Starting phenix.real_space_refine on Fri Oct 10 23:19:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gls_40207/10_2025/8gls_40207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gls_40207/10_2025/8gls_40207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gls_40207/10_2025/8gls_40207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gls_40207/10_2025/8gls_40207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gls_40207/10_2025/8gls_40207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gls_40207/10_2025/8gls_40207.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6321 2.51 5 N 1597 2.21 5 O 1708 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9682 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9450 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 32, 'TRANS': 1146} Chain breaks: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 147 Unusual residues: {' MG': 2, 'ATP': 2, 'POV': 5, 'ZRH': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 5, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 2.51, per 1000 atoms: 0.26 Number of scatterers: 9682 At special positions: 0 Unit cell: (78.28, 87.55, 143.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 F 1 9.00 O 1708 8.00 N 1597 7.00 C 6321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 364.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 4 sheets defined 69.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.742A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.572A pdb=" N LEU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 94 removed outlier: 3.883A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.532A pdb=" N LEU A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 164 removed outlier: 3.834A pdb=" N ILE A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.681A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 176 through 194 removed outlier: 4.274A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 removed outlier: 4.533A pdb=" N ALA A 198 " --> pdb=" O LEU A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.542A pdb=" N ALA A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 222 through 246 removed outlier: 3.561A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.868A pdb=" N ASN A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.803A pdb=" N VAL A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 329 removed outlier: 3.774A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.829A pdb=" N ILE A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 removed outlier: 3.504A pdb=" N ALA A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.552A pdb=" N GLY A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.689A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.603A pdb=" N ARG A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 606 through 613 removed outlier: 3.581A pdb=" N LEU A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.522A pdb=" N LEU A 850 " --> pdb=" O TRP A 846 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 886 removed outlier: 4.022A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 922 removed outlier: 4.001A pdb=" N SER A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 removed outlier: 3.604A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 958 removed outlier: 3.898A pdb=" N GLN A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 Processing helix chain 'A' and resid 969 through 986 removed outlier: 4.331A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1012 removed outlier: 4.413A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1046 removed outlier: 4.168A pdb=" N VAL A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 4.107A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.599A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A1058 " --> pdb=" O HIS A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 removed outlier: 3.533A pdb=" N LEU A1065 " --> pdb=" O GLY A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 3.584A pdb=" N PHE A1074 " --> pdb=" O ARG A1070 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1168 removed outlier: 3.685A pdb=" N ALA A1136 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1258 removed outlier: 3.789A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1284 removed outlier: 3.560A pdb=" N LYS A1284 " --> pdb=" O GLN A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1322 removed outlier: 3.746A pdb=" N ASP A1320 " --> pdb=" O TRP A1316 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1329 Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 3.706A pdb=" N LYS A1351 " --> pdb=" O SER A1347 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1390 removed outlier: 3.958A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A1390 " --> pdb=" O ARG A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 Processing helix chain 'A' and resid 1427 through 1434 Processing helix chain 'A' and resid 1434 through 1439 removed outlier: 3.793A pdb=" N ARG A1438 " --> pdb=" O ARG A1434 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A1439 " --> pdb=" O SER A1435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1434 through 1439' Processing helix chain 'A' and resid 1442 through 1450 removed outlier: 3.817A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 441 through 448 removed outlier: 6.752A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 397 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU A 479 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 490 through 491 removed outlier: 6.826A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 617 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1230 through 1234 removed outlier: 5.382A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL A1212 " --> pdb=" O GLN A1268 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN A1268 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP A1214 " --> pdb=" O GLU A1266 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A1266 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 6.239A pdb=" N ILE A1289 " --> pdb=" O ASP A1370 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1494 1.31 - 1.44: 2666 1.44 - 1.56: 5631 1.56 - 1.69: 11 1.69 - 1.81: 79 Bond restraints: 9881 Sorted by residual: bond pdb=" C4 ATP A1504 " pdb=" C5 ATP A1504 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP A1503 " pdb=" C5 ATP A1503 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C5 ATP A1504 " pdb=" C6 ATP A1504 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.42e+01 bond pdb=" C5 ATP A1503 " pdb=" C6 ATP A1503 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C15 ZRH A1510 " pdb=" N16 ZRH A1510 " ideal model delta sigma weight residual 1.358 1.453 -0.095 2.00e-02 2.50e+03 2.23e+01 ... (remaining 9876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 13268 4.52 - 9.04: 83 9.04 - 13.56: 0 13.56 - 18.08: 1 18.08 - 22.60: 3 Bond angle restraints: 13355 Sorted by residual: angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 117.27 22.60 1.00e+00 1.00e+00 5.11e+02 angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 119.52 20.35 1.00e+00 1.00e+00 4.14e+02 angle pdb=" PA ATP A1504 " pdb=" O3A ATP A1504 " pdb=" PB ATP A1504 " ideal model delta sigma weight residual 136.83 117.50 19.33 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP A1503 " pdb=" O3A ATP A1503 " pdb=" PB ATP A1503 " ideal model delta sigma weight residual 136.83 120.35 16.48 1.00e+00 1.00e+00 2.72e+02 angle pdb=" C5 ATP A1504 " pdb=" C4 ATP A1504 " pdb=" N3 ATP A1504 " ideal model delta sigma weight residual 126.80 118.82 7.98 1.00e+00 1.00e+00 6.37e+01 ... (remaining 13350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5032 18.00 - 36.00: 689 36.00 - 54.00: 164 54.00 - 72.00: 20 72.00 - 90.00: 7 Dihedral angle restraints: 5912 sinusoidal: 2436 harmonic: 3476 Sorted by residual: dihedral pdb=" CA MET A1137 " pdb=" C MET A1137 " pdb=" N ASN A1138 " pdb=" CA ASN A1138 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASN A 187 " pdb=" C ASN A 187 " pdb=" N LEU A 188 " pdb=" CA LEU A 188 " ideal model delta harmonic sigma weight residual -180.00 -161.73 -18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP A 112 " pdb=" C ASP A 112 " pdb=" N ASN A 113 " pdb=" CA ASN A 113 " ideal model delta harmonic sigma weight residual -180.00 -162.68 -17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1096 0.046 - 0.092: 336 0.092 - 0.137: 88 0.137 - 0.183: 10 0.183 - 0.229: 4 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA LYS A1060 " pdb=" N LYS A1060 " pdb=" C LYS A1060 " pdb=" CB LYS A1060 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASP A1305 " pdb=" N ASP A1305 " pdb=" C ASP A1305 " pdb=" CB ASP A1305 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU A 218 " pdb=" CB LEU A 218 " pdb=" CD1 LEU A 218 " pdb=" CD2 LEU A 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1531 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A1305 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" CG ASP A1305 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASP A1305 " -0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP A1305 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1034 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C LEU A1034 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A1034 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A1035 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 84 " 0.016 2.00e-02 2.50e+03 1.37e-02 3.73e+00 pdb=" CG TYR A 84 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 84 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 84 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 84 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 84 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 84 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 84 " 0.000 2.00e-02 2.50e+03 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 87 2.55 - 3.14: 8230 3.14 - 3.73: 15074 3.73 - 4.31: 19280 4.31 - 4.90: 31901 Nonbonded interactions: 74572 Sorted by model distance: nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 1.964 2.170 nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1501 " model vdw 1.974 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.057 2.170 nonbonded pdb=" NE2 GLN A1291 " pdb="MG MG A1502 " model vdw 2.109 2.250 nonbonded pdb=" NE2 GLN A 493 " pdb="MG MG A1501 " model vdw 2.171 2.250 ... (remaining 74567 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.006 0.095 9881 Z= 0.340 Angle : 1.011 22.598 13355 Z= 0.636 Chirality : 0.048 0.229 1534 Planarity : 0.004 0.038 1629 Dihedral : 17.077 89.999 3664 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.19 % Allowed : 1.26 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1169 helix: -0.06 (0.19), residues: 741 sheet: -1.50 (0.59), residues: 60 loop : -1.36 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1422 TYR 0.033 0.002 TYR A 84 PHE 0.027 0.002 PHE A 587 TRP 0.030 0.002 TRP A1274 HIS 0.012 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 9881) covalent geometry : angle 1.01143 (13355) hydrogen bonds : bond 0.16609 ( 560) hydrogen bonds : angle 6.28917 ( 1653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.377 Fit side-chains REVERT: A 265 MET cc_start: 0.8465 (tpp) cc_final: 0.8233 (tpp) REVERT: A 850 LEU cc_start: 0.9358 (mm) cc_final: 0.8757 (pp) REVERT: A 1157 MET cc_start: 0.7257 (ttm) cc_final: 0.6868 (tmm) outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.0883 time to fit residues: 16.6330 Evaluate side-chains 90 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 30.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN A 353 GLN ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1412 GLN A1432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.125355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.102894 restraints weight = 22441.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.106376 restraints weight = 11817.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.108823 restraints weight = 7757.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110320 restraints weight = 5809.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111542 restraints weight = 4809.225| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9881 Z= 0.151 Angle : 0.656 7.308 13355 Z= 0.334 Chirality : 0.043 0.194 1534 Planarity : 0.004 0.033 1629 Dihedral : 8.398 63.989 1408 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.35 % Allowed : 12.37 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.25), residues: 1169 helix: 0.61 (0.20), residues: 727 sheet: -1.25 (0.54), residues: 72 loop : -1.24 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1158 TYR 0.024 0.002 TYR A1219 PHE 0.018 0.001 PHE A1166 TRP 0.018 0.001 TRP A1274 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9881) covalent geometry : angle 0.65583 (13355) hydrogen bonds : bond 0.05578 ( 560) hydrogen bonds : angle 4.51318 ( 1653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.470 Fit side-chains REVERT: A 315 PHE cc_start: 0.8209 (t80) cc_final: 0.7881 (t80) REVERT: A 616 ILE cc_start: 0.9000 (mp) cc_final: 0.8620 (pt) REVERT: A 850 LEU cc_start: 0.9246 (mm) cc_final: 0.8690 (pp) REVERT: A 1114 VAL cc_start: 0.7736 (OUTLIER) cc_final: 0.7155 (p) REVERT: A 1157 MET cc_start: 0.7293 (ttm) cc_final: 0.6839 (tmm) outliers start: 14 outliers final: 8 residues processed: 116 average time/residue: 0.0816 time to fit residues: 14.6954 Evaluate side-chains 103 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 34 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 117 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** 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 = 0.3860 r_free = 0.3860 target = 0.122531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.100177 restraints weight = 22653.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.103607 restraints weight = 11730.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.105977 restraints weight = 7650.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.107450 restraints weight = 5738.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108581 restraints weight = 4758.025| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9881 Z= 0.183 Angle : 0.626 6.131 13355 Z= 0.322 Chirality : 0.042 0.162 1534 Planarity : 0.003 0.031 1629 Dihedral : 8.104 77.164 1408 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.80 % Allowed : 17.97 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.25), residues: 1169 helix: 0.77 (0.19), residues: 729 sheet: -1.20 (0.53), residues: 74 loop : -1.14 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1158 TYR 0.021 0.002 TYR A1219 PHE 0.022 0.002 PHE A 533 TRP 0.014 0.001 TRP A1274 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9881) covalent geometry : angle 0.62612 (13355) hydrogen bonds : bond 0.05613 ( 560) hydrogen bonds : angle 4.39271 ( 1653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.396 Fit side-chains REVERT: A 159 LEU cc_start: 0.8344 (tp) cc_final: 0.7975 (tt) REVERT: A 595 MET cc_start: 0.8087 (ppp) cc_final: 0.7880 (ppp) REVERT: A 616 ILE cc_start: 0.8978 (mp) cc_final: 0.8546 (pt) REVERT: A 850 LEU cc_start: 0.9240 (mm) cc_final: 0.8600 (pp) REVERT: A 1002 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 1157 MET cc_start: 0.7268 (ttm) cc_final: 0.6833 (tmm) outliers start: 29 outliers final: 19 residues processed: 117 average time/residue: 0.0781 time to fit residues: 14.3585 Evaluate side-chains 112 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 0.0010 chunk 110 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** 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 = 0.3900 r_free = 0.3900 target = 0.125496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.102972 restraints weight = 22468.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106348 restraints weight = 11876.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.108668 restraints weight = 7857.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.110348 restraints weight = 5960.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111311 restraints weight = 4883.612| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9881 Z= 0.133 Angle : 0.559 7.578 13355 Z= 0.288 Chirality : 0.040 0.151 1534 Planarity : 0.003 0.031 1629 Dihedral : 7.542 78.542 1408 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.00 % Allowed : 21.16 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.25), residues: 1169 helix: 0.97 (0.19), residues: 733 sheet: -0.71 (0.53), residues: 82 loop : -1.22 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1158 TYR 0.015 0.001 TYR A1219 PHE 0.014 0.001 PHE A 932 TRP 0.021 0.001 TRP A1274 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9881) covalent geometry : angle 0.55933 (13355) hydrogen bonds : bond 0.04938 ( 560) hydrogen bonds : angle 4.12092 ( 1653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.380 Fit side-chains REVERT: A 312 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 595 MET cc_start: 0.8051 (ppp) cc_final: 0.7721 (ppp) REVERT: A 616 ILE cc_start: 0.8975 (mp) cc_final: 0.8635 (pt) REVERT: A 850 LEU cc_start: 0.9240 (mm) cc_final: 0.8634 (pp) REVERT: A 948 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8303 (tt) REVERT: A 1002 ILE cc_start: 0.8494 (mm) cc_final: 0.8116 (tp) REVERT: A 1157 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6824 (tmm) REVERT: A 1166 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7569 (t80) outliers start: 31 outliers final: 17 residues processed: 120 average time/residue: 0.0707 time to fit residues: 13.5880 Evaluate side-chains 110 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1166 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 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 = 0.3911 r_free = 0.3911 target = 0.126840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.104374 restraints weight = 22741.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.107804 restraints weight = 11928.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.110217 restraints weight = 7823.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111853 restraints weight = 5865.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112818 restraints weight = 4812.452| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9881 Z= 0.121 Angle : 0.531 6.695 13355 Z= 0.273 Chirality : 0.039 0.149 1534 Planarity : 0.003 0.030 1629 Dihedral : 7.009 83.657 1408 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.19 % Allowed : 22.61 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1169 helix: 1.02 (0.19), residues: 743 sheet: -0.68 (0.55), residues: 84 loop : -1.05 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1158 TYR 0.012 0.001 TYR A1219 PHE 0.012 0.001 PHE A1026 TRP 0.019 0.001 TRP A1274 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9881) covalent geometry : angle 0.53119 (13355) hydrogen bonds : bond 0.04643 ( 560) hydrogen bonds : angle 3.99780 ( 1653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.416 Fit side-chains REVERT: A 312 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7741 (t80) REVERT: A 595 MET cc_start: 0.7937 (ppp) cc_final: 0.7492 (ppp) REVERT: A 616 ILE cc_start: 0.8948 (mp) cc_final: 0.8611 (pt) REVERT: A 850 LEU cc_start: 0.9203 (mm) cc_final: 0.8612 (pp) REVERT: A 948 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 1002 ILE cc_start: 0.8483 (mm) cc_final: 0.8120 (tp) REVERT: A 1110 PHE cc_start: 0.7982 (m-10) cc_final: 0.7738 (m-10) REVERT: A 1114 VAL cc_start: 0.7228 (OUTLIER) cc_final: 0.6882 (p) REVERT: A 1157 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6677 (tmm) REVERT: A 1166 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7413 (t80) REVERT: A 1314 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7575 (tp30) outliers start: 33 outliers final: 20 residues processed: 119 average time/residue: 0.0726 time to fit residues: 13.7833 Evaluate side-chains 122 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1314 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** 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 = 0.3926 r_free = 0.3926 target = 0.127489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.104907 restraints weight = 22491.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.108453 restraints weight = 11678.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110942 restraints weight = 7594.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112652 restraints weight = 5681.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.113788 restraints weight = 4627.115| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9881 Z= 0.118 Angle : 0.526 8.848 13355 Z= 0.268 Chirality : 0.038 0.144 1534 Planarity : 0.003 0.029 1629 Dihedral : 6.566 89.811 1408 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.96 % Allowed : 22.42 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1169 helix: 1.15 (0.19), residues: 744 sheet: -0.50 (0.57), residues: 84 loop : -1.01 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1158 TYR 0.011 0.001 TYR A1219 PHE 0.011 0.001 PHE A 932 TRP 0.021 0.001 TRP A1274 HIS 0.008 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9881) covalent geometry : angle 0.52608 (13355) hydrogen bonds : bond 0.04444 ( 560) hydrogen bonds : angle 3.91540 ( 1653) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.309 Fit side-chains REVERT: A 312 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7724 (t80) REVERT: A 595 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7510 (ppp) REVERT: A 616 ILE cc_start: 0.8947 (mp) cc_final: 0.8634 (pt) REVERT: A 850 LEU cc_start: 0.9209 (mm) cc_final: 0.8636 (pp) REVERT: A 918 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7560 (tp) REVERT: A 948 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 1002 ILE cc_start: 0.8501 (mm) cc_final: 0.8144 (tp) REVERT: A 1114 VAL cc_start: 0.7322 (OUTLIER) cc_final: 0.6748 (p) REVERT: A 1157 MET cc_start: 0.7239 (ttm) cc_final: 0.6746 (tmm) REVERT: A 1314 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7524 (tp30) outliers start: 41 outliers final: 23 residues processed: 134 average time/residue: 0.0781 time to fit residues: 16.0665 Evaluate side-chains 124 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1314 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** 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 = 0.3921 r_free = 0.3921 target = 0.127494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.104847 restraints weight = 22542.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108433 restraints weight = 11672.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110896 restraints weight = 7600.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.112554 restraints weight = 5695.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113695 restraints weight = 4663.655| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9881 Z= 0.124 Angle : 0.532 7.395 13355 Z= 0.271 Chirality : 0.039 0.151 1534 Planarity : 0.003 0.029 1629 Dihedral : 6.415 87.170 1408 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.29 % Allowed : 24.06 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1169 helix: 1.19 (0.19), residues: 744 sheet: -0.48 (0.57), residues: 84 loop : -1.00 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1102 TYR 0.017 0.001 TYR A 89 PHE 0.010 0.001 PHE A1026 TRP 0.030 0.001 TRP A1274 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9881) covalent geometry : angle 0.53179 (13355) hydrogen bonds : bond 0.04526 ( 560) hydrogen bonds : angle 3.92258 ( 1653) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.432 Fit side-chains REVERT: A 312 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7693 (t80) REVERT: A 595 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7498 (ppp) REVERT: A 616 ILE cc_start: 0.8915 (mp) cc_final: 0.8605 (pt) REVERT: A 850 LEU cc_start: 0.9208 (mm) cc_final: 0.8638 (pp) REVERT: A 918 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7501 (tp) REVERT: A 948 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 1002 ILE cc_start: 0.8492 (mm) cc_final: 0.8139 (tp) REVERT: A 1110 PHE cc_start: 0.7985 (m-10) cc_final: 0.7658 (m-10) REVERT: A 1114 VAL cc_start: 0.7283 (OUTLIER) cc_final: 0.6931 (p) REVERT: A 1157 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6977 (tmm) REVERT: A 1314 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7535 (tp30) outliers start: 34 outliers final: 21 residues processed: 121 average time/residue: 0.0806 time to fit residues: 15.2496 Evaluate side-chains 123 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1314 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 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 = 0.3923 r_free = 0.3923 target = 0.124496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103087 restraints weight = 21678.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106613 restraints weight = 11518.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.109027 restraints weight = 7563.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.110642 restraints weight = 5675.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.111663 restraints weight = 4656.876| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9881 Z= 0.126 Angle : 0.541 8.764 13355 Z= 0.275 Chirality : 0.039 0.150 1534 Planarity : 0.003 0.028 1629 Dihedral : 6.261 83.527 1408 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.29 % Allowed : 24.93 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.25), residues: 1169 helix: 1.22 (0.19), residues: 745 sheet: -0.42 (0.58), residues: 84 loop : -0.97 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1066 TYR 0.014 0.001 TYR A 89 PHE 0.013 0.001 PHE A1111 TRP 0.025 0.001 TRP A1274 HIS 0.010 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9881) covalent geometry : angle 0.54135 (13355) hydrogen bonds : bond 0.04500 ( 560) hydrogen bonds : angle 3.91375 ( 1653) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.348 Fit side-chains REVERT: A 595 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7513 (ppp) REVERT: A 616 ILE cc_start: 0.8880 (mp) cc_final: 0.8568 (pt) REVERT: A 850 LEU cc_start: 0.9212 (mm) cc_final: 0.8644 (pp) REVERT: A 918 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7517 (tp) REVERT: A 948 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8294 (tt) REVERT: A 1002 ILE cc_start: 0.8484 (mm) cc_final: 0.8132 (tp) REVERT: A 1114 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.6997 (p) REVERT: A 1157 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6954 (tmm) REVERT: A 1314 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7539 (tp30) outliers start: 34 outliers final: 23 residues processed: 125 average time/residue: 0.0730 time to fit residues: 14.4843 Evaluate side-chains 125 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1314 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 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 = 0.3911 r_free = 0.3911 target = 0.123779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.102551 restraints weight = 21840.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106015 restraints weight = 11523.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108377 restraints weight = 7553.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.109845 restraints weight = 5659.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.111019 restraints weight = 4692.360| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9881 Z= 0.141 Angle : 0.563 8.322 13355 Z= 0.285 Chirality : 0.039 0.145 1534 Planarity : 0.003 0.029 1629 Dihedral : 6.224 78.277 1408 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 25.02 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1169 helix: 1.28 (0.20), residues: 738 sheet: -0.30 (0.59), residues: 82 loop : -1.02 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1097 TYR 0.011 0.001 TYR A1219 PHE 0.014 0.001 PHE A1166 TRP 0.023 0.001 TRP A1274 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9881) covalent geometry : angle 0.56347 (13355) hydrogen bonds : bond 0.04714 ( 560) hydrogen bonds : angle 3.97366 ( 1653) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.378 Fit side-chains REVERT: A 281 MET cc_start: 0.6204 (mmp) cc_final: 0.5997 (mmp) REVERT: A 595 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7520 (ppp) REVERT: A 616 ILE cc_start: 0.8861 (mp) cc_final: 0.8534 (pt) REVERT: A 850 LEU cc_start: 0.9217 (mm) cc_final: 0.8647 (pp) REVERT: A 918 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 1002 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8137 (tp) REVERT: A 1157 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6932 (tmm) REVERT: A 1314 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7590 (tp30) outliers start: 31 outliers final: 23 residues processed: 120 average time/residue: 0.0642 time to fit residues: 12.4941 Evaluate side-chains 122 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1314 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** 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 = 0.3934 r_free = 0.3934 target = 0.125485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104073 restraints weight = 21707.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107613 restraints weight = 11490.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.110034 restraints weight = 7495.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111662 restraints weight = 5601.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112655 restraints weight = 4583.430| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9881 Z= 0.126 Angle : 0.564 9.114 13355 Z= 0.283 Chirality : 0.039 0.158 1534 Planarity : 0.003 0.029 1629 Dihedral : 6.059 76.116 1408 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.71 % Allowed : 25.41 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.25), residues: 1169 helix: 1.30 (0.20), residues: 742 sheet: -0.34 (0.59), residues: 84 loop : -0.97 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1066 TYR 0.010 0.001 TYR A1219 PHE 0.015 0.001 PHE A1111 TRP 0.020 0.001 TRP A1274 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9881) covalent geometry : angle 0.56390 (13355) hydrogen bonds : bond 0.04518 ( 560) hydrogen bonds : angle 3.95149 ( 1653) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.361 Fit side-chains REVERT: A 595 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7560 (ppp) REVERT: A 616 ILE cc_start: 0.8880 (mp) cc_final: 0.8579 (pt) REVERT: A 850 LEU cc_start: 0.9207 (mm) cc_final: 0.8645 (pp) REVERT: A 918 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7460 (tp) REVERT: A 1002 ILE cc_start: 0.8495 (mm) cc_final: 0.8125 (tp) REVERT: A 1157 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6954 (tmm) REVERT: A 1314 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7572 (tp30) outliers start: 28 outliers final: 23 residues processed: 119 average time/residue: 0.0686 time to fit residues: 13.1168 Evaluate side-chains 124 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1314 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 0.0470 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 359 GLN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.128504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106879 restraints weight = 21464.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110525 restraints weight = 11347.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.113018 restraints weight = 7413.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.114711 restraints weight = 5540.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.115887 restraints weight = 4524.811| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9881 Z= 0.113 Angle : 0.536 8.529 13355 Z= 0.269 Chirality : 0.038 0.152 1534 Planarity : 0.003 0.029 1629 Dihedral : 5.735 72.864 1408 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.51 % Allowed : 25.99 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1169 helix: 1.40 (0.20), residues: 746 sheet: -0.24 (0.60), residues: 84 loop : -0.87 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1259 TYR 0.010 0.001 TYR A 84 PHE 0.012 0.001 PHE A1111 TRP 0.023 0.001 TRP A1274 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9881) covalent geometry : angle 0.53639 (13355) hydrogen bonds : bond 0.04140 ( 560) hydrogen bonds : angle 3.86122 ( 1653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1522.78 seconds wall clock time: 27 minutes 11.03 seconds (1631.03 seconds total)