Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 04:57:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/04_2023/7vlt_32026_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/04_2023/7vlt_32026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/04_2023/7vlt_32026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/04_2023/7vlt_32026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/04_2023/7vlt_32026_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/04_2023/7vlt_32026_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.177 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 46 5.16 5 C 5849 2.51 5 N 1495 2.21 5 O 1627 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-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9024 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1151, 9024 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'ETJ': 1, 'Y01': 1} Classifications: {'peptide': 1145, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 33, 'TRANS': 1111, None: 6} Not linked: pdbres="MET A1545 " pdbres="ETJ A2001 " Not linked: pdbres="ETJ A2001 " pdbres="Y01 A2002 " Not linked: pdbres="Y01 A2002 " pdbres="ADP A2003 " Not linked: pdbres="ADP A2003 " pdbres=" MG A2004 " Not linked: pdbres=" MG A2004 " pdbres=" MG A2005 " Not linked: pdbres=" MG A2005 " pdbres="ATP A2006 " Chain breaks: 5 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Time building chain proxies: 5.50, per 1000 atoms: 0.61 Number of scatterers: 9024 At special positions: 0 Unit cell: (72.27, 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 46 16.00 P 5 15.00 Mg 2 11.99 O 1627 8.00 N 1495 7.00 C 5849 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: 3.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 72.1% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 278 removed outlier: 3.681A pdb=" N HIS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 312 removed outlier: 5.957A 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: 3.992A 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 397 through 402 Processing helix chain 'A' and resid 406 through 427 removed outlier: 3.599A pdb=" N GLU A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 3.501A 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 removed outlier: 3.541A pdb=" N ASN A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.999A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 498 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 507 through 559 Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 584 Proline residue: A 581 - end of helix removed outlier: 4.152A pdb=" N LEU A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 607 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 786 through 791 Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 853 through 859 removed outlier: 3.684A pdb=" N ASP A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 874 removed outlier: 4.022A 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 988 through 1016 removed outlier: 3.728A pdb=" N ASP A1008 " --> pdb=" O ILE A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1073 removed outlier: 4.000A pdb=" N VAL A1053 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.730A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1102 removed outlier: 3.897A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1163 removed outlier: 3.650A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 4.202A pdb=" N ASP A1155 " --> pdb=" O VAL A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.894A pdb=" N LEU A1167 " --> pdb=" O THR A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1186 through 1238 Processing helix chain 'A' and resid 1242 through 1280 removed outlier: 4.435A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1284 removed outlier: 3.665A pdb=" N MET A1284 " --> pdb=" O PHE A1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1281 through 1284' Processing helix chain 'A' and resid 1347 through 1355 removed outlier: 4.071A pdb=" N PHE A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1383 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: 3.856A pdb=" N GLU A1443 " --> pdb=" O GLU A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1462 removed outlier: 4.261A pdb=" N ARG A1461 " --> pdb=" O ARG A1457 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A1462 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 removed outlier: 3.694A pdb=" N ILE A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1509 removed outlier: 4.109A pdb=" N THR A1508 " --> pdb=" O THR A1505 " (cutoff:3.500A) removed outlier: 3.746A 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: 6.317A pdb=" N THR A 683 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER A 676 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER A 685 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR A 674 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE A 687 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 668 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 670 " --> pdb=" O VAL A 725 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 725 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A 672 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A 674 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.515A pdb=" N VAL A 829 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL A 865 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 831 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR A 697 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 696 " --> pdb=" O TRP A 877 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 879 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N MET A 698 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N MET A 881 " --> pdb=" O MET A 698 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 700 " --> pdb=" O MET A 881 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 878 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU A 889 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA A 880 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1332 removed outlier: 6.822A pdb=" N LYS A1326 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS A1314 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL A1328 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A1313 " --> pdb=" O ASP A1363 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP A1363 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A1315 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A1361 " --> pdb=" O VAL A1315 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A1371 " --> pdb=" O ILE A1368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 6.789A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A1338 " --> pdb=" O THR A1498 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS A1337 " --> pdb=" O LEU A1511 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A1513 " --> pdb=" O LYS A1337 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY A1339 " --> pdb=" O ILE A1513 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N MET A1515 " --> pdb=" O GLY A1339 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS A1341 " --> pdb=" O MET A1515 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1512 " --> pdb=" O TYR A1523 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR A1523 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 7.056A 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 616 hydrogen bonds defined for protein. 1815 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: 4.02 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1415 1.29 - 1.42: 2320 1.42 - 1.55: 5391 1.55 - 1.69: 8 1.69 - 1.82: 74 Bond restraints: 9208 Sorted by residual: bond pdb=" C13 ETJ A2001 " pdb=" C15 ETJ A2001 " ideal model delta sigma weight residual 1.424 1.286 0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" CAY Y01 A2002 " pdb=" OAW Y01 A2002 " ideal model delta sigma weight residual 1.332 1.461 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" CAX Y01 A2002 " pdb=" OAH Y01 A2002 " ideal model delta sigma weight residual 1.248 1.332 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C3 ETJ A2001 " pdb=" C6 ETJ A2001 " ideal model delta sigma weight residual 1.399 1.471 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N ETJ A2001 " pdb=" C7 ETJ A2001 " ideal model delta sigma weight residual 1.357 1.319 0.038 2.00e-02 2.50e+03 3.66e+00 ... (remaining 9203 not shown) Histogram of bond angle deviations from ideal: 99.58 - 115.21: 5987 115.21 - 130.84: 6491 130.84 - 146.47: 46 146.47 - 162.11: 0 162.11 - 177.74: 1 Bond angle restraints: 12525 Sorted by residual: angle pdb=" C1' ATP A2006 " pdb=" C2' ATP A2006 " pdb=" C3' ATP A2006 " ideal model delta sigma weight residual 101.56 105.39 -3.83 1.19e+00 7.05e-01 1.04e+01 angle pdb=" C2' ATP A2006 " pdb=" C3' ATP A2006 " pdb=" C4' ATP A2006 " ideal model delta sigma weight residual 102.49 105.56 -3.07 1.00e+00 1.00e+00 9.43e+00 angle pdb=" CAM Y01 A2002 " pdb=" CAY Y01 A2002 " pdb=" OAW Y01 A2002 " ideal model delta sigma weight residual 111.19 120.07 -8.88 3.00e+00 1.11e-01 8.77e+00 angle pdb=" C1' ATP A2006 " pdb=" C2' ATP A2006 " pdb=" O2' ATP A2006 " ideal model delta sigma weight residual 110.58 102.82 7.76 2.79e+00 1.28e-01 7.72e+00 angle pdb=" CAJ Y01 A2002 " pdb=" CAO Y01 A2002 " pdb=" CBB Y01 A2002 " ideal model delta sigma weight residual 115.08 106.90 8.18 3.00e+00 1.11e-01 7.44e+00 ... (remaining 12520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 5273 27.36 - 54.72: 151 54.72 - 82.08: 12 82.08 - 109.45: 2 109.45 - 136.81: 1 Dihedral angle restraints: 5439 sinusoidal: 2107 harmonic: 3332 Sorted by residual: dihedral pdb=" O2A ADP A2003 " pdb=" O3A ADP A2003 " pdb=" PA ADP A2003 " pdb=" PB ADP A2003 " ideal model delta sinusoidal sigma weight residual -60.00 76.81 -136.81 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" O1B ADP A2003 " pdb=" O3A ADP A2003 " pdb=" PB ADP A2003 " pdb=" PA ADP A2003 " ideal model delta sinusoidal sigma weight residual -60.00 31.44 -91.44 1 2.00e+01 2.50e-03 2.46e+01 dihedral pdb=" CA HIS A 278 " pdb=" C HIS A 278 " pdb=" N PRO A 279 " pdb=" CA PRO A 279 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1255 0.050 - 0.100: 190 0.100 - 0.150: 44 0.150 - 0.200: 4 0.200 - 0.250: 3 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C2' ATP A2006 " pdb=" C1' ATP A2006 " pdb=" C3' ATP A2006 " pdb=" O2' ATP A2006 " both_signs ideal model delta sigma weight residual False -2.68 -2.93 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3' ATP A2006 " pdb=" C2' ATP A2006 " pdb=" C4' ATP A2006 " pdb=" O3' ATP A2006 " both_signs ideal model delta sigma weight residual False -2.63 -2.88 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CBB Y01 A2002 " pdb=" CAC Y01 A2002 " pdb=" CAO Y01 A2002 " pdb=" CBE Y01 A2002 " both_signs ideal model delta sigma weight residual False 2.58 2.34 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1493 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 543 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO A 544 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 544 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 544 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 314 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 315 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 549 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C LEU A 549 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 549 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA A 550 " -0.012 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 27 2.55 - 3.14: 7510 3.14 - 3.73: 14022 3.73 - 4.31: 19822 4.31 - 4.90: 33304 Nonbonded interactions: 74685 Sorted by model distance: nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A2004 " model vdw 1.963 2.170 nonbonded pdb=" O1B ADP A2003 " pdb="MG MG A2005 " model vdw 2.075 2.170 nonbonded pdb=" OG SER A 708 " pdb="MG MG A2004 " model vdw 2.196 2.170 nonbonded pdb=" O2' ATP A2006 " pdb=" O3' ATP A2006 " model vdw 2.333 2.432 nonbonded pdb=" OH TYR A 674 " pdb=" OD1 ASN A 686 " model vdw 2.342 2.440 ... (remaining 74680 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: 0.960 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: 2.630 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.150 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 0.138 9208 Z= 0.241 Angle : 0.604 8.884 12525 Z= 0.303 Chirality : 0.041 0.250 1496 Planarity : 0.004 0.066 1529 Dihedral : 12.710 136.807 3281 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 2.19 % 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: 0.12 (0.24), residues: 1133 helix: 0.54 (0.18), residues: 758 sheet: 0.17 (0.59), residues: 65 loop : -0.84 (0.34), residues: 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 1.119 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 198 average time/residue: 0.2897 time to fit residues: 74.2020 Evaluate side-chains 106 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1651 time to fit residues: 3.4226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 0.0980 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1097 ASN A1259 ASN A1379 HIS A1444 ASN A1504 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9208 Z= 0.170 Angle : 0.526 6.835 12525 Z= 0.264 Chirality : 0.040 0.232 1496 Planarity : 0.004 0.053 1529 Dihedral : 6.769 124.289 1257 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 0.83 % 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: 1.99 (0.25), residues: 1133 helix: 2.01 (0.19), residues: 752 sheet: 0.58 (0.62), residues: 65 loop : -0.14 (0.34), residues: 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.047 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 126 average time/residue: 0.2514 time to fit residues: 42.9421 Evaluate side-chains 106 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1514 time to fit residues: 2.8261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 412 ASN A 447 ASN A 841 HIS A1259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9208 Z= 0.215 Angle : 0.525 7.172 12525 Z= 0.260 Chirality : 0.040 0.232 1496 Planarity : 0.004 0.054 1529 Dihedral : 6.551 126.177 1257 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 2.19 % 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: 2.23 (0.25), residues: 1133 helix: 2.21 (0.19), residues: 757 sheet: 0.53 (0.63), residues: 65 loop : -0.12 (0.35), residues: 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.032 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 118 average time/residue: 0.2322 time to fit residues: 37.7919 Evaluate side-chains 109 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1028 time to fit residues: 4.2478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0020 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 9208 Z= 0.218 Angle : 0.524 6.974 12525 Z= 0.259 Chirality : 0.040 0.232 1496 Planarity : 0.004 0.052 1529 Dihedral : 6.410 127.413 1257 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 0.94 % 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: 2.29 (0.25), residues: 1133 helix: 2.25 (0.19), residues: 758 sheet: 0.61 (0.62), residues: 65 loop : -0.09 (0.35), residues: 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.956 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 121 average time/residue: 0.2629 time to fit residues: 42.9798 Evaluate side-chains 103 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1025 time to fit residues: 2.6971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9208 Z= 0.191 Angle : 0.502 6.760 12525 Z= 0.247 Chirality : 0.039 0.226 1496 Planarity : 0.004 0.049 1529 Dihedral : 6.279 128.028 1257 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 0.52 % 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: 2.41 (0.25), residues: 1133 helix: 2.39 (0.19), residues: 757 sheet: 0.72 (0.63), residues: 65 loop : -0.19 (0.34), residues: 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.067 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 105 average time/residue: 0.2509 time to fit residues: 36.3390 Evaluate side-chains 102 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0993 time to fit residues: 2.3859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1402 ASN A1451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 9208 Z= 0.267 Angle : 0.558 7.772 12525 Z= 0.273 Chirality : 0.041 0.235 1496 Planarity : 0.004 0.049 1529 Dihedral : 6.309 129.578 1257 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.25 % 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: 2.20 (0.25), residues: 1133 helix: 2.22 (0.19), residues: 757 sheet: 0.52 (0.62), residues: 65 loop : -0.22 (0.34), residues: 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.955 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.2528 time to fit residues: 36.8143 Evaluate side-chains 109 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1156 time to fit residues: 3.7040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 0.0050 chunk 93 optimal weight: 7.9990 chunk 110 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9208 Z= 0.166 Angle : 0.492 7.286 12525 Z= 0.241 Chirality : 0.039 0.226 1496 Planarity : 0.004 0.047 1529 Dihedral : 6.060 127.767 1257 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.52 % 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: 1133 helix: 2.49 (0.19), residues: 759 sheet: 0.67 (0.63), residues: 65 loop : -0.19 (0.35), residues: 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.117 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 112 average time/residue: 0.2641 time to fit residues: 40.1306 Evaluate side-chains 103 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1119 time to fit residues: 2.2954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 9208 Z= 0.312 Angle : 0.578 8.428 12525 Z= 0.283 Chirality : 0.042 0.239 1496 Planarity : 0.004 0.048 1529 Dihedral : 6.259 130.252 1257 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 1.15 % 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: 2.11 (0.25), residues: 1133 helix: 2.16 (0.18), residues: 757 sheet: 0.47 (0.63), residues: 65 loop : -0.26 (0.35), residues: 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.077 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 0.2797 time to fit residues: 36.2279 Evaluate side-chains 98 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0965 time to fit residues: 2.4965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.0670 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9208 Z= 0.168 Angle : 0.500 7.184 12525 Z= 0.247 Chirality : 0.039 0.227 1496 Planarity : 0.004 0.047 1529 Dihedral : 6.020 127.463 1257 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.31 % 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: 2.44 (0.25), residues: 1133 helix: 2.43 (0.19), residues: 760 sheet: 0.56 (0.63), residues: 65 loop : -0.20 (0.35), residues: 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.084 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 99 average time/residue: 0.2817 time to fit residues: 37.7767 Evaluate side-chains 99 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1037 time to fit residues: 1.9039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 9208 Z= 0.311 Angle : 0.585 8.398 12525 Z= 0.287 Chirality : 0.042 0.238 1496 Planarity : 0.004 0.048 1529 Dihedral : 6.271 131.207 1257 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 0.10 % 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: 2.13 (0.25), residues: 1133 helix: 2.14 (0.18), residues: 758 sheet: 0.58 (0.63), residues: 65 loop : -0.20 (0.35), residues: 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.181 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.2865 time to fit residues: 38.6096 Evaluate side-chains 100 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1437 time to fit residues: 1.7808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 0.0970 chunk 13 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123020 restraints weight = 10422.730| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.89 r_work: 0.3282 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9208 Z= 0.153 Angle : 0.499 7.749 12525 Z= 0.247 Chirality : 0.038 0.224 1496 Planarity : 0.003 0.046 1529 Dihedral : 5.969 126.358 1257 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.10 % 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: 1133 helix: 2.49 (0.19), residues: 760 sheet: 0.63 (0.63), residues: 65 loop : -0.18 (0.35), residues: 308 =============================================================================== Job complete usr+sys time: 1977.10 seconds wall clock time: 36 minutes 43.23 seconds (2203.23 seconds total)