 0.00303 (15152) covalent geometry : angle 0.61479 (20564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 1.677 Fit side-chains REVERT: B 512 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7361 (ptt90) REVERT: B 527 ASP cc_start: 0.7017 (t0) cc_final: 0.6766 (p0) REVERT: B 567 TRP cc_start: 0.8204 (m100) cc_final: 0.7724 (m100) REVERT: B 1489 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8688 (mm) REVERT: C 50 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7434 (ptp-110) REVERT: C 61 GLU cc_start: 0.8605 (pp20) cc_final: 0.8276 (pt0) REVERT: C 184 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.7840 (p-80) REVERT: C 240 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8772 (t80) REVERT: D 33 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8152 (mm-30) REVERT: D 127 VAL cc_start: 0.7608 (m) cc_final: 0.7367 (t) REVERT: D 221 HIS cc_start: 0.7399 (m-70) cc_final: 0.7180 (m-70) REVERT: E 456 GLU cc_start: 0.7683 (mp0) cc_final: 0.7473 (mp0) outliers start: 38 outliers final: 28 residues processed: 144 average time/residue: 0.2641 time to fit residues: 58.5004 Evaluate side-chains 141 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1502 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 453 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 70 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 180 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 0.0270 chunk 162 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 157 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS B1291 ASN D 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.065241 restraints weight = 32264.319| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.15 r_work: 0.2667 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15152 Z= 0.148 Angle : 0.624 11.726 20564 Z= 0.324 Chirality : 0.042 0.177 2322 Planarity : 0.004 0.053 2616 Dihedral : 4.868 32.735 2029 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.22 % Favored : 90.62 % Rotamer: Outliers : 3.14 % Allowed : 16.31 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1888 helix: 2.81 (0.16), residues: 952 sheet: -0.90 (0.32), residues: 238 loop : -2.75 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1524 HIS 0.008 0.001 HIS D 126 PHE 0.037 0.001 PHE B1316 TYR 0.015 0.001 TYR B1525 ARG 0.011 0.001 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 817) hydrogen bonds : angle 3.54871 ( 2379) covalent geometry : bond 0.00343 (15152) covalent geometry : angle 0.62398 (20564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 1.568 Fit side-chains REVERT: B 527 ASP cc_start: 0.6876 (t0) cc_final: 0.6607 (p0) REVERT: B 567 TRP cc_start: 0.8075 (m100) cc_final: 0.7669 (m100) REVERT: B 588 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: B 1489 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8711 (mm) REVERT: C 12 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8178 (tp30) REVERT: C 50 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7443 (ptp-110) REVERT: C 61 GLU cc_start: 0.8641 (pp20) cc_final: 0.8312 (pt0) REVERT: C 184 HIS cc_start: 0.8692 (OUTLIER) cc_final: 0.7842 (p-80) REVERT: C 240 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8702 (t80) REVERT: D 33 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8165 (mm-30) REVERT: D 127 VAL cc_start: 0.7810 (m) cc_final: 0.7461 (t) REVERT: D 221 HIS cc_start: 0.7419 (m-70) cc_final: 0.7203 (m-70) REVERT: D 240 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.7576 (t80) outliers start: 50 outliers final: 35 residues processed: 154 average time/residue: 0.2506 time to fit residues: 59.4749 Evaluate side-chains 148 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1502 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain A residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 175 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.063800 restraints weight = 32153.567| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.22 r_work: 0.2615 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15152 Z= 0.200 Angle : 0.680 17.327 20564 Z= 0.354 Chirality : 0.044 0.184 2322 Planarity : 0.004 0.046 2616 Dihedral : 5.087 34.376 2029 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.01 % Favored : 89.83 % Rotamer: Outliers : 2.95 % Allowed : 16.50 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1888 helix: 2.68 (0.16), residues: 951 sheet: -0.92 (0.33), residues: 240 loop : -2.76 (0.20), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1524 HIS 0.013 0.001 HIS D 126 PHE 0.013 0.002 PHE D 9 TYR 0.013 0.001 TYR B1525 ARG 0.007 0.001 ARG B 512 Details of bonding type rmsd hydrogen bonds : bond 0.05725 ( 817) hydrogen bonds : angle 3.73723 ( 2379) covalent geometry : bond 0.00478 (15152) covalent geometry : angle 0.67973 (20564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 1.586 Fit side-chains REVERT: B 527 ASP cc_start: 0.6750 (t0) cc_final: 0.6504 (p0) REVERT: B 567 TRP cc_start: 0.8008 (m100) cc_final: 0.7415 (m100) REVERT: B 570 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7372 (mtm-85) REVERT: B 588 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7283 (pm20) REVERT: B 1489 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8739 (mm) REVERT: C 50 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7417 (ptp-110) REVERT: C 61 GLU cc_start: 0.8647 (pp20) cc_final: 0.8161 (pt0) REVERT: C 184 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.7866 (p-80) REVERT: C 240 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8841 (t80) REVERT: D 33 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8282 (mm-30) REVERT: D 50 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7682 (ptp-110) REVERT: D 203 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: D 221 HIS cc_start: 0.7454 (m-70) cc_final: 0.7253 (m-70) REVERT: D 240 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7580 (t80) outliers start: 47 outliers final: 35 residues processed: 148 average time/residue: 0.2632 time to fit residues: 59.6160 Evaluate side-chains 148 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1502 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain A residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 60 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.0060 chunk 84 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 150 optimal weight: 0.0980 chunk 130 optimal weight: 0.0570 chunk 38 optimal weight: 0.0980 chunk 184 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS C 237 ASN A 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.067297 restraints weight = 31756.464| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.15 r_work: 0.2709 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15152 Z= 0.120 Angle : 0.608 14.843 20564 Z= 0.314 Chirality : 0.041 0.179 2322 Planarity : 0.004 0.044 2616 Dihedral : 4.769 31.260 2029 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.79 % Favored : 91.05 % Rotamer: Outliers : 2.32 % Allowed : 17.63 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1888 helix: 2.86 (0.17), residues: 953 sheet: -0.73 (0.33), residues: 230 loop : -2.69 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.006 0.001 HIS B1151 PHE 0.011 0.001 PHE C 247 TYR 0.015 0.001 TYR B1525 ARG 0.006 0.000 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 817) hydrogen bonds : angle 3.45815 ( 2379) covalent geometry : bond 0.00258 (15152) covalent geometry : angle 0.60762 (20564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: B 567 TRP cc_start: 0.7972 (m100) cc_final: 0.7544 (m100) REVERT: B 588 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7325 (pm20) REVERT: B 611 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7202 (ttp-110) REVERT: C 50 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7495 (ptp-110) REVERT: C 61 GLU cc_start: 0.8612 (pp20) cc_final: 0.8181 (pt0) REVERT: C 184 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.7886 (p-80) REVERT: C 240 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8742 (t80) REVERT: D 33 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8173 (mm-30) REVERT: D 50 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7591 (ptp-110) REVERT: D 221 HIS cc_start: 0.7371 (m-70) cc_final: 0.7054 (m170) outliers start: 37 outliers final: 31 residues processed: 148 average time/residue: 0.2801 time to fit residues: 63.5697 Evaluate side-chains 145 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1502 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 173 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 152 optimal weight: 0.1980 chunk 73 optimal weight: 0.1980 chunk 120 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.066922 restraints weight = 32150.409| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.17 r_work: 0.2692 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15152 Z= 0.128 Angle : 0.616 14.490 20564 Z= 0.319 Chirality : 0.041 0.238 2322 Planarity : 0.004 0.044 2616 Dihedral : 4.682 30.804 2029 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.16 % Favored : 90.68 % Rotamer: Outliers : 2.45 % Allowed : 17.57 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1888 helix: 2.89 (0.16), residues: 953 sheet: -0.83 (0.32), residues: 240 loop : -2.65 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.007 0.001 HIS B1151 PHE 0.043 0.001 PHE B1316 TYR 0.015 0.001 TYR B1525 ARG 0.005 0.000 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 817) hydrogen bonds : angle 3.43868 ( 2379) covalent geometry : bond 0.00284 (15152) covalent geometry : angle 0.61616 (20564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.787 Fit side-chains revert: symmetry clash REVERT: B 567 TRP cc_start: 0.8003 (m100) cc_final: 0.7593 (m100) REVERT: B 611 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.7213 (ttp-110) REVERT: B 1489 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8713 (mm) REVERT: C 50 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7436 (ptp-110) REVERT: C 184 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.7874 (p-80) REVERT: C 240 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8750 (t80) REVERT: D 33 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8181 (mm-30) REVERT: D 50 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7618 (ptp-110) REVERT: D 221 HIS cc_start: 0.7364 (m-70) cc_final: 0.7055 (m170) outliers start: 39 outliers final: 33 residues processed: 148 average time/residue: 0.2677 time to fit residues: 60.4172 Evaluate side-chains 146 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1502 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain A residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 142 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 0.0970 chunk 182 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.062862 restraints weight = 32247.984| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.78 r_work: 0.2633 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15152 Z= 0.201 Angle : 0.700 15.468 20564 Z= 0.363 Chirality : 0.045 0.249 2322 Planarity : 0.005 0.045 2616 Dihedral : 5.039 34.056 2029 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.80 % Favored : 90.04 % Rotamer: Outliers : 2.70 % Allowed : 17.57 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1888 helix: 2.75 (0.16), residues: 949 sheet: -0.68 (0.32), residues: 246 loop : -2.74 (0.20), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 601 HIS 0.013 0.001 HIS D 126 PHE 0.014 0.002 PHE C 150 TYR 0.014 0.001 TYR C 156 ARG 0.004 0.001 ARG B1528 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 817) hydrogen bonds : angle 3.72015 ( 2379) covalent geometry : bond 0.00481 (15152) covalent geometry : angle 0.70026 (20564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7599.84 seconds wall clock time: 135 minutes 43.36 seconds (8143.36 seconds total)