Starting phenix.real_space_refine on Sun Dec 29 02:17:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vls_32025/12_2024/7vls_32025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vls_32025/12_2024/7vls_32025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vls_32025/12_2024/7vls_32025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vls_32025/12_2024/7vls_32025.map" model { file = "/net/cci-nas-00/data/ceres_data/7vls_32025/12_2024/7vls_32025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vls_32025/12_2024/7vls_32025.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.154 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 5837 2.51 5 N 1493 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9003 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8891 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 33, 'TRANS': 1107} Chain breaks: 6 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'ESV': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.56, per 1000 atoms: 0.62 Number of scatterers: 9003 At special positions: 0 Unit cell: (70.956, 90.666, 135.342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 5 15.00 Mg 2 11.99 O 1619 8.00 N 1493 7.00 C 5837 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 72.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 278 removed outlier: 3.520A pdb=" N ASN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 312 removed outlier: 3.575A pdb=" N ALA A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.020A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 395 Processing helix chain 'A' and resid 396 through 402 removed outlier: 4.153A pdb=" N LEU A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 428 removed outlier: 4.477A pdb=" N THR A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 450 Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.233A pdb=" N LEU A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 506 removed outlier: 6.089A pdb=" N LYS A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 559 removed outlier: 3.603A pdb=" N SER A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 607 Proline residue: A 581 - end of helix removed outlier: 4.008A pdb=" N LEU A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 785 through 791 removed outlier: 4.458A pdb=" N ASP A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 839 through 853 Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.548A pdb=" N ASP A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 874 removed outlier: 4.046A pdb=" N THR A 873 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 911 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 1017 removed outlier: 3.626A pdb=" N PHE A 991 " --> pdb=" O PHE A 987 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A1008 " --> pdb=" O ILE A1004 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1074 removed outlier: 3.727A pdb=" N LEU A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A1052 " --> pdb=" O VAL A1048 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL A1053 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.781A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1102 removed outlier: 3.883A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1128 removed outlier: 3.721A pdb=" N THR A1106 " --> pdb=" O HIS A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 3.732A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.956A pdb=" N ASP A1155 " --> pdb=" O VAL A1151 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1186 through 1236 Processing helix chain 'A' and resid 1242 through 1282 removed outlier: 3.809A pdb=" N LEU A1246 " --> pdb=" O GLY A1242 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A1251 " --> pdb=" O GLY A1247 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR A1253 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A1277 " --> pdb=" O GLY A1273 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A1278 " --> pdb=" O ALA A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1356 removed outlier: 3.921A pdb=" N PHE A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A1356 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1384 Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1432 through 1435 Processing helix chain 'A' and resid 1439 through 1443 removed outlier: 3.913A pdb=" N GLU A1443 " --> pdb=" O GLU A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1460 Processing helix chain 'A' and resid 1476 through 1491 Processing helix chain 'A' and resid 1502 through 1509 removed outlier: 4.130A pdb=" N THR A1508 " --> pdb=" O THR A1505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A1509 " --> pdb=" O ILE A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1532 Processing helix chain 'A' and resid 1535 through 1545 Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 692 removed outlier: 7.040A pdb=" N PHE A 675 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER A 685 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 673 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 687 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A 671 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 689 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS A 669 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 691 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 673 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU A 722 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 675 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A 720 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 749 through 751 removed outlier: 6.320A pdb=" N ALA A 749 " --> pdb=" O PHE A 830 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP A 832 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 751 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 696 " --> pdb=" O TRP A 877 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A 879 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N MET A 698 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N MET A 881 " --> pdb=" O MET A 698 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A 700 " --> pdb=" O MET A 881 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 888 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LYS A 882 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1332 removed outlier: 6.910A pdb=" N LYS A1326 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS A1314 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL A1328 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A1313 " --> pdb=" O ASP A1363 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP A1363 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A1315 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE A1361 " --> pdb=" O VAL A1315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1385 through 1388 removed outlier: 6.416A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A1338 " --> pdb=" O THR A1498 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS A1337 " --> pdb=" O LEU A1511 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE A1513 " --> pdb=" O LYS A1337 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A1339 " --> pdb=" O ILE A1513 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET A1515 " --> pdb=" O GLY A1339 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS A1341 " --> pdb=" O MET A1515 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A1512 " --> pdb=" O TYR A1523 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR A1523 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1514 " --> pdb=" O LEU A1521 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398 627 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1410 1.27 - 1.41: 2219 1.41 - 1.54: 5453 1.54 - 1.68: 26 1.68 - 1.82: 76 Bond restraints: 9184 Sorted by residual: bond pdb=" C17 ESV A1606 " pdb=" N3 ESV A1606 " ideal model delta sigma weight residual 1.323 1.459 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" CAY Y01 A1601 " pdb=" OAW Y01 A1601 " ideal model delta sigma weight residual 1.332 1.462 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C11 ESV A1606 " pdb=" N2 ESV A1606 " ideal model delta sigma weight residual 1.380 1.474 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" CAX Y01 A1601 " pdb=" OAH Y01 A1601 " ideal model delta sigma weight residual 1.248 1.332 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C12 ESV A1606 " pdb=" N2 ESV A1606 " ideal model delta sigma weight residual 1.402 1.466 -0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 9179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 12380 2.65 - 5.30: 87 5.30 - 7.94: 15 7.94 - 10.59: 2 10.59 - 13.24: 1 Bond angle restraints: 12485 Sorted by residual: angle pdb=" N2 ESV A1606 " pdb=" C11 ESV A1606 " pdb=" N3 ESV A1606 " ideal model delta sigma weight residual 112.24 125.48 -13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CA GLY A 701 " pdb=" C GLY A 701 " pdb=" N GLN A 702 " ideal model delta sigma weight residual 114.58 117.31 -2.73 8.60e-01 1.35e+00 1.01e+01 angle pdb=" C1' ATP A1605 " pdb=" C2' ATP A1605 " pdb=" C3' ATP A1605 " ideal model delta sigma weight residual 101.56 105.17 -3.61 1.19e+00 7.05e-01 9.19e+00 angle pdb=" C2' ATP A1605 " pdb=" C3' ATP A1605 " pdb=" C4' ATP A1605 " ideal model delta sigma weight residual 102.49 105.44 -2.95 1.00e+00 1.00e+00 8.73e+00 angle pdb=" CAJ Y01 A1601 " pdb=" CAO Y01 A1601 " pdb=" CBB Y01 A1601 " ideal model delta sigma weight residual 115.08 106.36 8.72 3.00e+00 1.11e-01 8.46e+00 ... (remaining 12480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 5346 27.64 - 55.28: 150 55.28 - 82.92: 18 82.92 - 110.57: 0 110.57 - 138.21: 1 Dihedral angle restraints: 5515 sinusoidal: 2194 harmonic: 3321 Sorted by residual: dihedral pdb=" O2A ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PA ADP A1602 " pdb=" PB ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 78.21 -138.21 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" O1B ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PB ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 14.54 -74.54 1 2.00e+01 2.50e-03 1.76e+01 dihedral pdb=" CA PHE A 795 " pdb=" C PHE A 795 " pdb=" N GLY A 796 " pdb=" CA GLY A 796 " ideal model delta harmonic sigma weight residual -180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 5512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1247 0.049 - 0.099: 193 0.099 - 0.148: 45 0.148 - 0.198: 5 0.198 - 0.247: 1 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CBB Y01 A1601 " pdb=" CAC Y01 A1601 " pdb=" CAO Y01 A1601 " pdb=" CBE Y01 A1601 " both_signs ideal model delta sigma weight residual False 2.58 2.33 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C2' ATP A1605 " pdb=" C1' ATP A1605 " pdb=" C3' ATP A1605 " pdb=" O2' ATP A1605 " both_signs ideal model delta sigma weight residual False -2.68 -2.87 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" C3' ATP A1605 " pdb=" C2' ATP A1605 " pdb=" C4' ATP A1605 " pdb=" O3' ATP A1605 " both_signs ideal model delta sigma weight residual False -2.63 -2.82 0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 1488 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1092 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C PHE A1092 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE A1092 " -0.017 2.00e-02 2.50e+03 pdb=" N SER A1093 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 580 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO A 581 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 847 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C MET A 847 " 0.041 2.00e-02 2.50e+03 pdb=" O MET A 847 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 848 " -0.014 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 10 2.52 - 3.12: 7233 3.12 - 3.71: 13971 3.71 - 4.31: 20045 4.31 - 4.90: 33770 Nonbonded interactions: 75029 Sorted by model distance: nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1603 " model vdw 1.926 2.170 nonbonded pdb=" O1B ADP A1602 " pdb="MG MG A1604 " model vdw 2.149 2.170 nonbonded pdb=" OG SER A1349 " pdb="MG MG A1604 " model vdw 2.219 2.170 nonbonded pdb=" OG SER A 708 " pdb="MG MG A1603 " model vdw 2.272 2.170 nonbonded pdb=" OE2 GLU A 717 " pdb=" NH2 ARG A1182 " model vdw 2.300 3.120 ... (remaining 75024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.120 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.930 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.004 0.136 9184 Z= 0.262 Angle : 0.619 13.240 12485 Z= 0.314 Chirality : 0.040 0.247 1491 Planarity : 0.005 0.060 1524 Dihedral : 13.156 138.207 3363 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.46 % Allowed : 4.49 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1127 helix: 0.34 (0.19), residues: 743 sheet: -0.64 (0.58), residues: 69 loop : -1.00 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 727 HIS 0.004 0.001 HIS A1001 PHE 0.010 0.001 PHE A 552 TYR 0.011 0.001 TYR A 290 ARG 0.002 0.000 ARG A1461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.8600 (mtp) cc_final: 0.8382 (ttt) REVERT: A 402 MET cc_start: 0.8189 (mmm) cc_final: 0.7830 (mmm) REVERT: A 422 MET cc_start: 0.8779 (ttp) cc_final: 0.8528 (ttp) REVERT: A 440 MET cc_start: 0.8193 (mmm) cc_final: 0.7973 (mtt) REVERT: A 539 MET cc_start: 0.8175 (mmt) cc_final: 0.7843 (mmm) REVERT: A 698 MET cc_start: 0.8495 (mtp) cc_final: 0.7926 (mtp) REVERT: A 724 LYS cc_start: 0.7892 (mttt) cc_final: 0.7579 (mmmt) REVERT: A 795 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: A 808 LEU cc_start: 0.9007 (mt) cc_final: 0.8628 (mt) REVERT: A 836 SER cc_start: 0.8573 (p) cc_final: 0.8353 (m) REVERT: A 881 MET cc_start: 0.8379 (mtp) cc_final: 0.8091 (mtm) REVERT: A 910 MET cc_start: 0.8531 (mtp) cc_final: 0.8243 (mtp) REVERT: A 1004 ILE cc_start: 0.8121 (mt) cc_final: 0.7668 (mm) REVERT: A 1013 THR cc_start: 0.7894 (m) cc_final: 0.7552 (p) REVERT: A 1078 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7570 (mtm110) REVERT: A 1126 TYR cc_start: 0.8275 (t80) cc_final: 0.8051 (t80) REVERT: A 1165 LEU cc_start: 0.8785 (tt) cc_final: 0.8485 (mt) REVERT: A 1213 ARG cc_start: 0.8017 (mmt-90) cc_final: 0.7411 (ttp80) REVERT: A 1358 MET cc_start: 0.9345 (mmm) cc_final: 0.9007 (mtp) REVERT: A 1409 CYS cc_start: 0.6715 (m) cc_final: 0.6473 (m) REVERT: A 1508 THR cc_start: 0.8632 (p) cc_final: 0.8372 (t) outliers start: 14 outliers final: 4 residues processed: 200 average time/residue: 0.2659 time to fit residues: 70.0708 Evaluate side-chains 110 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1410 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 702 GLN A 719 GLN A 911 ASN A1102 HIS A1379 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9184 Z= 0.226 Angle : 0.584 9.808 12485 Z= 0.294 Chirality : 0.041 0.195 1491 Planarity : 0.005 0.052 1524 Dihedral : 8.603 138.720 1346 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.71 % Allowed : 10.02 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1127 helix: 1.87 (0.18), residues: 755 sheet: -0.38 (0.60), residues: 69 loop : -0.45 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1260 HIS 0.005 0.001 HIS A 576 PHE 0.018 0.001 PHE A1149 TYR 0.009 0.001 TYR A 305 ARG 0.006 0.000 ARG A1150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 402 MET cc_start: 0.8313 (mmm) cc_final: 0.8081 (mmm) REVERT: A 422 MET cc_start: 0.8761 (ttp) cc_final: 0.8492 (ttp) REVERT: A 440 MET cc_start: 0.7977 (mmm) cc_final: 0.7619 (mtm) REVERT: A 539 MET cc_start: 0.8158 (mmt) cc_final: 0.7888 (mmm) REVERT: A 698 MET cc_start: 0.8540 (mtp) cc_final: 0.8075 (mtp) REVERT: A 724 LYS cc_start: 0.7814 (mttt) cc_final: 0.7601 (mmmt) REVERT: A 795 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: A 881 MET cc_start: 0.8460 (mtp) cc_final: 0.7971 (mtm) REVERT: A 1013 THR cc_start: 0.7481 (m) cc_final: 0.7213 (p) REVERT: A 1213 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.7371 (ttp80) REVERT: A 1358 MET cc_start: 0.9386 (mmm) cc_final: 0.9097 (mtp) REVERT: A 1443 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7877 (mp0) REVERT: A 1508 THR cc_start: 0.8664 (p) cc_final: 0.8413 (t) outliers start: 26 outliers final: 15 residues processed: 134 average time/residue: 0.2667 time to fit residues: 47.8671 Evaluate side-chains 108 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9184 Z= 0.191 Angle : 0.541 8.140 12485 Z= 0.269 Chirality : 0.040 0.206 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.436 137.980 1344 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.67 % Allowed : 13.57 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.25), residues: 1127 helix: 2.45 (0.19), residues: 746 sheet: -0.18 (0.63), residues: 69 loop : -0.41 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1260 HIS 0.013 0.001 HIS A1379 PHE 0.013 0.001 PHE A 356 TYR 0.010 0.001 TYR A1126 ARG 0.004 0.000 ARG A1150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.030 Fit side-chains REVERT: A 422 MET cc_start: 0.8786 (ttp) cc_final: 0.8491 (ttp) REVERT: A 440 MET cc_start: 0.8028 (mmm) cc_final: 0.7477 (mtt) REVERT: A 539 MET cc_start: 0.7897 (mmt) cc_final: 0.7578 (mmm) REVERT: A 698 MET cc_start: 0.8653 (mtp) cc_final: 0.8291 (mtp) REVERT: A 724 LYS cc_start: 0.7806 (mttt) cc_final: 0.7587 (mmmt) REVERT: A 795 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: A 881 MET cc_start: 0.8516 (mtp) cc_final: 0.7982 (mtm) REVERT: A 883 ASP cc_start: 0.8181 (m-30) cc_final: 0.7934 (m-30) REVERT: A 1013 THR cc_start: 0.7417 (m) cc_final: 0.7100 (p) REVERT: A 1213 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7269 (ttp80) REVERT: A 1358 MET cc_start: 0.9307 (mmm) cc_final: 0.9091 (mtp) REVERT: A 1391 ASP cc_start: 0.7998 (p0) cc_final: 0.7785 (p0) REVERT: A 1443 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7921 (mp0) REVERT: A 1508 THR cc_start: 0.8707 (p) cc_final: 0.8482 (t) outliers start: 16 outliers final: 9 residues processed: 108 average time/residue: 0.2511 time to fit residues: 37.0575 Evaluate side-chains 95 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1379 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN A 848 GLN A1212 ASN A1311 HIS A1379 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9184 Z= 0.346 Angle : 0.625 10.061 12485 Z= 0.307 Chirality : 0.044 0.239 1491 Planarity : 0.004 0.047 1524 Dihedral : 9.023 155.167 1344 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.24 % Allowed : 12.84 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.25), residues: 1127 helix: 2.20 (0.18), residues: 751 sheet: 0.13 (0.68), residues: 63 loop : -0.65 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1302 HIS 0.006 0.001 HIS A1001 PHE 0.013 0.002 PHE A 356 TYR 0.009 0.001 TYR A1317 ARG 0.004 0.001 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.093 Fit side-chains REVERT: A 278 HIS cc_start: 0.7183 (m90) cc_final: 0.6542 (t70) REVERT: A 422 MET cc_start: 0.8801 (ttp) cc_final: 0.8486 (ttp) REVERT: A 440 MET cc_start: 0.8174 (mmm) cc_final: 0.7784 (mtm) REVERT: A 539 MET cc_start: 0.8016 (mmt) cc_final: 0.7718 (mmm) REVERT: A 569 PHE cc_start: 0.8078 (m-80) cc_final: 0.7875 (m-10) REVERT: A 698 MET cc_start: 0.8646 (mtp) cc_final: 0.8311 (mtp) REVERT: A 795 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: A 883 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: A 887 LEU cc_start: 0.9187 (tt) cc_final: 0.8933 (tp) REVERT: A 1013 THR cc_start: 0.7788 (m) cc_final: 0.7439 (p) REVERT: A 1143 TYR cc_start: 0.7979 (t80) cc_final: 0.7691 (t80) REVERT: A 1213 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7391 (ttp80) REVERT: A 1358 MET cc_start: 0.9225 (mmm) cc_final: 0.8942 (mtp) REVERT: A 1508 THR cc_start: 0.8794 (p) cc_final: 0.8587 (t) outliers start: 31 outliers final: 20 residues processed: 125 average time/residue: 0.2502 time to fit residues: 44.8492 Evaluate side-chains 114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.0050 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN A 807 ASN A1065 HIS A1311 HIS A1379 HIS A1402 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9184 Z= 0.183 Angle : 0.526 8.230 12485 Z= 0.260 Chirality : 0.039 0.204 1491 Planarity : 0.004 0.045 1524 Dihedral : 8.787 155.140 1342 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.61 % Allowed : 13.99 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.25), residues: 1127 helix: 2.53 (0.19), residues: 752 sheet: 0.15 (0.69), residues: 63 loop : -0.60 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 727 HIS 0.009 0.001 HIS A1379 PHE 0.011 0.001 PHE A 356 TYR 0.009 0.001 TYR A1257 ARG 0.005 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.263 Fit side-chains REVERT: A 422 MET cc_start: 0.8804 (ttp) cc_final: 0.8498 (ttp) REVERT: A 440 MET cc_start: 0.8104 (mmm) cc_final: 0.7891 (ttm) REVERT: A 539 MET cc_start: 0.7923 (mmt) cc_final: 0.7581 (mmm) REVERT: A 699 ILE cc_start: 0.8759 (mt) cc_final: 0.8540 (mt) REVERT: A 881 MET cc_start: 0.8661 (mtp) cc_final: 0.8349 (mtm) REVERT: A 883 ASP cc_start: 0.8171 (m-30) cc_final: 0.7895 (m-30) REVERT: A 1013 THR cc_start: 0.7366 (m) cc_final: 0.7048 (p) REVERT: A 1213 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7304 (ttp80) REVERT: A 1391 ASP cc_start: 0.8169 (p0) cc_final: 0.7919 (p0) REVERT: A 1508 THR cc_start: 0.8836 (p) cc_final: 0.8620 (t) outliers start: 25 outliers final: 16 residues processed: 123 average time/residue: 0.2295 time to fit residues: 39.2133 Evaluate side-chains 108 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1097 ASN A1311 HIS A1379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9184 Z= 0.198 Angle : 0.529 9.046 12485 Z= 0.260 Chirality : 0.040 0.199 1491 Planarity : 0.004 0.046 1524 Dihedral : 8.669 156.199 1340 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.40 % Allowed : 14.93 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.25), residues: 1127 helix: 2.58 (0.19), residues: 754 sheet: 0.16 (0.69), residues: 63 loop : -0.53 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 727 HIS 0.004 0.001 HIS A1001 PHE 0.012 0.001 PHE A 569 TYR 0.009 0.001 TYR A1257 ARG 0.006 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.990 Fit side-chains REVERT: A 285 ILE cc_start: 0.8879 (mt) cc_final: 0.8643 (mt) REVERT: A 422 MET cc_start: 0.8792 (ttp) cc_final: 0.8490 (ttp) REVERT: A 440 MET cc_start: 0.8123 (mmm) cc_final: 0.7896 (ttm) REVERT: A 539 MET cc_start: 0.7917 (mmt) cc_final: 0.7547 (mmm) REVERT: A 881 MET cc_start: 0.8651 (mtp) cc_final: 0.8282 (mtm) REVERT: A 883 ASP cc_start: 0.8159 (m-30) cc_final: 0.7885 (m-30) REVERT: A 1013 THR cc_start: 0.7370 (m) cc_final: 0.7045 (p) REVERT: A 1391 ASP cc_start: 0.8185 (p0) cc_final: 0.7942 (p0) REVERT: A 1508 THR cc_start: 0.8915 (p) cc_final: 0.8711 (t) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.2202 time to fit residues: 37.0886 Evaluate side-chains 113 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1311 HIS A1379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9184 Z= 0.188 Angle : 0.525 8.852 12485 Z= 0.256 Chirality : 0.039 0.197 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.584 155.495 1340 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.03 % Allowed : 14.51 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.25), residues: 1127 helix: 2.61 (0.19), residues: 754 sheet: 0.15 (0.69), residues: 63 loop : -0.52 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 727 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 356 TYR 0.009 0.001 TYR A1257 ARG 0.007 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.079 Fit side-chains REVERT: A 422 MET cc_start: 0.8779 (ttp) cc_final: 0.8485 (ttp) REVERT: A 440 MET cc_start: 0.8127 (mmm) cc_final: 0.7899 (ttm) REVERT: A 539 MET cc_start: 0.7891 (mmt) cc_final: 0.7510 (mmm) REVERT: A 881 MET cc_start: 0.8649 (mtp) cc_final: 0.8250 (mtm) REVERT: A 883 ASP cc_start: 0.8150 (m-30) cc_final: 0.7875 (m-30) REVERT: A 1013 THR cc_start: 0.7351 (m) cc_final: 0.7024 (p) REVERT: A 1281 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6752 (t80) REVERT: A 1391 ASP cc_start: 0.8203 (p0) cc_final: 0.7956 (p0) REVERT: A 1508 THR cc_start: 0.8939 (p) cc_final: 0.8720 (t) outliers start: 29 outliers final: 22 residues processed: 121 average time/residue: 0.2162 time to fit residues: 37.6871 Evaluate side-chains 121 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1311 HIS A1379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9184 Z= 0.204 Angle : 0.532 8.939 12485 Z= 0.259 Chirality : 0.040 0.194 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.561 155.178 1340 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.13 % Allowed : 14.51 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.25), residues: 1127 helix: 2.59 (0.19), residues: 755 sheet: 0.23 (0.69), residues: 63 loop : -0.51 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1302 HIS 0.008 0.001 HIS A1379 PHE 0.011 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.005 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 1.066 Fit side-chains REVERT: A 422 MET cc_start: 0.8784 (ttp) cc_final: 0.8484 (ttp) REVERT: A 440 MET cc_start: 0.8139 (mmm) cc_final: 0.7908 (ttm) REVERT: A 539 MET cc_start: 0.7895 (mmt) cc_final: 0.7509 (mmm) REVERT: A 705 CYS cc_start: 0.8653 (m) cc_final: 0.7972 (m) REVERT: A 883 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 1013 THR cc_start: 0.7344 (m) cc_final: 0.7019 (p) REVERT: A 1281 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6687 (t80) REVERT: A 1284 MET cc_start: 0.7168 (ttm) cc_final: 0.6775 (ttt) REVERT: A 1391 ASP cc_start: 0.8212 (p0) cc_final: 0.7966 (p0) outliers start: 30 outliers final: 22 residues processed: 118 average time/residue: 0.2385 time to fit residues: 40.1499 Evaluate side-chains 117 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9184 Z= 0.204 Angle : 0.532 8.939 12485 Z= 0.259 Chirality : 0.040 0.194 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.561 155.178 1340 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.51 % Allowed : 15.45 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.25), residues: 1127 helix: 2.59 (0.19), residues: 755 sheet: 0.23 (0.69), residues: 63 loop : -0.51 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1302 HIS 0.008 0.001 HIS A1379 PHE 0.011 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.005 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.068 Fit side-chains REVERT: A 422 MET cc_start: 0.8784 (ttp) cc_final: 0.8484 (ttp) REVERT: A 440 MET cc_start: 0.8146 (mmm) cc_final: 0.7908 (ttm) REVERT: A 539 MET cc_start: 0.7895 (mmt) cc_final: 0.7509 (mmm) REVERT: A 705 CYS cc_start: 0.8658 (m) cc_final: 0.7972 (m) REVERT: A 883 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 1013 THR cc_start: 0.7346 (m) cc_final: 0.7019 (p) REVERT: A 1281 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6687 (t80) REVERT: A 1284 MET cc_start: 0.7167 (ttm) cc_final: 0.6775 (ttt) REVERT: A 1391 ASP cc_start: 0.8210 (p0) cc_final: 0.7966 (p0) outliers start: 24 outliers final: 22 residues processed: 110 average time/residue: 0.2400 time to fit residues: 37.6080 Evaluate side-chains 117 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A1186 HIS A1311 HIS A1379 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9184 Z= 0.172 Angle : 0.517 8.724 12485 Z= 0.251 Chirality : 0.039 0.192 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.470 153.917 1340 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.40 % Allowed : 15.55 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.25), residues: 1127 helix: 2.67 (0.19), residues: 756 sheet: 0.31 (0.70), residues: 63 loop : -0.47 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1302 HIS 0.003 0.001 HIS A1001 PHE 0.010 0.001 PHE A 356 TYR 0.007 0.001 TYR A1257 ARG 0.005 0.000 ARG A1078 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.089 Fit side-chains REVERT: A 278 HIS cc_start: 0.7493 (m90) cc_final: 0.6509 (t70) REVERT: A 422 MET cc_start: 0.8753 (ttp) cc_final: 0.8455 (ttp) REVERT: A 440 MET cc_start: 0.8143 (mmm) cc_final: 0.7903 (ttm) REVERT: A 539 MET cc_start: 0.7861 (mmt) cc_final: 0.7458 (mmm) REVERT: A 705 CYS cc_start: 0.8410 (m) cc_final: 0.7659 (m) REVERT: A 883 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: A 887 LEU cc_start: 0.9018 (tt) cc_final: 0.8808 (tp) REVERT: A 1013 THR cc_start: 0.7258 (m) cc_final: 0.6970 (p) REVERT: A 1281 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6742 (t80) REVERT: A 1284 MET cc_start: 0.7214 (ttm) cc_final: 0.6920 (ttt) REVERT: A 1391 ASP cc_start: 0.8223 (p0) cc_final: 0.7983 (p0) outliers start: 23 outliers final: 21 residues processed: 117 average time/residue: 0.2150 time to fit residues: 35.6505 Evaluate side-chains 118 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1311 HIS A1379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109741 restraints weight = 11573.988| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.20 r_work: 0.3106 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9184 Z= 0.198 Angle : 0.528 8.855 12485 Z= 0.256 Chirality : 0.040 0.187 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.455 153.599 1340 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.92 % Allowed : 14.82 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.25), residues: 1127 helix: 2.64 (0.19), residues: 756 sheet: 0.24 (0.68), residues: 63 loop : -0.45 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1302 HIS 0.005 0.001 HIS A1379 PHE 0.011 0.001 PHE A 356 TYR 0.007 0.001 TYR A1257 ARG 0.005 0.000 ARG A1078 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1982.55 seconds wall clock time: 37 minutes 21.07 seconds (2241.07 seconds total)