Starting phenix.real_space_refine on Wed Feb 14 09:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/02_2024/7vls_32025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/02_2024/7vls_32025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/02_2024/7vls_32025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/02_2024/7vls_32025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/02_2024/7vls_32025.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9003 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9003 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'ESV': 1, 'Y01': 1} Classifications: {'peptide': 1141, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 33, 'TRANS': 1107, None: 6} Not linked: pdbres="MET A1545 " pdbres="Y01 A1601 " Not linked: pdbres="Y01 A1601 " pdbres="ADP A1602 " Not linked: pdbres="ADP A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres=" MG A1604 " Not linked: pdbres=" MG A1604 " pdbres="ATP A1605 " Not linked: pdbres="ATP A1605 " pdbres="ESV A1606 " 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 Time building chain proxies: 5.70, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 4.40 Conformation dependent library (CDL) restraints added in 1.7 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: 1.18 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: 3.50 Time building geometry restraints manager: 4.59 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: 100.52 - 116.37: 6244 116.37 - 132.22: 6216 132.22 - 148.07: 24 148.07 - 163.92: 0 163.92 - 179.76: 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 2.520 ... (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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.220 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 30.460 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 1.164 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: 0.2979 time to fit residues: 78.6714 Evaluate side-chains 110 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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: 2.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 0.0370 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN A 911 ASN A1102 HIS A1379 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2125 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= 0.185 Angle : 0.555 9.231 12485 Z= 0.280 Chirality : 0.040 0.202 1491 Planarity : 0.005 0.053 1524 Dihedral : 8.704 135.371 1346 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.19 % Allowed : 10.44 % Favored : 87.37 % 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: 1.80 (0.25), residues: 1127 helix: 1.98 (0.19), residues: 752 sheet: -0.29 (0.60), residues: 69 loop : -0.38 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 432 HIS 0.004 0.001 HIS A 576 PHE 0.016 0.001 PHE A1149 TYR 0.009 0.001 TYR A1317 ARG 0.005 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 133 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.8600 (mtp) cc_final: 0.8352 (ttt) REVERT: A 402 MET cc_start: 0.8235 (mmm) cc_final: 0.7978 (mmm) REVERT: A 422 MET cc_start: 0.8716 (ttp) cc_final: 0.8437 (ttp) REVERT: A 440 MET cc_start: 0.7931 (mmm) cc_final: 0.7595 (mtm) REVERT: A 539 MET cc_start: 0.8115 (mmt) cc_final: 0.7861 (mmm) REVERT: A 698 MET cc_start: 0.8533 (mtp) cc_final: 0.8046 (mtp) REVERT: A 724 LYS cc_start: 0.7837 (mttt) cc_final: 0.7617 (mmmt) REVERT: A 795 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: A 881 MET cc_start: 0.8367 (mtp) cc_final: 0.7867 (mtm) REVERT: A 1013 THR cc_start: 0.7480 (m) cc_final: 0.7208 (p) REVERT: A 1213 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7284 (ttp80) REVERT: A 1350 SER cc_start: 0.9148 (m) cc_final: 0.8821 (p) REVERT: A 1358 MET cc_start: 0.9374 (mmm) cc_final: 0.9034 (mtp) REVERT: A 1443 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7923 (mp0) REVERT: A 1508 THR cc_start: 0.8674 (p) cc_final: 0.8418 (t) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.2510 time to fit residues: 43.3322 Evaluate side-chains 99 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.1980 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2681 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= 0.176 Angle : 0.530 8.148 12485 Z= 0.262 Chirality : 0.039 0.184 1491 Planarity : 0.004 0.045 1524 Dihedral : 8.430 138.003 1344 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.88 % Allowed : 12.84 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.43 (0.25), residues: 1127 helix: 2.57 (0.19), residues: 744 sheet: -0.09 (0.62), residues: 69 loop : -0.36 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1260 HIS 0.017 0.001 HIS A1379 PHE 0.013 0.001 PHE A 356 TYR 0.015 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 113 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.964 Fit side-chains REVERT: A 255 MET cc_start: 0.8255 (mmm) cc_final: 0.8050 (mmm) REVERT: A 387 MET cc_start: 0.8675 (mtp) cc_final: 0.8453 (ttt) REVERT: A 422 MET cc_start: 0.8646 (ttp) cc_final: 0.8317 (ttp) REVERT: A 440 MET cc_start: 0.7982 (mmm) cc_final: 0.7453 (mtt) REVERT: A 539 MET cc_start: 0.7859 (mmt) cc_final: 0.7536 (mmm) REVERT: A 698 MET cc_start: 0.8627 (mtp) cc_final: 0.8263 (mtp) REVERT: A 724 LYS cc_start: 0.7912 (mttt) cc_final: 0.7657 (mmmt) REVERT: A 881 MET cc_start: 0.8416 (mtp) cc_final: 0.7888 (mtm) REVERT: A 883 ASP cc_start: 0.8195 (m-30) cc_final: 0.7933 (m-30) REVERT: A 1013 THR cc_start: 0.7402 (m) cc_final: 0.7091 (p) REVERT: A 1213 ARG cc_start: 0.7796 (mmt-90) cc_final: 0.7243 (ttp80) REVERT: A 1284 MET cc_start: 0.8020 (ttm) cc_final: 0.7626 (ttm) REVERT: A 1358 MET cc_start: 0.9329 (mmm) cc_final: 0.8469 (mtp) REVERT: A 1391 ASP cc_start: 0.7939 (p0) cc_final: 0.7626 (p0) REVERT: A 1443 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7939 (mp0) REVERT: A 1508 THR cc_start: 0.8685 (p) cc_final: 0.8458 (t) outliers start: 18 outliers final: 10 residues processed: 109 average time/residue: 0.2607 time to fit residues: 38.2468 Evaluate side-chains 96 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 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 681 LEU Chi-restraints excluded: chain A residue 808 LEU 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 102 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN A1311 HIS A1379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9184 Z= 0.262 Angle : 0.574 9.758 12485 Z= 0.280 Chirality : 0.041 0.186 1491 Planarity : 0.004 0.048 1524 Dihedral : 8.786 153.313 1342 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.13 % Allowed : 12.73 % 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: 2.34 (0.25), residues: 1127 helix: 2.47 (0.19), residues: 751 sheet: -0.01 (0.63), residues: 69 loop : -0.42 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1260 HIS 0.005 0.001 HIS A1001 PHE 0.012 0.001 PHE A 356 TYR 0.009 0.001 TYR A1257 ARG 0.005 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 130 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8370 (mmm) cc_final: 0.8153 (mmm) REVERT: A 278 HIS cc_start: 0.7290 (m90) cc_final: 0.6568 (t70) REVERT: A 422 MET cc_start: 0.8820 (ttp) cc_final: 0.8515 (ttp) REVERT: A 440 MET cc_start: 0.8098 (mmm) cc_final: 0.7544 (mtt) REVERT: A 539 MET cc_start: 0.7906 (mmt) cc_final: 0.7565 (mmm) REVERT: A 698 MET cc_start: 0.8618 (mtp) cc_final: 0.8336 (mtp) REVERT: A 881 MET cc_start: 0.8612 (mtp) cc_final: 0.8041 (mtm) REVERT: A 883 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: A 1013 THR cc_start: 0.7419 (m) cc_final: 0.7075 (p) REVERT: A 1213 ARG cc_start: 0.7875 (mmt-90) cc_final: 0.7309 (ttp80) REVERT: A 1443 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7894 (mp0) outliers start: 30 outliers final: 17 residues processed: 124 average time/residue: 0.2280 time to fit residues: 39.2690 Evaluate side-chains 102 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 808 LEU 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 1128 THR 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 1493 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN A 848 GLN A1311 HIS A1379 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9184 Z= 0.302 Angle : 0.577 10.095 12485 Z= 0.284 Chirality : 0.042 0.198 1491 Planarity : 0.004 0.047 1524 Dihedral : 9.032 166.939 1342 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.71 % Allowed : 13.15 % 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: 2.19 (0.25), residues: 1127 helix: 2.33 (0.19), residues: 754 sheet: -0.02 (0.63), residues: 69 loop : -0.45 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1302 HIS 0.019 0.001 HIS A1379 PHE 0.014 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 120 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.048 Fit side-chains REVERT: A 422 MET cc_start: 0.8824 (ttp) cc_final: 0.8540 (ttp) REVERT: A 440 MET cc_start: 0.8147 (mmm) cc_final: 0.7576 (mtt) REVERT: A 539 MET cc_start: 0.7981 (mmt) cc_final: 0.7659 (mmm) REVERT: A 698 MET cc_start: 0.8595 (mtp) cc_final: 0.8307 (mtp) REVERT: A 881 MET cc_start: 0.8703 (mtp) cc_final: 0.8173 (mtm) REVERT: A 883 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: A 1013 THR cc_start: 0.7606 (m) cc_final: 0.7273 (p) REVERT: A 1143 TYR cc_start: 0.7990 (t80) cc_final: 0.7719 (t80) REVERT: A 1358 MET cc_start: 0.9148 (mtp) cc_final: 0.8946 (mtp) outliers start: 26 outliers final: 20 residues processed: 114 average time/residue: 0.2066 time to fit residues: 33.9646 Evaluate side-chains 110 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 808 LEU 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 1254 ILE 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 1493 ASP 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: 0.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN A1311 HIS A1379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3487 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= 0.197 Angle : 0.525 8.914 12485 Z= 0.259 Chirality : 0.039 0.203 1491 Planarity : 0.004 0.045 1524 Dihedral : 8.983 172.734 1342 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.61 % Allowed : 14.72 % 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: 2.42 (0.25), residues: 1127 helix: 2.53 (0.19), residues: 754 sheet: -0.02 (0.63), residues: 69 loop : -0.39 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 727 HIS 0.011 0.001 HIS A1379 PHE 0.012 0.001 PHE A 356 TYR 0.009 0.001 TYR A1257 ARG 0.004 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 123 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 1.073 Fit side-chains REVERT: A 285 ILE cc_start: 0.8897 (mt) cc_final: 0.8669 (mt) REVERT: A 422 MET cc_start: 0.8792 (ttp) cc_final: 0.8510 (ttp) REVERT: A 440 MET cc_start: 0.8126 (mmm) cc_final: 0.7910 (ttm) REVERT: A 539 MET cc_start: 0.7925 (mmt) cc_final: 0.7575 (mmm) REVERT: A 698 MET cc_start: 0.8575 (mtp) cc_final: 0.8300 (mtp) REVERT: A 881 MET cc_start: 0.8674 (mtp) cc_final: 0.8173 (mtm) REVERT: A 883 ASP cc_start: 0.8198 (m-30) cc_final: 0.7927 (m-30) REVERT: A 1013 THR cc_start: 0.7361 (m) cc_final: 0.7038 (p) outliers start: 25 outliers final: 22 residues processed: 118 average time/residue: 0.2217 time to fit residues: 36.7721 Evaluate side-chains 111 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 406 THR 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 808 LEU 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 1254 ILE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1360 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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: 0.8217 moved from start: 0.3599 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= 0.182 Angle : 0.518 9.333 12485 Z= 0.253 Chirality : 0.039 0.199 1491 Planarity : 0.004 0.045 1524 Dihedral : 8.918 176.948 1342 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.55 % Allowed : 14.20 % 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: 2.53 (0.25), residues: 1127 helix: 2.61 (0.19), residues: 754 sheet: 0.03 (0.63), residues: 69 loop : -0.35 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1302 HIS 0.011 0.001 HIS A1379 PHE 0.011 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.006 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 132 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.077 Fit side-chains REVERT: A 285 ILE cc_start: 0.8911 (mt) cc_final: 0.8693 (mt) REVERT: A 422 MET cc_start: 0.8788 (ttp) cc_final: 0.8467 (ttp) REVERT: A 440 MET cc_start: 0.8128 (mmm) cc_final: 0.7913 (ttm) REVERT: A 539 MET cc_start: 0.7900 (mmt) cc_final: 0.7525 (mmm) REVERT: A 698 MET cc_start: 0.8579 (mtp) cc_final: 0.8320 (mtp) REVERT: A 883 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: A 1013 THR cc_start: 0.7352 (m) cc_final: 0.7024 (p) outliers start: 34 outliers final: 25 residues processed: 120 average time/residue: 0.2084 time to fit residues: 35.6946 Evaluate side-chains 120 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 THR 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 808 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 1128 THR 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 1360 ASP Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1493 ASP 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: 0.8980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 105 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: 0.8214 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9184 Z= 0.188 Angle : 0.517 8.743 12485 Z= 0.253 Chirality : 0.039 0.197 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.842 179.016 1342 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.55 % Allowed : 14.61 % Favored : 81.84 % 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: 2.62 (0.19), residues: 755 sheet: 0.01 (0.63), residues: 69 loop : -0.33 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 727 HIS 0.004 0.001 HIS A1001 PHE 0.011 0.001 PHE A 356 TYR 0.008 0.001 TYR A1257 ARG 0.006 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 133 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 1.101 Fit side-chains REVERT: A 278 HIS cc_start: 0.7486 (m90) cc_final: 0.6508 (t70) REVERT: A 285 ILE cc_start: 0.8898 (mt) cc_final: 0.8686 (mt) REVERT: A 422 MET cc_start: 0.8784 (ttp) cc_final: 0.8464 (ttp) REVERT: A 440 MET cc_start: 0.8135 (mmm) cc_final: 0.7919 (ttm) REVERT: A 539 MET cc_start: 0.7894 (mmt) cc_final: 0.7506 (mmm) REVERT: A 698 MET cc_start: 0.8577 (mtp) cc_final: 0.8300 (mtp) REVERT: A 705 CYS cc_start: 0.8525 (m) cc_final: 0.7898 (m) REVERT: A 883 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: A 1013 THR cc_start: 0.7336 (m) cc_final: 0.7010 (p) outliers start: 34 outliers final: 29 residues processed: 123 average time/residue: 0.2344 time to fit residues: 40.0408 Evaluate side-chains 128 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 406 THR 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 808 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 993 MET Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1128 THR 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 1360 ASP 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 1493 ASP Chi-restraints excluded: chain A residue 1508 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 96 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8207 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9184 Z= 0.179 Angle : 0.519 8.632 12485 Z= 0.254 Chirality : 0.039 0.196 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.804 179.712 1342 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.24 % Allowed : 14.93 % Favored : 81.84 % 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: 2.57 (0.25), residues: 1127 helix: 2.64 (0.19), residues: 756 sheet: 0.07 (0.63), residues: 69 loop : -0.37 (0.36), residues: 302 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 A1079 TYR 0.009 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 128 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 0.898 Fit side-chains REVERT: A 278 HIS cc_start: 0.7487 (m90) cc_final: 0.6518 (t70) REVERT: A 422 MET cc_start: 0.8777 (ttp) cc_final: 0.8459 (ttp) REVERT: A 440 MET cc_start: 0.8131 (mmm) cc_final: 0.7919 (ttm) REVERT: A 539 MET cc_start: 0.7882 (mmt) cc_final: 0.7488 (mmm) REVERT: A 698 MET cc_start: 0.8557 (mtp) cc_final: 0.8316 (mtp) REVERT: A 705 CYS cc_start: 0.8549 (m) cc_final: 0.7822 (m) REVERT: A 883 ASP cc_start: 0.8194 (m-30) cc_final: 0.7852 (m-30) REVERT: A 1013 THR cc_start: 0.7320 (m) cc_final: 0.7002 (p) outliers start: 31 outliers final: 29 residues processed: 119 average time/residue: 0.2090 time to fit residues: 35.0265 Evaluate side-chains 124 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 406 THR 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 700 VAL Chi-restraints excluded: chain A residue 808 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 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1493 ASP Chi-restraints excluded: chain A residue 1508 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 51 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9184 Z= 0.188 Angle : 0.522 8.633 12485 Z= 0.256 Chirality : 0.039 0.189 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.602 177.656 1340 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.03 % Allowed : 15.03 % Favored : 81.94 % 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: 2.59 (0.26), residues: 1127 helix: 2.66 (0.19), residues: 757 sheet: 0.08 (0.63), residues: 69 loop : -0.39 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.007 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 123 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.096 Fit side-chains REVERT: A 278 HIS cc_start: 0.7503 (m90) cc_final: 0.6529 (t70) REVERT: A 324 ARG cc_start: 0.7678 (tpt170) cc_final: 0.7397 (tpt-90) REVERT: A 422 MET cc_start: 0.8773 (ttp) cc_final: 0.8459 (ttp) REVERT: A 440 MET cc_start: 0.8151 (mmm) cc_final: 0.7931 (ttm) REVERT: A 539 MET cc_start: 0.7888 (mmt) cc_final: 0.7483 (mmm) REVERT: A 698 MET cc_start: 0.8581 (mtp) cc_final: 0.8335 (mtp) REVERT: A 705 CYS cc_start: 0.8503 (m) cc_final: 0.7781 (m) REVERT: A 883 ASP cc_start: 0.8163 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1013 THR cc_start: 0.7265 (m) cc_final: 0.6983 (p) outliers start: 29 outliers final: 28 residues processed: 114 average time/residue: 0.2098 time to fit residues: 34.1776 Evaluate side-chains 119 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 406 THR 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 700 VAL Chi-restraints excluded: chain A residue 808 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 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1493 ASP Chi-restraints excluded: chain A residue 1508 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 83 optimal weight: 0.0670 chunk 13 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1186 HIS A1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112259 restraints weight = 11622.159| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.04 r_work: 0.3064 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9184 Z= 0.168 Angle : 0.511 7.926 12485 Z= 0.249 Chirality : 0.039 0.191 1491 Planarity : 0.004 0.047 1524 Dihedral : 8.423 176.036 1340 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.61 % Allowed : 15.03 % 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: 2.68 (0.26), residues: 1127 helix: 2.73 (0.19), residues: 757 sheet: 0.14 (0.63), residues: 69 loop : -0.34 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1260 HIS 0.003 0.001 HIS A1065 PHE 0.010 0.001 PHE A 356 TYR 0.007 0.001 TYR A1523 ARG 0.007 0.000 ARG A1078 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.65 seconds wall clock time: 36 minutes 32.58 seconds (2192.58 seconds total)