Starting phenix.real_space_refine on Fri Mar 14 05:06:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vls_32025/03_2025/7vls_32025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vls_32025/03_2025/7vls_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_32025/03_2025/7vls_32025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vls_32025/03_2025/7vls_32025.map" model { file = "/net/cci-nas-00/data/ceres_data/7vls_32025/03_2025/7vls_32025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vls_32025/03_2025/7vls_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-5624/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: 5.51, per 1000 atoms: 0.61 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: 2.53 Conformation dependent library (CDL) restraints added in 1.0 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: 1.06 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: 3.46 Time building geometry restraints manager: 2.96 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: 0.350 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- 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 : 0.964 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: 0.2569 time to fit residues: 67.7533 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 : 0.911 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111370 restraints weight = 11316.756| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.14 r_work: 0.3025 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 : 0.886 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8482 (mmm) REVERT: A 402 MET cc_start: 0.8069 (mmm) cc_final: 0.7764 (mmm) REVERT: A 440 MET cc_start: 0.7985 (mmm) cc_final: 0.7174 (mtm) REVERT: A 539 MET cc_start: 0.7601 (mmt) cc_final: 0.7294 (mmm) REVERT: A 698 MET cc_start: 0.8737 (mtp) cc_final: 0.8207 (mtp) REVERT: A 724 LYS cc_start: 0.7715 (mttt) cc_final: 0.7337 (mmmt) REVERT: A 795 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: A 881 MET cc_start: 0.8477 (mtp) cc_final: 0.7892 (mtm) REVERT: A 1013 THR cc_start: 0.6720 (m) cc_final: 0.6362 (p) REVERT: A 1126 TYR cc_start: 0.8412 (t80) cc_final: 0.8132 (t80) REVERT: A 1213 ARG cc_start: 0.7758 (mmt-90) cc_final: 0.6346 (ttp80) REVERT: A 1276 LYS cc_start: 0.8127 (tttp) cc_final: 0.7708 (tptm) REVERT: A 1284 MET cc_start: 0.8039 (ttp) cc_final: 0.7804 (ttm) REVERT: A 1358 MET cc_start: 0.9409 (mmm) cc_final: 0.9069 (mtp) REVERT: A 1443 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7826 (mp0) REVERT: A 1508 THR cc_start: 0.8771 (p) cc_final: 0.8514 (t) outliers start: 26 outliers final: 15 residues processed: 134 average time/residue: 0.2340 time to fit residues: 42.8303 Evaluate side-chains 110 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET 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 21 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111283 restraints weight = 11477.091| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.17 r_work: 0.3100 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2749 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= 0.187 Angle : 0.538 8.602 12485 Z= 0.267 Chirality : 0.040 0.196 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.437 137.869 1344 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.77 % Allowed : 13.78 % Favored : 84.45 % 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: -0.17 (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 0.016 0.001 HIS A1379 PHE 0.013 0.001 PHE A 356 TYR 0.009 0.001 TYR A1317 ARG 0.004 0.000 ARG A1078 *********************** 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 114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.053 Fit side-chains REVERT: A 255 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8271 (mmm) REVERT: A 402 MET cc_start: 0.8134 (mmm) cc_final: 0.7924 (mmm) REVERT: A 440 MET cc_start: 0.8150 (mmm) cc_final: 0.7159 (mtt) REVERT: A 539 MET cc_start: 0.7577 (mmt) cc_final: 0.7231 (mmm) REVERT: A 698 MET cc_start: 0.8885 (mtp) cc_final: 0.8479 (mtp) REVERT: A 724 LYS cc_start: 0.7824 (mttt) cc_final: 0.7460 (mmmt) REVERT: A 795 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: A 881 MET cc_start: 0.8536 (mtp) cc_final: 0.7988 (mtm) REVERT: A 883 ASP cc_start: 0.8255 (m-30) cc_final: 0.8004 (m-30) REVERT: A 983 THR cc_start: 0.8287 (m) cc_final: 0.8060 (p) REVERT: A 1013 THR cc_start: 0.6811 (m) cc_final: 0.6421 (p) REVERT: A 1126 TYR cc_start: 0.8554 (t80) cc_final: 0.8231 (t80) REVERT: A 1213 ARG cc_start: 0.7731 (mmt-90) cc_final: 0.6473 (ttp80) REVERT: A 1276 LYS cc_start: 0.8272 (tttp) cc_final: 0.7866 (tptm) REVERT: A 1358 MET cc_start: 0.9338 (mmm) cc_final: 0.9126 (mtp) REVERT: A 1443 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7999 (mp0) REVERT: A 1508 THR cc_start: 0.8819 (p) cc_final: 0.8576 (t) outliers start: 17 outliers final: 8 residues processed: 109 average time/residue: 0.2452 time to fit residues: 36.5223 Evaluate side-chains 97 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 42 optimal weight: 0.0020 chunk 106 optimal weight: 4.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1212 ASN A1311 HIS A1379 HIS A1402 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109816 restraints weight = 11536.705| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.21 r_work: 0.3093 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3089 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= 0.192 Angle : 0.529 8.235 12485 Z= 0.259 Chirality : 0.040 0.190 1491 Planarity : 0.004 0.046 1524 Dihedral : 8.446 142.688 1344 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.51 % Allowed : 13.47 % Favored : 84.03 % 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: 2.46 (0.25), residues: 1127 helix: 2.59 (0.19), residues: 751 sheet: -0.06 (0.65), residues: 69 loop : -0.42 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1260 HIS 0.004 0.001 HIS A1001 PHE 0.011 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.004 0.000 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 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.203 Fit side-chains REVERT: A 255 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8285 (mmm) REVERT: A 278 HIS cc_start: 0.7331 (m90) cc_final: 0.6334 (t70) REVERT: A 440 MET cc_start: 0.8156 (mmm) cc_final: 0.7160 (mtt) REVERT: A 539 MET cc_start: 0.7509 (mmt) cc_final: 0.7119 (mmm) REVERT: A 698 MET cc_start: 0.8840 (mtp) cc_final: 0.8468 (mtp) REVERT: A 699 ILE cc_start: 0.8768 (mt) cc_final: 0.8512 (mt) REVERT: A 705 CYS cc_start: 0.8512 (m) cc_final: 0.7796 (m) REVERT: A 724 LYS cc_start: 0.7720 (mttt) cc_final: 0.7514 (tptp) REVERT: A 881 MET cc_start: 0.8681 (mtp) cc_final: 0.8212 (mtm) REVERT: A 883 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: A 983 THR cc_start: 0.8301 (m) cc_final: 0.8095 (p) REVERT: A 1013 THR cc_start: 0.6760 (m) cc_final: 0.6367 (p) REVERT: A 1126 TYR cc_start: 0.8576 (t80) cc_final: 0.8205 (t80) REVERT: A 1213 ARG cc_start: 0.7769 (mmt-90) cc_final: 0.6456 (ttp80) REVERT: A 1276 LYS cc_start: 0.8241 (tttp) cc_final: 0.7832 (tptm) REVERT: A 1284 MET cc_start: 0.8328 (ttm) cc_final: 0.8037 (ttm) REVERT: A 1443 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8071 (mp0) REVERT: A 1508 THR cc_start: 0.8838 (p) cc_final: 0.8629 (t) outliers start: 24 outliers final: 15 residues processed: 121 average time/residue: 0.2417 time to fit residues: 41.5213 Evaluate side-chains 106 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 360 ILE 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 681 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 883 ASP 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 1379 HIS Chi-restraints excluded: chain A residue 1486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 807 ASN A1311 HIS A1379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109831 restraints weight = 11505.354| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.20 r_work: 0.3093 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3226 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 : 0.515 8.462 12485 Z= 0.253 Chirality : 0.039 0.189 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.411 144.961 1342 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.82 % Allowed : 13.05 % Favored : 84.13 % 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: 2.53 (0.25), residues: 1127 helix: 2.65 (0.19), residues: 751 sheet: -0.02 (0.65), residues: 69 loop : -0.42 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1260 HIS 0.004 0.001 HIS A1001 PHE 0.012 0.001 PHE A 356 TYR 0.008 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 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.662 Fit side-chains REVERT: A 255 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8280 (mmm) REVERT: A 387 MET cc_start: 0.8744 (ttp) cc_final: 0.8473 (ttm) REVERT: A 440 MET cc_start: 0.8165 (mmm) cc_final: 0.7636 (ttm) REVERT: A 539 MET cc_start: 0.7496 (mmt) cc_final: 0.7083 (mmm) REVERT: A 698 MET cc_start: 0.8843 (mtp) cc_final: 0.8477 (mtp) REVERT: A 705 CYS cc_start: 0.8469 (m) cc_final: 0.7902 (m) REVERT: A 724 LYS cc_start: 0.7815 (mttt) cc_final: 0.7548 (tptp) REVERT: A 883 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: A 1013 THR cc_start: 0.6739 (m) cc_final: 0.6373 (p) REVERT: A 1096 THR cc_start: 0.8542 (m) cc_final: 0.8296 (m) REVERT: A 1115 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8818 (tt) REVERT: A 1126 TYR cc_start: 0.8590 (t80) cc_final: 0.8197 (t80) REVERT: A 1213 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.6483 (ttp80) REVERT: A 1276 LYS cc_start: 0.8243 (tttp) cc_final: 0.7837 (tptm) REVERT: A 1284 MET cc_start: 0.8264 (ttm) cc_final: 0.8008 (ttm) REVERT: A 1443 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8063 (mp0) REVERT: A 1508 THR cc_start: 0.8904 (p) cc_final: 0.8667 (t) outliers start: 27 outliers final: 17 residues processed: 120 average time/residue: 0.3558 time to fit residues: 60.7647 Evaluate side-chains 111 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 418 THR 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 840 ILE Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1115 LEU 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 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 97 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.135975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110727 restraints weight = 11510.046| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.21 r_work: 0.3103 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3357 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= 0.171 Angle : 0.506 8.807 12485 Z= 0.249 Chirality : 0.039 0.190 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.421 145.419 1342 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.61 % Allowed : 13.57 % Favored : 83.82 % 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: 2.61 (0.26), residues: 1127 helix: 2.69 (0.19), residues: 753 sheet: 0.32 (0.69), residues: 63 loop : -0.45 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1260 HIS 0.007 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 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 120 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.909 Fit side-chains REVERT: A 387 MET cc_start: 0.8756 (ttp) cc_final: 0.8487 (ttm) REVERT: A 440 MET cc_start: 0.8173 (mmm) cc_final: 0.7647 (ttm) REVERT: A 539 MET cc_start: 0.7476 (mmt) cc_final: 0.7049 (mmm) REVERT: A 698 MET cc_start: 0.8818 (mtp) cc_final: 0.8405 (mtp) REVERT: A 705 CYS cc_start: 0.8425 (m) cc_final: 0.7732 (m) REVERT: A 724 LYS cc_start: 0.7884 (mttt) cc_final: 0.7596 (tptp) REVERT: A 881 MET cc_start: 0.8732 (mtp) cc_final: 0.8239 (mtm) REVERT: A 883 ASP cc_start: 0.8202 (m-30) cc_final: 0.7891 (m-30) REVERT: A 1013 THR cc_start: 0.6710 (m) cc_final: 0.6342 (p) REVERT: A 1096 THR cc_start: 0.8531 (m) cc_final: 0.8310 (m) REVERT: A 1115 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8831 (tt) REVERT: A 1126 TYR cc_start: 0.8601 (t80) cc_final: 0.8258 (t80) REVERT: A 1213 ARG cc_start: 0.7668 (mmt-90) cc_final: 0.6316 (ttp80) REVERT: A 1276 LYS cc_start: 0.8233 (tttp) cc_final: 0.7825 (tptm) REVERT: A 1284 MET cc_start: 0.8215 (ttm) cc_final: 0.7754 (ttm) REVERT: A 1358 MET cc_start: 0.9062 (mtp) cc_final: 0.8612 (mtp) REVERT: A 1440 GLU cc_start: 0.7495 (tt0) cc_final: 0.7240 (tt0) REVERT: A 1443 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7982 (mp0) REVERT: A 1508 THR cc_start: 0.8914 (p) cc_final: 0.8690 (t) outliers start: 25 outliers final: 18 residues processed: 115 average time/residue: 0.2355 time to fit residues: 37.1036 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 : 0.899 ------------------------------------------------------------------------------- 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 987 PHE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1253 THR 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 49 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 GLN A1311 HIS A1379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106763 restraints weight = 11821.317| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.22 r_work: 0.3078 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9184 Z= 0.291 Angle : 0.566 9.802 12485 Z= 0.278 Chirality : 0.041 0.181 1491 Planarity : 0.004 0.046 1524 Dihedral : 8.579 151.168 1340 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.82 % Allowed : 13.57 % Favored : 83.61 % 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: 2.36 (0.25), residues: 1127 helix: 2.50 (0.19), residues: 754 sheet: 0.35 (0.69), residues: 63 loop : -0.56 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1260 HIS 0.015 0.001 HIS A1379 PHE 0.013 0.001 PHE A 356 TYR 0.009 0.001 TYR A1257 ARG 0.006 0.001 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 124 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.442 Fit side-chains REVERT: A 387 MET cc_start: 0.8843 (ttp) cc_final: 0.8559 (ttm) REVERT: A 440 MET cc_start: 0.8273 (mmm) cc_final: 0.7272 (mtt) REVERT: A 539 MET cc_start: 0.7576 (mmt) cc_final: 0.7168 (mmm) REVERT: A 698 MET cc_start: 0.8854 (mtp) cc_final: 0.8480 (mtp) REVERT: A 705 CYS cc_start: 0.8564 (m) cc_final: 0.7929 (m) REVERT: A 724 LYS cc_start: 0.7847 (mttt) cc_final: 0.7617 (tptp) REVERT: A 881 MET cc_start: 0.8805 (mtp) cc_final: 0.8420 (mtm) REVERT: A 883 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: A 1013 THR cc_start: 0.6783 (m) cc_final: 0.6408 (p) REVERT: A 1126 TYR cc_start: 0.8656 (t80) cc_final: 0.8301 (t80) REVERT: A 1276 LYS cc_start: 0.8346 (tttp) cc_final: 0.7913 (tptm) REVERT: A 1284 MET cc_start: 0.8196 (ttm) cc_final: 0.7758 (ttm) REVERT: A 1360 ASP cc_start: 0.8450 (m-30) cc_final: 0.8093 (m-30) REVERT: A 1379 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.7349 (t70) REVERT: A 1508 THR cc_start: 0.8946 (p) cc_final: 0.8721 (t) outliers start: 27 outliers final: 17 residues processed: 118 average time/residue: 0.2289 time to fit residues: 38.7984 Evaluate side-chains 112 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 883 ASP Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 994 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 103 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 HIS A1311 HIS A1379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109327 restraints weight = 11698.883| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.28 r_work: 0.3034 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9184 Z= 0.163 Angle : 0.513 8.522 12485 Z= 0.251 Chirality : 0.039 0.196 1491 Planarity : 0.004 0.044 1524 Dihedral : 8.433 148.584 1340 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.09 % Allowed : 14.61 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.26), residues: 1127 helix: 2.71 (0.19), residues: 753 sheet: 0.35 (0.69), residues: 63 loop : -0.47 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1260 HIS 0.006 0.001 HIS A1379 PHE 0.010 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.007 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 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.074 Fit side-chains REVERT: A 278 HIS cc_start: 0.7491 (m90) cc_final: 0.6259 (t70) REVERT: A 387 MET cc_start: 0.8765 (ttp) cc_final: 0.8533 (ttm) REVERT: A 440 MET cc_start: 0.8190 (mmm) cc_final: 0.7641 (ttm) REVERT: A 539 MET cc_start: 0.7445 (mmt) cc_final: 0.7010 (mmm) REVERT: A 698 MET cc_start: 0.8811 (mtp) cc_final: 0.8461 (mtp) REVERT: A 705 CYS cc_start: 0.8391 (m) cc_final: 0.7671 (m) REVERT: A 724 LYS cc_start: 0.7783 (mttt) cc_final: 0.7544 (tptp) REVERT: A 881 MET cc_start: 0.8777 (mtp) cc_final: 0.8369 (mtm) REVERT: A 883 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: A 1013 THR cc_start: 0.6632 (m) cc_final: 0.6272 (p) REVERT: A 1108 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7260 (tp30) REVERT: A 1126 TYR cc_start: 0.8677 (t80) cc_final: 0.8287 (t80) REVERT: A 1263 ARG cc_start: 0.8265 (mmm160) cc_final: 0.8044 (mmm160) REVERT: A 1276 LYS cc_start: 0.8191 (tttp) cc_final: 0.7775 (tptm) REVERT: A 1281 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6770 (t80) REVERT: A 1284 MET cc_start: 0.8039 (ttm) cc_final: 0.7269 (ttm) REVERT: A 1360 ASP cc_start: 0.8438 (m-30) cc_final: 0.8235 (m-30) REVERT: A 1379 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7164 (t-90) REVERT: A 1508 THR cc_start: 0.9007 (p) cc_final: 0.8796 (t) outliers start: 20 outliers final: 16 residues processed: 120 average time/residue: 0.2294 time to fit residues: 38.7269 Evaluate side-chains 114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 413 LEU 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 883 ASP Chi-restraints excluded: chain A residue 987 PHE 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 1514 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111592 restraints weight = 11672.095| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.05 r_work: 0.3062 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3663 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= 0.180 Angle : 0.521 8.925 12485 Z= 0.254 Chirality : 0.039 0.198 1491 Planarity : 0.004 0.045 1524 Dihedral : 8.383 148.240 1340 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.09 % Allowed : 14.82 % Favored : 83.09 % 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: 2.64 (0.25), residues: 1127 helix: 2.71 (0.19), residues: 754 sheet: 0.38 (0.69), residues: 63 loop : -0.43 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1260 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.008 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 118 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.040 Fit side-chains REVERT: A 278 HIS cc_start: 0.7435 (m90) cc_final: 0.6207 (t70) REVERT: A 387 MET cc_start: 0.8573 (ttp) cc_final: 0.8339 (ttm) REVERT: A 440 MET cc_start: 0.7934 (mmm) cc_final: 0.7366 (ttm) REVERT: A 539 MET cc_start: 0.7162 (mmt) cc_final: 0.6723 (mmm) REVERT: A 698 MET cc_start: 0.8728 (mtp) cc_final: 0.8393 (mtp) REVERT: A 705 CYS cc_start: 0.8343 (m) cc_final: 0.7490 (m) REVERT: A 724 LYS cc_start: 0.7658 (mttt) cc_final: 0.7386 (tptp) REVERT: A 881 MET cc_start: 0.8736 (mtp) cc_final: 0.8253 (mtm) REVERT: A 883 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: A 1013 THR cc_start: 0.6398 (m) cc_final: 0.6062 (p) REVERT: A 1108 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7132 (tp30) REVERT: A 1126 TYR cc_start: 0.8628 (t80) cc_final: 0.8211 (t80) REVERT: A 1263 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7884 (mmm160) REVERT: A 1276 LYS cc_start: 0.7976 (tttp) cc_final: 0.7537 (tptm) REVERT: A 1281 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6658 (t80) REVERT: A 1284 MET cc_start: 0.7903 (ttm) cc_final: 0.7088 (ttm) REVERT: A 1360 ASP cc_start: 0.8381 (m-30) cc_final: 0.8150 (m-30) REVERT: A 1379 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6698 (t-90) REVERT: A 1407 CYS cc_start: 0.8583 (t) cc_final: 0.8335 (t) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.2172 time to fit residues: 34.5206 Evaluate side-chains 111 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 413 LEU 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 883 ASP Chi-restraints excluded: chain A residue 987 PHE 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 1514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111344 restraints weight = 11782.939| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.06 r_work: 0.3085 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3664 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= 0.180 Angle : 0.521 8.925 12485 Z= 0.254 Chirality : 0.039 0.198 1491 Planarity : 0.004 0.045 1524 Dihedral : 8.385 148.240 1340 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.98 % Allowed : 15.14 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.64 (0.25), residues: 1127 helix: 2.71 (0.19), residues: 754 sheet: 0.38 (0.69), residues: 63 loop : -0.43 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1260 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.008 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 111 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.941 Fit side-chains REVERT: A 278 HIS cc_start: 0.7481 (m90) cc_final: 0.6251 (t70) REVERT: A 387 MET cc_start: 0.8695 (ttp) cc_final: 0.8449 (ttm) REVERT: A 440 MET cc_start: 0.8037 (mmm) cc_final: 0.7483 (ttm) REVERT: A 539 MET cc_start: 0.7319 (mmt) cc_final: 0.6874 (mmm) REVERT: A 698 MET cc_start: 0.8785 (mtp) cc_final: 0.8444 (mtp) REVERT: A 705 CYS cc_start: 0.8390 (m) cc_final: 0.7599 (m) REVERT: A 724 LYS cc_start: 0.7719 (mttt) cc_final: 0.7487 (tptp) REVERT: A 881 MET cc_start: 0.8754 (mtp) cc_final: 0.8302 (mtm) REVERT: A 883 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: A 1013 THR cc_start: 0.6532 (m) cc_final: 0.6188 (p) REVERT: A 1108 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7238 (tp30) REVERT: A 1126 TYR cc_start: 0.8653 (t80) cc_final: 0.8258 (t80) REVERT: A 1263 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7954 (mmm160) REVERT: A 1276 LYS cc_start: 0.8096 (tttp) cc_final: 0.7663 (tptm) REVERT: A 1281 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.6725 (t80) REVERT: A 1284 MET cc_start: 0.7961 (ttm) cc_final: 0.7149 (ttm) REVERT: A 1360 ASP cc_start: 0.8422 (m-30) cc_final: 0.8212 (m-30) REVERT: A 1379 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.6819 (t-90) REVERT: A 1407 CYS cc_start: 0.8596 (t) cc_final: 0.8344 (t) outliers start: 19 outliers final: 16 residues processed: 106 average time/residue: 0.2046 time to fit residues: 30.6926 Evaluate side-chains 111 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 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 413 LEU 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 883 ASP Chi-restraints excluded: chain A residue 987 PHE 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 1514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111342 restraints weight = 11745.871| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.07 r_work: 0.3085 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3664 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= 0.180 Angle : 0.521 8.925 12485 Z= 0.254 Chirality : 0.039 0.197 1491 Planarity : 0.004 0.045 1524 Dihedral : 8.399 148.240 1340 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.98 % Allowed : 15.14 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.64 (0.25), residues: 1127 helix: 2.71 (0.19), residues: 754 sheet: 0.38 (0.69), residues: 63 loop : -0.43 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1260 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.007 0.000 ARG A1078 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4460.91 seconds wall clock time: 79 minutes 7.91 seconds (4747.91 seconds total)