Starting phenix.real_space_refine on Sun Dec 29 21:12:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tj8_25919/12_2024/7tj8_25919_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj8_25919/12_2024/7tj8_25919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tj8_25919/12_2024/7tj8_25919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj8_25919/12_2024/7tj8_25919.map" model { file = "/net/cci-nas-00/data/ceres_data/7tj8_25919/12_2024/7tj8_25919_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj8_25919/12_2024/7tj8_25919_neut.cif" } resolution = 3.2 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= -0.008 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 C 7087 2.51 5 N 1598 2.21 5 O 1774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10551 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8805 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 1045} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "A" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 382 Unusual residues: {'CLR': 1, 'NAG': 2, 'PEV': 3, 'PLM': 6, 'POV': 3} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 1, 'PLM:plan-1': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.11, per 1000 atoms: 0.67 Number of scatterers: 10551 At special positions: 0 Unit cell: (129.897, 110.37, 115.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 4 15.00 O 1774 8.00 N 1598 7.00 C 7087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1087 " - pdb=" SG CYS A1107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2412 " - " ASN A 309 " " NAG A2414 " - " ASN A1103 " " NAG B 301 " - " ASN B 121 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 5 sheets defined 69.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.657A pdb=" N VAL A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 137 removed outlier: 4.054A pdb=" N GLN A 121 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 166 removed outlier: 3.919A pdb=" N GLU A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.906A pdb=" N LEU A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.609A pdb=" N MET A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 285 through 289 removed outlier: 3.941A pdb=" N ILE A 289 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 382 removed outlier: 4.205A pdb=" N PHE A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.906A pdb=" N GLU A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 524 removed outlier: 4.749A pdb=" N ASN A 518 " --> pdb=" O CYS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 556 removed outlier: 4.583A pdb=" N LEU A 536 " --> pdb=" O GLN A 532 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.620A pdb=" N VAL A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 4.866A pdb=" N MET A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 609 removed outlier: 3.773A pdb=" N PHE A 598 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 600 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 656 removed outlier: 3.631A pdb=" N SER A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 removed outlier: 4.168A pdb=" N ILE A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 687 Processing helix chain 'A' and resid 688 through 701 removed outlier: 4.176A pdb=" N THR A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 733 Proline residue: A 707 - end of helix removed outlier: 3.656A pdb=" N SER A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 931 Processing helix chain 'A' and resid 933 through 950 Processing helix chain 'A' and resid 951 through 954 Processing helix chain 'A' and resid 955 through 960 removed outlier: 4.412A pdb=" N ASP A 959 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 990 removed outlier: 3.547A pdb=" N LYS A 965 " --> pdb=" O ARG A 961 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 998 removed outlier: 3.517A pdb=" N TYR A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1018 removed outlier: 3.528A pdb=" N LEU A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1033 removed outlier: 7.106A pdb=" N GLU A1022 " --> pdb=" O THR A1019 " (cutoff:3.500A) Proline residue: A1025 - end of helix removed outlier: 3.605A pdb=" N LYS A1030 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1041 removed outlier: 4.100A pdb=" N LEU A1038 " --> pdb=" O PRO A1034 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A1041 " --> pdb=" O VAL A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1056 removed outlier: 3.694A pdb=" N LYS A1045 " --> pdb=" O PHE A1041 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A1046 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.639A pdb=" N LEU A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A1064 " --> pdb=" O ASN A1060 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A1079 " --> pdb=" O MET A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1108 removed outlier: 3.516A pdb=" N CYS A1107 " --> pdb=" O ASN A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1140 removed outlier: 3.610A pdb=" N LEU A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1154 removed outlier: 3.577A pdb=" N ILE A1147 " --> pdb=" O GLY A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1169 through 1180 removed outlier: 3.937A pdb=" N PHE A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1204 removed outlier: 3.548A pdb=" N SER A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A1191 " --> pdb=" O MET A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1222 removed outlier: 3.880A pdb=" N GLN A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1249 removed outlier: 3.733A pdb=" N THR A1249 " --> pdb=" O PHE A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1270 removed outlier: 3.513A pdb=" N ILE A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A1270 " --> pdb=" O ILE A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1302 removed outlier: 3.607A pdb=" N ALA A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A1286 " --> pdb=" O ALA A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1330 removed outlier: 3.521A pdb=" N PHE A1319 " --> pdb=" O ASN A1315 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1351 removed outlier: 3.919A pdb=" N LEU A1347 " --> pdb=" O SER A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 7.268A pdb=" N LEU A1359 " --> pdb=" O MET A1356 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY A1360 " --> pdb=" O LEU A1357 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY A1362 " --> pdb=" O LEU A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1402 removed outlier: 3.770A pdb=" N HIS A1367 " --> pdb=" O PRO A1363 " (cutoff:3.500A) Proline residue: A1372 - end of helix Proline residue: A1378 - end of helix Processing helix chain 'A' and resid 1419 through 1432 Processing helix chain 'A' and resid 1436 through 1444 removed outlier: 3.753A pdb=" N ALA A1442 " --> pdb=" O GLY A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1449 removed outlier: 3.785A pdb=" N TRP A1448 " --> pdb=" O ASN A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1502 removed outlier: 3.693A pdb=" N PHE A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A1489 " --> pdb=" O LEU A1485 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A1494 " --> pdb=" O MET A1490 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1497 " --> pdb=" O VAL A1493 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 186 removed outlier: 5.295A pdb=" N GLU B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA2, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.704A pdb=" N ALA B 35 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 119 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.696A pdb=" N VAL B 122 " --> pdb=" O THR B 137 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1590 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: 3.03 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1618 1.32 - 1.45: 2939 1.45 - 1.57: 5925 1.57 - 1.69: 172 1.69 - 1.82: 151 Bond restraints: 10805 Sorted by residual: bond pdb=" C29 POV A2403 " pdb="C210 POV A2403 " ideal model delta sigma weight residual 1.333 1.642 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" O14 POV A2408 " pdb=" P POV A2408 " ideal model delta sigma weight residual 1.496 1.752 -0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C31 POV A2402 " pdb=" O31 POV A2402 " ideal model delta sigma weight residual 1.327 1.507 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C31 POV A2408 " pdb=" O31 POV A2408 " ideal model delta sigma weight residual 1.327 1.506 -0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C21 POV A2402 " pdb=" O21 POV A2402 " ideal model delta sigma weight residual 1.330 1.505 -0.175 2.00e-02 2.50e+03 7.69e+01 ... (remaining 10800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 14372 3.74 - 7.48: 141 7.48 - 11.22: 28 11.22 - 14.95: 4 14.95 - 18.69: 7 Bond angle restraints: 14552 Sorted by residual: angle pdb=" N PHE B 72 " pdb=" CA PHE B 72 " pdb=" C PHE B 72 " ideal model delta sigma weight residual 111.37 130.06 -18.69 1.64e+00 3.72e-01 1.30e+02 angle pdb=" C PRO B 66 " pdb=" CA PRO B 66 " pdb=" CB PRO B 66 " ideal model delta sigma weight residual 111.56 96.54 15.02 1.65e+00 3.67e-01 8.28e+01 angle pdb=" N TYR B 64 " pdb=" CA TYR B 64 " pdb=" C TYR B 64 " ideal model delta sigma weight residual 111.33 121.18 -9.85 1.21e+00 6.83e-01 6.63e+01 angle pdb=" C PHE B 63 " pdb=" N TYR B 64 " pdb=" CA TYR B 64 " ideal model delta sigma weight residual 120.38 129.17 -8.79 1.37e+00 5.33e-01 4.12e+01 angle pdb=" O VAL B 84 " pdb=" C VAL B 84 " pdb=" N GLU B 85 " ideal model delta sigma weight residual 122.06 115.75 6.31 1.14e+00 7.69e-01 3.07e+01 ... (remaining 14547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 6248 34.29 - 68.58: 231 68.58 - 102.87: 28 102.87 - 137.16: 4 137.16 - 171.45: 2 Dihedral angle restraints: 6513 sinusoidal: 2878 harmonic: 3635 Sorted by residual: dihedral pdb=" C PRO B 66 " pdb=" N PRO B 66 " pdb=" CA PRO B 66 " pdb=" CB PRO B 66 " ideal model delta harmonic sigma weight residual -120.70 -101.90 -18.80 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" CA LEU A 581 " pdb=" C LEU A 581 " pdb=" N ILE A 582 " pdb=" CA ILE A 582 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA MET B 177 " pdb=" C MET B 177 " pdb=" N ILE B 178 " pdb=" CA ILE B 178 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1595 0.119 - 0.239: 36 0.239 - 0.358: 4 0.358 - 0.478: 2 0.478 - 0.597: 4 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C1 NAG A2414 " pdb=" ND2 ASN A1103 " pdb=" C2 NAG A2414 " pdb=" O5 NAG A2414 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.91e+00 chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 121 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" C2 POV A2402 " pdb=" C1 POV A2402 " pdb=" C3 POV A2402 " pdb=" O21 POV A2402 " both_signs ideal model delta sigma weight residual False 2.43 2.94 -0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 1638 not shown) Planarity restraints: 1739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A2403 " 0.235 2.00e-02 2.50e+03 2.35e-01 5.51e+02 pdb=" C29 POV A2403 " -0.236 2.00e-02 2.50e+03 pdb="C210 POV A2403 " -0.233 2.00e-02 2.50e+03 pdb="C211 POV A2403 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1331 " -0.109 5.00e-02 4.00e+02 1.63e-01 4.26e+01 pdb=" N PRO A1332 " 0.282 5.00e-02 4.00e+02 pdb=" CA PRO A1332 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO A1332 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 84 " -0.032 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C VAL B 84 " 0.104 2.00e-02 2.50e+03 pdb=" O VAL B 84 " -0.037 2.00e-02 2.50e+03 pdb=" N GLU B 85 " -0.034 2.00e-02 2.50e+03 ... (remaining 1736 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 69 2.61 - 3.19: 9475 3.19 - 3.76: 14138 3.76 - 4.33: 20285 4.33 - 4.90: 33619 Nonbonded interactions: 77586 Sorted by model distance: nonbonded pdb=" O ASN B 95 " pdb=" OD1 ASN B 95 " model vdw 2.042 3.040 nonbonded pdb=" ND2 ASN B 95 " pdb=" C1 NAG B 302 " model vdw 2.086 3.550 nonbonded pdb=" ND2 ASN B 109 " pdb=" C1 NAG B 303 " model vdw 2.173 3.550 nonbonded pdb=" O ILE A1016 " pdb=" OG1 THR A1019 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR B 138 " pdb=" O7 NAG B 301 " model vdw 2.292 3.040 ... (remaining 77581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.015 0.309 10805 Z= 0.964 Angle : 1.032 18.692 14552 Z= 0.522 Chirality : 0.057 0.597 1641 Planarity : 0.010 0.235 1736 Dihedral : 17.586 171.453 4155 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.95 % Favored : 93.39 % Rotamer: Outliers : 0.80 % Allowed : 7.83 % Favored : 91.37 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.21), residues: 1226 helix: -1.82 (0.15), residues: 746 sheet: -2.10 (0.56), residues: 69 loop : -1.58 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 610 HIS 0.012 0.002 HIS B 131 PHE 0.026 0.002 PHE B 63 TYR 0.028 0.003 TYR A 354 ARG 0.037 0.003 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 229 time to evaluate : 1.179 Fit side-chains REVERT: A 538 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.8033 (m-40) REVERT: A 661 ASP cc_start: 0.8171 (t70) cc_final: 0.7836 (t0) REVERT: A 1256 ILE cc_start: 0.8828 (mm) cc_final: 0.8529 (mt) REVERT: A 1361 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7814 (mmpt) REVERT: A 1496 MET cc_start: 0.8201 (mmm) cc_final: 0.7902 (mmm) REVERT: A 1497 GLU cc_start: 0.8114 (tp30) cc_final: 0.7894 (tp30) outliers start: 9 outliers final: 4 residues processed: 233 average time/residue: 0.2082 time to fit residues: 70.9909 Evaluate side-chains 192 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10805 Z= 0.203 Angle : 0.677 11.824 14552 Z= 0.349 Chirality : 0.045 0.357 1641 Planarity : 0.007 0.150 1736 Dihedral : 15.374 179.754 1784 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.85 % Favored : 96.98 % Rotamer: Outliers : 2.31 % Allowed : 10.50 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.69 (0.23), residues: 1226 helix: 0.18 (0.18), residues: 754 sheet: -1.64 (0.60), residues: 69 loop : -1.29 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 610 HIS 0.009 0.001 HIS A1199 PHE 0.023 0.001 PHE A 246 TYR 0.015 0.001 TYR A 354 ARG 0.003 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 510 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6529 (t80) REVERT: A 538 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7751 (m-40) REVERT: A 560 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5463 (m90) REVERT: A 1361 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7731 (mmtt) outliers start: 26 outliers final: 8 residues processed: 221 average time/residue: 0.2028 time to fit residues: 65.9405 Evaluate side-chains 198 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1263 PHE Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 659 HIS A1264 GLN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 10805 Z= 0.296 Angle : 0.685 10.992 14552 Z= 0.351 Chirality : 0.046 0.329 1641 Planarity : 0.006 0.138 1736 Dihedral : 14.436 175.788 1776 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 2.67 % Allowed : 12.19 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.27 (0.24), residues: 1226 helix: 0.65 (0.19), residues: 757 sheet: -1.66 (0.62), residues: 69 loop : -1.40 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.010 0.001 HIS B 131 PHE 0.024 0.002 PHE A 246 TYR 0.019 0.002 TYR A1218 ARG 0.007 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.026 Fit side-chains REVERT: A 538 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7994 (m-40) REVERT: A 560 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5755 (m90) REVERT: A 1110 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7943 (pp) REVERT: A 1361 LYS cc_start: 0.8062 (mmtp) cc_final: 0.7726 (mmtt) REVERT: B 50 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8196 (mtmt) outliers start: 30 outliers final: 11 residues processed: 213 average time/residue: 0.2171 time to fit residues: 68.6665 Evaluate side-chains 203 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1414 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS B 81 HIS B 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10805 Z= 0.145 Angle : 0.586 11.338 14552 Z= 0.294 Chirality : 0.042 0.299 1641 Planarity : 0.005 0.097 1736 Dihedral : 13.420 175.881 1776 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 2.14 % Allowed : 14.06 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.34 (0.25), residues: 1226 helix: 1.22 (0.20), residues: 753 sheet: -1.46 (0.62), residues: 69 loop : -1.33 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 94 HIS 0.003 0.001 HIS B 81 PHE 0.022 0.001 PHE A 246 TYR 0.023 0.001 TYR A1218 ARG 0.005 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 510 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6285 (t80) REVERT: A 538 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7837 (m-40) REVERT: A 617 MET cc_start: 0.7829 (tpt) cc_final: 0.7607 (tpt) REVERT: A 1324 PHE cc_start: 0.8394 (m-80) cc_final: 0.8045 (m-80) REVERT: A 1361 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7539 (mmtt) REVERT: B 50 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8220 (mtmt) outliers start: 24 outliers final: 12 residues processed: 216 average time/residue: 0.1958 time to fit residues: 62.5155 Evaluate side-chains 207 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.0170 chunk 82 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10805 Z= 0.198 Angle : 0.588 11.604 14552 Z= 0.296 Chirality : 0.042 0.305 1641 Planarity : 0.004 0.095 1736 Dihedral : 12.891 179.694 1776 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 2.67 % Allowed : 14.68 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.55 (0.25), residues: 1226 helix: 1.42 (0.20), residues: 748 sheet: -1.59 (0.62), residues: 69 loop : -1.23 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 94 HIS 0.004 0.001 HIS B 131 PHE 0.022 0.001 PHE A 246 TYR 0.018 0.001 TYR A1218 ARG 0.006 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.953 Fit side-chains REVERT: A 510 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6498 (t80) REVERT: A 538 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7915 (m-40) REVERT: A 617 MET cc_start: 0.7878 (tpt) cc_final: 0.7672 (tpt) REVERT: A 1356 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6643 (mtt) REVERT: A 1361 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7526 (mmtt) outliers start: 30 outliers final: 17 residues processed: 212 average time/residue: 0.2116 time to fit residues: 65.8093 Evaluate side-chains 208 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1356 MET Chi-restraints excluded: chain A residue 1414 VAL Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.0000 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS A1195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10805 Z= 0.222 Angle : 0.601 10.752 14552 Z= 0.307 Chirality : 0.043 0.302 1641 Planarity : 0.005 0.093 1736 Dihedral : 12.675 175.462 1776 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 2.49 % Allowed : 16.28 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.58 (0.25), residues: 1226 helix: 1.47 (0.20), residues: 747 sheet: -1.59 (0.61), residues: 69 loop : -1.27 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.004 0.001 HIS B 131 PHE 0.022 0.001 PHE A 246 TYR 0.022 0.001 TYR A1218 ARG 0.005 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.068 Fit side-chains REVERT: A 538 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7950 (m-40) REVERT: A 617 MET cc_start: 0.7888 (tpt) cc_final: 0.7670 (tpt) REVERT: A 1361 LYS cc_start: 0.7944 (mmtp) cc_final: 0.7497 (mmtt) outliers start: 28 outliers final: 20 residues processed: 207 average time/residue: 0.2103 time to fit residues: 63.6211 Evaluate side-chains 210 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 10805 Z= 0.143 Angle : 0.559 11.381 14552 Z= 0.283 Chirality : 0.041 0.299 1641 Planarity : 0.004 0.092 1736 Dihedral : 11.910 169.981 1776 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 1.51 % Allowed : 17.70 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.84 (0.25), residues: 1226 helix: 1.69 (0.20), residues: 747 sheet: -1.42 (0.60), residues: 69 loop : -1.22 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 94 HIS 0.003 0.001 HIS A 560 PHE 0.021 0.001 PHE A 246 TYR 0.020 0.001 TYR A1218 ARG 0.004 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.117 Fit side-chains REVERT: A 510 PHE cc_start: 0.7006 (t80) cc_final: 0.6205 (t80) REVERT: A 538 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7924 (m-40) REVERT: A 1166 ASN cc_start: 0.7628 (p0) cc_final: 0.7374 (p0) REVERT: B 51 ARG cc_start: 0.8424 (mmm160) cc_final: 0.8153 (mtp85) outliers start: 17 outliers final: 11 residues processed: 202 average time/residue: 0.2226 time to fit residues: 64.9289 Evaluate side-chains 195 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1501 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0770 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS A1254 ASN B 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10805 Z= 0.135 Angle : 0.561 11.297 14552 Z= 0.280 Chirality : 0.041 0.309 1641 Planarity : 0.004 0.091 1736 Dihedral : 11.515 164.237 1776 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 1.42 % Allowed : 18.06 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.05 (0.25), residues: 1226 helix: 1.87 (0.20), residues: 747 sheet: -1.35 (0.59), residues: 71 loop : -1.16 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 94 HIS 0.002 0.000 HIS A1199 PHE 0.020 0.001 PHE A 246 TYR 0.019 0.001 TYR A1218 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 1.125 Fit side-chains REVERT: A 510 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6130 (t80) REVERT: A 538 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7943 (m-40) outliers start: 16 outliers final: 11 residues processed: 197 average time/residue: 0.1949 time to fit residues: 57.0839 Evaluate side-chains 191 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1501 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS B 93 GLN B 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 10805 Z= 0.139 Angle : 0.562 11.475 14552 Z= 0.280 Chirality : 0.041 0.311 1641 Planarity : 0.004 0.087 1736 Dihedral : 11.180 159.186 1776 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.25 % Allowed : 18.68 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.17 (0.25), residues: 1226 helix: 2.02 (0.20), residues: 742 sheet: -1.43 (0.59), residues: 71 loop : -1.16 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 94 HIS 0.003 0.000 HIS A 560 PHE 0.020 0.001 PHE A 246 TYR 0.018 0.001 TYR A1218 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 510 PHE cc_start: 0.6936 (t80) cc_final: 0.6120 (t80) REVERT: A 1166 ASN cc_start: 0.7625 (p0) cc_final: 0.7369 (p0) REVERT: A 1256 ILE cc_start: 0.8685 (mm) cc_final: 0.8258 (mp) outliers start: 14 outliers final: 12 residues processed: 199 average time/residue: 0.2139 time to fit residues: 62.5153 Evaluate side-chains 195 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1414 VAL Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10805 Z= 0.202 Angle : 0.599 11.053 14552 Z= 0.301 Chirality : 0.042 0.313 1641 Planarity : 0.004 0.087 1736 Dihedral : 11.251 154.280 1774 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 1.16 % Allowed : 19.04 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.03 (0.25), residues: 1226 helix: 1.91 (0.20), residues: 741 sheet: -1.86 (0.56), residues: 74 loop : -1.13 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 94 HIS 0.004 0.001 HIS B 131 PHE 0.022 0.001 PHE A 246 TYR 0.023 0.001 TYR A1218 ARG 0.004 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 1.222 Fit side-chains REVERT: A 510 PHE cc_start: 0.7243 (t80) cc_final: 0.6425 (t80) REVERT: A 1116 MET cc_start: 0.6211 (mtt) cc_final: 0.5752 (mtt) REVERT: A 1220 ARG cc_start: 0.8059 (tmt170) cc_final: 0.7844 (tmt170) outliers start: 13 outliers final: 11 residues processed: 198 average time/residue: 0.2300 time to fit residues: 68.9212 Evaluate side-chains 197 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 658 CYS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115478 restraints weight = 16191.628| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.40 r_work: 0.3269 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10805 Z= 0.279 Angle : 0.647 10.617 14552 Z= 0.328 Chirality : 0.044 0.299 1641 Planarity : 0.005 0.086 1736 Dihedral : 11.717 148.703 1774 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 1.42 % Allowed : 18.86 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.25), residues: 1226 helix: 1.71 (0.19), residues: 739 sheet: -1.87 (0.55), residues: 74 loop : -1.26 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 94 HIS 0.004 0.001 HIS B 131 PHE 0.026 0.002 PHE B 63 TYR 0.022 0.002 TYR A1218 ARG 0.004 0.000 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.56 seconds wall clock time: 45 minutes 10.91 seconds (2710.91 seconds total)