Starting phenix.real_space_refine on Thu Mar 14 14:04:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/03_2024/7vlt_32026_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/03_2024/7vlt_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_32026/03_2024/7vlt_32026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/03_2024/7vlt_32026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/03_2024/7vlt_32026_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/03_2024/7vlt_32026_neut.pdb" } resolution = 3.1 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= 0.008 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-dev-5265/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: 5.29, per 1000 atoms: 0.59 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: 3.60 Conformation dependent library (CDL) restraints added in 1.6 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: 0.94 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: 2.94 Time building geometry restraints manager: 3.88 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: 5366 27.36 - 54.72: 162 54.72 - 82.08: 15 82.08 - 109.45: 2 109.45 - 136.81: 1 Dihedral angle restraints: 5546 sinusoidal: 2214 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 5543 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: 0.370 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: 2.250 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.020 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- 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 : 13.021 136.807 3388 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 % Allowed : 4.17 % Favored : 93.64 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1415 HIS 0.005 0.001 HIS A1001 PHE 0.011 0.001 PHE A1035 TYR 0.016 0.001 TYR A1250 ARG 0.003 0.000 ARG A1461 *********************** 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 : 1.101 Fit side-chains REVERT: A 387 MET cc_start: 0.8508 (mtp) cc_final: 0.8255 (ttt) REVERT: A 394 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7481 (mtm110) REVERT: A 412 ASN cc_start: 0.8184 (t0) cc_final: 0.7971 (t0) REVERT: A 416 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8380 (mt) REVERT: A 486 THR cc_start: 0.8868 (m) cc_final: 0.7956 (p) REVERT: A 500 LYS cc_start: 0.8657 (tttp) cc_final: 0.8359 (tttt) REVERT: A 722 GLU cc_start: 0.7305 (tt0) cc_final: 0.6992 (mt-10) REVERT: A 724 LYS cc_start: 0.7643 (mptt) cc_final: 0.7110 (mmmt) REVERT: A 795 PHE cc_start: 0.8568 (m-80) cc_final: 0.8250 (m-80) REVERT: A 817 CYS cc_start: 0.8226 (t) cc_final: 0.7873 (m) REVERT: A 842 LEU cc_start: 0.8607 (mp) cc_final: 0.8326 (mt) REVERT: A 848 GLN cc_start: 0.8115 (tp40) cc_final: 0.7712 (mm-40) REVERT: A 888 ARG cc_start: 0.8041 (tpt170) cc_final: 0.7814 (tpt90) REVERT: A 976 LYS cc_start: 0.7797 (mttp) cc_final: 0.7460 (tptp) REVERT: A 1309 LYS cc_start: 0.8074 (mttt) cc_final: 0.7452 (mptt) REVERT: A 1358 MET cc_start: 0.8643 (mmm) cc_final: 0.8151 (mmm) REVERT: A 1430 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8682 (mt) REVERT: A 1468 MET cc_start: 0.8646 (mtm) cc_final: 0.8224 (mtp) REVERT: A 1520 ILE cc_start: 0.8941 (mt) cc_final: 0.8714 (mt) outliers start: 21 outliers final: 8 residues processed: 198 average time/residue: 0.2748 time to fit residues: 70.5212 Evaluate side-chains 115 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1446 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 841 HIS A1097 ASN A1259 ASN A1379 HIS A1444 ASN A1504 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9208 Z= 0.276 Angle : 0.580 7.745 12525 Z= 0.288 Chirality : 0.042 0.201 1496 Planarity : 0.005 0.056 1529 Dihedral : 9.749 128.900 1384 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.40 % Allowed : 11.57 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1133 helix: 1.69 (0.19), residues: 753 sheet: 0.49 (0.63), residues: 65 loop : -0.16 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1055 HIS 0.009 0.001 HIS A1504 PHE 0.017 0.002 PHE A1142 TYR 0.015 0.002 TYR A 484 ARG 0.005 0.001 ARG A 820 *********************** 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 149 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.864 Fit side-chains REVERT: A 273 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7410 (ttpp) REVERT: A 412 ASN cc_start: 0.8567 (t0) cc_final: 0.8354 (t0) REVERT: A 416 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8750 (mt) REVERT: A 486 THR cc_start: 0.8968 (m) cc_final: 0.8058 (p) REVERT: A 539 MET cc_start: 0.8752 (mmt) cc_final: 0.8435 (mmt) REVERT: A 591 PHE cc_start: 0.8812 (m-80) cc_final: 0.8476 (m-10) REVERT: A 724 LYS cc_start: 0.7806 (mptt) cc_final: 0.7189 (mtpp) REVERT: A 763 GLU cc_start: 0.8248 (tt0) cc_final: 0.7972 (tt0) REVERT: A 764 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7730 (mt-10) REVERT: A 795 PHE cc_start: 0.8534 (m-80) cc_final: 0.8188 (m-80) REVERT: A 797 ASP cc_start: 0.7824 (t70) cc_final: 0.7612 (t0) REVERT: A 817 CYS cc_start: 0.8427 (t) cc_final: 0.8192 (m) REVERT: A 847 MET cc_start: 0.8742 (tpp) cc_final: 0.8380 (tpt) REVERT: A 848 GLN cc_start: 0.8184 (tp40) cc_final: 0.7747 (mm-40) REVERT: A 889 GLU cc_start: 0.7837 (tt0) cc_final: 0.7637 (tt0) REVERT: A 910 MET cc_start: 0.7528 (mtp) cc_final: 0.7282 (mtp) REVERT: A 976 LYS cc_start: 0.7806 (mttp) cc_final: 0.7483 (tptp) REVERT: A 1158 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7608 (tp30) REVERT: A 1309 LYS cc_start: 0.8224 (mttt) cc_final: 0.7510 (mptt) REVERT: A 1468 MET cc_start: 0.8818 (mtm) cc_final: 0.8406 (mtp) outliers start: 23 outliers final: 16 residues processed: 141 average time/residue: 0.2392 time to fit residues: 45.6805 Evaluate side-chains 123 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1463 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 326 ASN A 447 ASN A 807 ASN A1259 ASN A1379 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9208 Z= 0.191 Angle : 0.515 6.778 12525 Z= 0.256 Chirality : 0.039 0.210 1496 Planarity : 0.004 0.053 1529 Dihedral : 8.952 126.962 1376 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.71 % Allowed : 12.83 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.25), residues: 1133 helix: 2.15 (0.19), residues: 755 sheet: 0.52 (0.63), residues: 65 loop : -0.05 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1055 HIS 0.008 0.001 HIS A1379 PHE 0.013 0.001 PHE A1149 TYR 0.009 0.001 TYR A 532 ARG 0.003 0.000 ARG A 888 *********************** 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 138 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.974 Fit side-chains REVERT: A 273 LYS cc_start: 0.7825 (mtpp) cc_final: 0.7574 (ttpp) REVERT: A 412 ASN cc_start: 0.8534 (t0) cc_final: 0.8326 (t0) REVERT: A 539 MET cc_start: 0.8736 (mmt) cc_final: 0.8433 (mmt) REVERT: A 724 LYS cc_start: 0.7894 (mptt) cc_final: 0.7310 (mtpp) REVERT: A 764 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7640 (mt-10) REVERT: A 795 PHE cc_start: 0.8506 (m-80) cc_final: 0.8119 (m-80) REVERT: A 817 CYS cc_start: 0.8597 (t) cc_final: 0.8226 (m) REVERT: A 847 MET cc_start: 0.8736 (tpp) cc_final: 0.8331 (tpt) REVERT: A 848 GLN cc_start: 0.7997 (tp40) cc_final: 0.7523 (mm-40) REVERT: A 888 ARG cc_start: 0.7777 (tpt90) cc_final: 0.7499 (ttm-80) REVERT: A 889 GLU cc_start: 0.7668 (tt0) cc_final: 0.7450 (tt0) REVERT: A 898 LYS cc_start: 0.8242 (mmtp) cc_final: 0.7843 (mmtm) REVERT: A 910 MET cc_start: 0.7477 (mtp) cc_final: 0.7194 (mtp) REVERT: A 976 LYS cc_start: 0.7747 (mttp) cc_final: 0.7473 (tptp) REVERT: A 1158 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7647 (tp30) REVERT: A 1254 ILE cc_start: 0.8851 (mt) cc_final: 0.8511 (tp) REVERT: A 1309 LYS cc_start: 0.8148 (mttt) cc_final: 0.7379 (mptt) REVERT: A 1311 HIS cc_start: 0.6986 (m90) cc_final: 0.6747 (m170) REVERT: A 1426 MET cc_start: 0.6533 (ttt) cc_final: 0.6105 (ttt) REVERT: A 1468 MET cc_start: 0.8727 (mtm) cc_final: 0.8311 (mtp) outliers start: 26 outliers final: 19 residues processed: 129 average time/residue: 0.2420 time to fit residues: 42.7698 Evaluate side-chains 118 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1536 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1259 ASN A1379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9208 Z= 0.197 Angle : 0.512 6.971 12525 Z= 0.253 Chirality : 0.039 0.204 1496 Planarity : 0.004 0.050 1529 Dihedral : 8.689 127.166 1373 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.50 % Allowed : 13.56 % Favored : 83.94 % 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: 2.33 (0.25), residues: 1133 helix: 2.27 (0.19), residues: 758 sheet: 0.63 (0.63), residues: 65 loop : -0.06 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1055 HIS 0.008 0.001 HIS A1504 PHE 0.012 0.001 PHE A1362 TYR 0.016 0.001 TYR A1250 ARG 0.003 0.000 ARG A 774 *********************** 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 125 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.998 Fit side-chains REVERT: A 273 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7617 (ttpp) REVERT: A 539 MET cc_start: 0.8636 (mmt) cc_final: 0.8342 (mmt) REVERT: A 591 PHE cc_start: 0.8849 (m-80) cc_final: 0.8512 (m-10) REVERT: A 724 LYS cc_start: 0.7914 (mptt) cc_final: 0.7327 (mtpp) REVERT: A 795 PHE cc_start: 0.8417 (m-80) cc_final: 0.8017 (m-80) REVERT: A 817 CYS cc_start: 0.8573 (t) cc_final: 0.8211 (m) REVERT: A 848 GLN cc_start: 0.7969 (tp40) cc_final: 0.7504 (mm-40) REVERT: A 898 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7838 (mmtm) REVERT: A 910 MET cc_start: 0.7483 (mtp) cc_final: 0.7210 (mtp) REVERT: A 976 LYS cc_start: 0.7757 (mttp) cc_final: 0.7477 (tptp) REVERT: A 1161 ASP cc_start: 0.7525 (m-30) cc_final: 0.7158 (m-30) REVERT: A 1254 ILE cc_start: 0.8898 (mt) cc_final: 0.8550 (tp) REVERT: A 1283 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8358 (t) REVERT: A 1309 LYS cc_start: 0.8189 (mttt) cc_final: 0.7389 (mptt) REVERT: A 1406 GLU cc_start: 0.7910 (mp0) cc_final: 0.7585 (mp0) REVERT: A 1426 MET cc_start: 0.6736 (ttt) cc_final: 0.6458 (ttt) REVERT: A 1468 MET cc_start: 0.8718 (mtm) cc_final: 0.8331 (mtp) outliers start: 24 outliers final: 18 residues processed: 119 average time/residue: 0.2446 time to fit residues: 39.8481 Evaluate side-chains 115 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1283 THR Chi-restraints excluded: chain A residue 1430 LEU 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: 0.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3026 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= 0.183 Angle : 0.500 6.458 12525 Z= 0.247 Chirality : 0.039 0.196 1496 Planarity : 0.004 0.047 1529 Dihedral : 8.377 128.092 1373 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.61 % Allowed : 13.45 % Favored : 83.94 % 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: 2.49 (0.25), residues: 1133 helix: 2.43 (0.19), residues: 757 sheet: 0.80 (0.64), residues: 65 loop : -0.10 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 677 HIS 0.008 0.001 HIS A1504 PHE 0.009 0.001 PHE A1149 TYR 0.009 0.001 TYR A1250 ARG 0.002 0.000 ARG A 888 *********************** 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 132 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.027 Fit side-chains REVERT: A 273 LYS cc_start: 0.7847 (mtpp) cc_final: 0.7621 (ttpp) REVERT: A 387 MET cc_start: 0.8694 (ttt) cc_final: 0.8479 (mtp) REVERT: A 705 CYS cc_start: 0.8144 (m) cc_final: 0.7871 (p) REVERT: A 724 LYS cc_start: 0.7932 (mptt) cc_final: 0.7320 (mtpp) REVERT: A 764 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7701 (mt-10) REVERT: A 795 PHE cc_start: 0.8334 (m-80) cc_final: 0.7915 (m-80) REVERT: A 817 CYS cc_start: 0.8542 (t) cc_final: 0.8278 (m) REVERT: A 848 GLN cc_start: 0.7964 (tp40) cc_final: 0.7520 (mm-40) REVERT: A 898 LYS cc_start: 0.8292 (mmtp) cc_final: 0.7861 (mmtm) REVERT: A 910 MET cc_start: 0.7520 (mtp) cc_final: 0.7039 (mtp) REVERT: A 976 LYS cc_start: 0.7757 (mttp) cc_final: 0.7492 (tptp) REVERT: A 1073 ILE cc_start: 0.8655 (tt) cc_final: 0.8298 (tt) REVERT: A 1254 ILE cc_start: 0.8937 (mt) cc_final: 0.8650 (tp) REVERT: A 1283 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8374 (t) REVERT: A 1309 LYS cc_start: 0.8208 (mttt) cc_final: 0.7286 (mppt) REVERT: A 1406 GLU cc_start: 0.7738 (mp0) cc_final: 0.7394 (mp0) REVERT: A 1468 MET cc_start: 0.8662 (mtm) cc_final: 0.8306 (mtp) outliers start: 25 outliers final: 22 residues processed: 128 average time/residue: 0.2432 time to fit residues: 42.3151 Evaluate side-chains 121 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1283 THR Chi-restraints excluded: chain A residue 1301 HIS Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1536 VAL 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: 2.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 HIS A1379 HIS A1402 ASN A1451 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9208 Z= 0.321 Angle : 0.580 9.026 12525 Z= 0.284 Chirality : 0.043 0.209 1496 Planarity : 0.004 0.047 1529 Dihedral : 8.563 133.749 1373 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.13 % Allowed : 13.56 % Favored : 83.32 % 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: 2.10 (0.25), residues: 1133 helix: 2.11 (0.19), residues: 756 sheet: 0.56 (0.63), residues: 65 loop : -0.19 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1302 HIS 0.009 0.001 HIS A1379 PHE 0.015 0.002 PHE A1362 TYR 0.015 0.002 TYR A1250 ARG 0.004 0.001 ARG A1461 *********************** 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 134 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 1.049 Fit side-chains REVERT: A 273 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7679 (ttpp) REVERT: A 406 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8765 (p) REVERT: A 591 PHE cc_start: 0.8965 (m-80) cc_final: 0.8650 (m-10) REVERT: A 690 ARG cc_start: 0.8009 (ptt-90) cc_final: 0.7552 (ptm160) REVERT: A 705 CYS cc_start: 0.8144 (m) cc_final: 0.7757 (p) REVERT: A 724 LYS cc_start: 0.7885 (mptt) cc_final: 0.7299 (mtpp) REVERT: A 795 PHE cc_start: 0.8462 (m-80) cc_final: 0.8110 (m-80) REVERT: A 817 CYS cc_start: 0.8695 (t) cc_final: 0.8327 (m) REVERT: A 976 LYS cc_start: 0.7797 (mttp) cc_final: 0.7512 (tptp) REVERT: A 1192 GLN cc_start: 0.7890 (tp40) cc_final: 0.7420 (mt0) REVERT: A 1309 LYS cc_start: 0.8185 (mttt) cc_final: 0.7204 (mptt) REVERT: A 1406 GLU cc_start: 0.7736 (mp0) cc_final: 0.7308 (mp0) REVERT: A 1468 MET cc_start: 0.8714 (mtm) cc_final: 0.8315 (mtp) outliers start: 30 outliers final: 27 residues processed: 127 average time/residue: 0.2567 time to fit residues: 44.4174 Evaluate side-chains 128 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1301 HIS Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1536 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8076 moved from start: 0.3282 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= 0.189 Angle : 0.500 6.624 12525 Z= 0.247 Chirality : 0.039 0.198 1496 Planarity : 0.004 0.045 1529 Dihedral : 8.265 132.666 1373 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.71 % Allowed : 14.39 % Favored : 82.90 % 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: 756 sheet: 0.63 (0.63), residues: 65 loop : -0.16 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1055 HIS 0.008 0.001 HIS A1504 PHE 0.010 0.001 PHE A1362 TYR 0.013 0.001 TYR A1250 ARG 0.005 0.000 ARG A 774 *********************** 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 129 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.8666 (ttt) cc_final: 0.8462 (mtp) REVERT: A 406 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 591 PHE cc_start: 0.8937 (m-80) cc_final: 0.8634 (m-10) REVERT: A 690 ARG cc_start: 0.8001 (ptt-90) cc_final: 0.7570 (ptm160) REVERT: A 722 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 724 LYS cc_start: 0.8005 (mptt) cc_final: 0.7434 (mtpp) REVERT: A 795 PHE cc_start: 0.8342 (m-80) cc_final: 0.7935 (m-80) REVERT: A 817 CYS cc_start: 0.8599 (t) cc_final: 0.8332 (m) REVERT: A 976 LYS cc_start: 0.7776 (mttp) cc_final: 0.7486 (tptp) REVERT: A 1073 ILE cc_start: 0.8691 (tt) cc_final: 0.8370 (tt) REVERT: A 1254 ILE cc_start: 0.8900 (mt) cc_final: 0.8534 (tp) REVERT: A 1309 LYS cc_start: 0.8179 (mttt) cc_final: 0.7193 (mptt) REVERT: A 1406 GLU cc_start: 0.7774 (mp0) cc_final: 0.7303 (mp0) REVERT: A 1468 MET cc_start: 0.8673 (mtm) cc_final: 0.8330 (mtp) outliers start: 26 outliers final: 24 residues processed: 122 average time/residue: 0.2506 time to fit residues: 41.2741 Evaluate side-chains 128 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1301 HIS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1536 VAL 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: 1.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.3348 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= 0.223 Angle : 0.518 7.179 12525 Z= 0.255 Chirality : 0.040 0.197 1496 Planarity : 0.004 0.045 1529 Dihedral : 8.177 131.328 1370 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.92 % Allowed : 14.29 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.37 (0.25), residues: 1133 helix: 2.37 (0.19), residues: 756 sheet: 0.63 (0.63), residues: 65 loop : -0.20 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1055 HIS 0.009 0.001 HIS A1504 PHE 0.009 0.001 PHE A 469 TYR 0.011 0.001 TYR A1250 ARG 0.004 0.000 ARG A 774 *********************** 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 128 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 406 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8721 (p) REVERT: A 591 PHE cc_start: 0.8944 (m-80) cc_final: 0.8641 (m-10) REVERT: A 690 ARG cc_start: 0.8005 (ptt-90) cc_final: 0.7575 (ptm160) REVERT: A 722 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 724 LYS cc_start: 0.8020 (mptt) cc_final: 0.7443 (mtpp) REVERT: A 774 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7622 (tpp-160) REVERT: A 795 PHE cc_start: 0.8369 (m-80) cc_final: 0.8023 (m-80) REVERT: A 817 CYS cc_start: 0.8636 (t) cc_final: 0.8315 (m) REVERT: A 910 MET cc_start: 0.7503 (mtp) cc_final: 0.7125 (mtp) REVERT: A 976 LYS cc_start: 0.7763 (mttp) cc_final: 0.7497 (tptp) REVERT: A 1073 ILE cc_start: 0.8734 (tt) cc_final: 0.8405 (tt) REVERT: A 1254 ILE cc_start: 0.8929 (mt) cc_final: 0.8565 (tp) REVERT: A 1309 LYS cc_start: 0.8173 (mttt) cc_final: 0.7188 (mptt) REVERT: A 1406 GLU cc_start: 0.7703 (mp0) cc_final: 0.7245 (mp0) REVERT: A 1468 MET cc_start: 0.8665 (mtm) cc_final: 0.8339 (mtp) REVERT: A 1484 GLN cc_start: 0.6740 (tt0) cc_final: 0.6451 (tp40) outliers start: 28 outliers final: 26 residues processed: 119 average time/residue: 0.2529 time to fit residues: 40.7812 Evaluate side-chains 127 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1301 HIS Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1536 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 62 optimal weight: 0.0070 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 0.0000 overall best weight: 0.1618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN A1090 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.002 0.034 9208 Z= 0.131 Angle : 0.468 8.061 12525 Z= 0.231 Chirality : 0.037 0.187 1496 Planarity : 0.003 0.046 1529 Dihedral : 7.688 125.141 1370 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.77 % Allowed : 15.85 % Favored : 82.38 % 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: 2.88 (0.25), residues: 1133 helix: 2.79 (0.19), residues: 758 sheet: 0.80 (0.64), residues: 65 loop : -0.12 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1214 HIS 0.010 0.001 HIS A1504 PHE 0.006 0.001 PHE A 772 TYR 0.009 0.001 TYR A1250 ARG 0.004 0.000 ARG A 774 *********************** 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 141 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.125 Fit side-chains REVERT: A 323 GLN cc_start: 0.7955 (tt0) cc_final: 0.7570 (tp40) REVERT: A 406 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8560 (p) REVERT: A 690 ARG cc_start: 0.7911 (ptt-90) cc_final: 0.7469 (ptm160) REVERT: A 724 LYS cc_start: 0.7951 (mptt) cc_final: 0.7446 (mtpp) REVERT: A 764 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7644 (mt-10) REVERT: A 774 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7697 (tpp-160) REVERT: A 976 LYS cc_start: 0.7771 (mttp) cc_final: 0.7485 (tptp) REVERT: A 1055 TRP cc_start: 0.7591 (t-100) cc_final: 0.7009 (t-100) REVERT: A 1254 ILE cc_start: 0.8728 (mt) cc_final: 0.8410 (tp) REVERT: A 1309 LYS cc_start: 0.8256 (mttt) cc_final: 0.7109 (mptt) REVERT: A 1329 LYS cc_start: 0.8446 (ptmt) cc_final: 0.7242 (mttm) REVERT: A 1406 GLU cc_start: 0.7698 (mp0) cc_final: 0.7313 (mp0) REVERT: A 1416 GLU cc_start: 0.7892 (tp30) cc_final: 0.7609 (tt0) REVERT: A 1468 MET cc_start: 0.8582 (mtm) cc_final: 0.8334 (mtp) outliers start: 17 outliers final: 9 residues processed: 136 average time/residue: 0.2550 time to fit residues: 47.1741 Evaluate side-chains 116 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1536 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8050 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9208 Z= 0.185 Angle : 0.508 8.262 12525 Z= 0.249 Chirality : 0.039 0.173 1496 Planarity : 0.004 0.045 1529 Dihedral : 7.749 125.469 1370 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.15 % Allowed : 17.21 % Favored : 81.65 % 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: 2.73 (0.25), residues: 1133 helix: 2.66 (0.19), residues: 761 sheet: 0.84 (0.64), residues: 65 loop : -0.19 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1302 HIS 0.010 0.001 HIS A1504 PHE 0.014 0.001 PHE A1540 TYR 0.014 0.001 TYR A1250 ARG 0.004 0.000 ARG A 774 ********************** 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 116 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 GLN cc_start: 0.7977 (tt0) cc_final: 0.7601 (tp40) REVERT: A 406 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 690 ARG cc_start: 0.7992 (ptt-90) cc_final: 0.7516 (ptm160) REVERT: A 724 LYS cc_start: 0.7934 (mptt) cc_final: 0.7499 (mtpp) REVERT: A 976 LYS cc_start: 0.7763 (mttp) cc_final: 0.7480 (tptp) REVERT: A 1254 ILE cc_start: 0.8995 (mt) cc_final: 0.8681 (tp) REVERT: A 1329 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7358 (mtpp) REVERT: A 1416 GLU cc_start: 0.7923 (tp30) cc_final: 0.7640 (tt0) REVERT: A 1426 MET cc_start: 0.6724 (ttt) cc_final: 0.6449 (ttt) REVERT: A 1468 MET cc_start: 0.8643 (mtm) cc_final: 0.8339 (mtp) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.2539 time to fit residues: 38.6290 Evaluate side-chains 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.151972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121424 restraints weight = 10426.239| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.87 r_work: 0.3257 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9208 Z= 0.190 Angle : 0.521 9.287 12525 Z= 0.252 Chirality : 0.039 0.180 1496 Planarity : 0.003 0.044 1529 Dihedral : 7.817 125.985 1370 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.15 % Allowed : 17.41 % Favored : 81.44 % 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: 2.66 (0.25), residues: 1133 helix: 2.59 (0.19), residues: 761 sheet: 0.81 (0.64), residues: 65 loop : -0.18 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 286 HIS 0.010 0.001 HIS A1504 PHE 0.012 0.001 PHE A1540 TYR 0.013 0.001 TYR A 505 ARG 0.003 0.000 ARG A1461 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.44 seconds wall clock time: 37 minutes 50.34 seconds (2270.34 seconds total)