Starting phenix.real_space_refine on Sat Mar 16 03:01:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf2_31946/03_2024/7vf2_31946.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf2_31946/03_2024/7vf2_31946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf2_31946/03_2024/7vf2_31946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf2_31946/03_2024/7vf2_31946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf2_31946/03_2024/7vf2_31946.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf2_31946/03_2024/7vf2_31946.pdb" } resolution = 3.0 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= 0.005 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 8551 2.51 5 N 2301 2.21 5 O 2630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 426": "OD1" <-> "OD2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 541": "OD1" <-> "OD2" Residue "A TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ASP 706": "OD1" <-> "OD2" Residue "A TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 742": "OD1" <-> "OD2" Residue "A ASP 750": "OD1" <-> "OD2" Residue "A ASP 755": "OD1" <-> "OD2" Residue "A ASP 791": "OD1" <-> "OD2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A ASP 882": "OD1" <-> "OD2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A ASP 1186": "OD1" <-> "OD2" Residue "A ASP 1213": "OD1" <-> "OD2" Residue "A GLU 1215": "OE1" <-> "OE2" Residue "A ASP 1253": "OD1" <-> "OD2" Residue "A ASP 1272": "OD1" <-> "OD2" Residue "A ASP 1294": "OD1" <-> "OD2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A GLU 1356": "OE1" <-> "OE2" Residue "A ASP 1358": "OD1" <-> "OD2" Residue "A PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1389": "OD1" <-> "OD2" Residue "A ASP 1526": "OD1" <-> "OD2" Residue "A PHE 1533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1546": "OD1" <-> "OD2" Residue "A ASP 1562": "OD1" <-> "OD2" Residue "A ARG 1571": "NH1" <-> "NH2" Residue "B ASP 1494": "OD1" <-> "OD2" Residue "B ARG 1512": "NH1" <-> "NH2" Residue "B GLU 1540": "OE1" <-> "OE2" Residue "B ARG 1577": "NH1" <-> "NH2" Residue "B GLU 1580": "OE1" <-> "OE2" Residue "B ARG 1581": "NH1" <-> "NH2" Residue "B ARG 1598": "NH1" <-> "NH2" Residue "B GLU 1611": "OE1" <-> "OE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C ASP 206": "OD1" <-> "OD2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13565 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9390 Classifications: {'peptide': 1196} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1149} Chain breaks: 2 Chain: "B" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1187 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "C" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Time building chain proxies: 7.51, per 1000 atoms: 0.55 Number of scatterers: 13565 At special positions: 0 Unit cell: (112.34, 115.62, 150.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 83 16.00 O 2630 8.00 N 2301 7.00 C 8551 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: 5.47 Conformation dependent library (CDL) restraints added in 2.5 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 3 sheets defined 74.5% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 374 through 390 removed outlier: 3.899A pdb=" N ALA A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 426 through 439 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.570A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 3.878A pdb=" N GLY A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 removed outlier: 4.083A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 543 through 579 removed outlier: 3.688A pdb=" N LYS A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 640 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 668 through 679 removed outlier: 4.074A pdb=" N ARG A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 691 Processing helix chain 'A' and resid 691 through 697 removed outlier: 3.963A pdb=" N HIS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.766A pdb=" N LEU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.681A pdb=" N MET A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.962A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU A 743 " --> pdb=" O TYR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 776 Processing helix chain 'A' and resid 789 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 805 through 816 Processing helix chain 'A' and resid 822 through 833 Processing helix chain 'A' and resid 845 through 862 removed outlier: 3.652A pdb=" N ASN A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.934A pdb=" N GLU A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 871 " --> pdb=" O MET A 867 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER A 874 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'A' and resid 928 through 940 removed outlier: 4.078A pdb=" N THR A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 937 " --> pdb=" O ALA A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 966 removed outlier: 3.775A pdb=" N VAL A 960 " --> pdb=" O TRP A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 989 removed outlier: 3.512A pdb=" N ILE A 973 " --> pdb=" O MET A 969 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN A 985 " --> pdb=" O SER A 981 " (cutoff:3.500A) Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 995 through 1021 Processing helix chain 'A' and resid 1032 through 1045 removed outlier: 3.962A pdb=" N THR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A1042 " --> pdb=" O VAL A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1070 Processing helix chain 'A' and resid 1076 through 1080 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1089 through 1100 Processing helix chain 'A' and resid 1108 through 1120 removed outlier: 3.949A pdb=" N GLU A1118 " --> pdb=" O ILE A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.513A pdb=" N ILE A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1165 removed outlier: 3.801A pdb=" N GLU A1160 " --> pdb=" O LYS A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1184 removed outlier: 3.935A pdb=" N VAL A1182 " --> pdb=" O ARG A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1208 Processing helix chain 'A' and resid 1219 through 1234 Processing helix chain 'A' and resid 1235 through 1247 removed outlier: 3.584A pdb=" N LEU A1245 " --> pdb=" O ALA A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1268 removed outlier: 3.670A pdb=" N ALA A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1291 removed outlier: 4.401A pdb=" N GLU A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1314 removed outlier: 3.601A pdb=" N SER A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1336 removed outlier: 3.687A pdb=" N SER A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A1334 " --> pdb=" O LEU A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 3.601A pdb=" N LEU A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1369 Processing helix chain 'A' and resid 1373 through 1385 Processing helix chain 'A' and resid 1390 through 1406 Processing helix chain 'A' and resid 1434 through 1443 Processing helix chain 'A' and resid 1447 through 1461 Processing helix chain 'A' and resid 1468 through 1486 removed outlier: 3.556A pdb=" N SER A1472 " --> pdb=" O ASP A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1514 Processing helix chain 'A' and resid 1525 through 1530 Processing helix chain 'A' and resid 1554 through 1559 removed outlier: 4.388A pdb=" N LYS A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1575 removed outlier: 3.868A pdb=" N PHE A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A1575 " --> pdb=" O ARG A1571 " (cutoff:3.500A) Processing helix chain 'B' and resid 1517 through 1521 removed outlier: 4.200A pdb=" N LYS B1520 " --> pdb=" O ALA B1517 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B1521 " --> pdb=" O LEU B1518 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1517 through 1521' Processing helix chain 'B' and resid 1522 through 1531 Processing helix chain 'B' and resid 1533 through 1538 removed outlier: 3.762A pdb=" N GLY B1538 " --> pdb=" O LYS B1534 " (cutoff:3.500A) Processing helix chain 'B' and resid 1538 through 1551 Processing helix chain 'B' and resid 1555 through 1561 Processing helix chain 'B' and resid 1567 through 1583 Processing helix chain 'B' and resid 1596 through 1608 Processing helix chain 'B' and resid 1626 through 1643 Processing helix chain 'C' and resid 65 through 98 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 114 through 146 Processing helix chain 'C' and resid 151 through 175 Processing helix chain 'C' and resid 176 through 243 Processing helix chain 'D' and resid 66 through 100 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 114 through 145 removed outlier: 3.604A pdb=" N SER D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 178 removed outlier: 3.634A pdb=" N GLN D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 244 removed outlier: 3.790A pdb=" N GLU D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 657 through 658 Processing sheet with id=AA2, first strand: chain 'A' and resid 1126 through 1128 removed outlier: 6.178A pdb=" N MET A1126 " --> pdb=" O VAL A1519 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1549 through 1551 902 hydrogen bonds defined for protein. 2688 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: 4.38 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2859 1.33 - 1.45: 2695 1.45 - 1.57: 8074 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 13760 Sorted by residual: bond pdb=" C GLN A 647 " pdb=" N GLN A 648 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.47e-02 4.63e+03 1.03e+01 bond pdb=" N ARG B1512 " pdb=" CA ARG B1512 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.72e+00 bond pdb=" N LYS C 146 " pdb=" CA LYS C 146 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.25e-02 6.40e+03 7.07e+00 bond pdb=" C TRP C 145 " pdb=" N LYS C 146 " ideal model delta sigma weight residual 1.333 1.366 -0.034 1.36e-02 5.41e+03 6.08e+00 bond pdb=" N GLU D 141 " pdb=" CA GLU D 141 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.28e-02 6.10e+03 5.73e+00 ... (remaining 13755 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 278 106.03 - 113.03: 7762 113.03 - 120.02: 4877 120.02 - 127.02: 5545 127.02 - 134.02: 120 Bond angle restraints: 18582 Sorted by residual: angle pdb=" N ILE A1541 " pdb=" CA ILE A1541 " pdb=" C ILE A1541 " ideal model delta sigma weight residual 113.47 105.93 7.54 1.01e+00 9.80e-01 5.58e+01 angle pdb=" N VAL A1274 " pdb=" CA VAL A1274 " pdb=" C VAL A1274 " ideal model delta sigma weight residual 113.42 107.22 6.20 1.17e+00 7.31e-01 2.81e+01 angle pdb=" CA GLU B1513 " pdb=" C GLU B1513 " pdb=" N PRO B1514 " ideal model delta sigma weight residual 118.75 123.54 -4.79 9.70e-01 1.06e+00 2.44e+01 angle pdb=" N ALA A 783 " pdb=" CA ALA A 783 " pdb=" C ALA A 783 " ideal model delta sigma weight residual 113.38 107.55 5.83 1.23e+00 6.61e-01 2.24e+01 angle pdb=" N SER A1444 " pdb=" CA SER A1444 " pdb=" C SER A1444 " ideal model delta sigma weight residual 114.75 109.41 5.34 1.26e+00 6.30e-01 1.80e+01 ... (remaining 18577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7715 17.96 - 35.92: 661 35.92 - 53.88: 124 53.88 - 71.84: 42 71.84 - 89.80: 39 Dihedral angle restraints: 8581 sinusoidal: 3540 harmonic: 5041 Sorted by residual: dihedral pdb=" CA HIS A1463 " pdb=" C HIS A1463 " pdb=" N SER A1464 " pdb=" CA SER A1464 " ideal model delta harmonic sigma weight residual 180.00 -156.51 -23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LYS A1251 " pdb=" C LYS A1251 " pdb=" N GLY A1252 " pdb=" CA GLY A1252 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LYS A1465 " pdb=" C LYS A1465 " pdb=" N ASP A1466 " pdb=" CA ASP A1466 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 8578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1579 0.041 - 0.081: 479 0.081 - 0.122: 110 0.122 - 0.162: 13 0.162 - 0.203: 5 Chirality restraints: 2186 Sorted by residual: chirality pdb=" CA GLU D 136 " pdb=" N GLU D 136 " pdb=" C GLU D 136 " pdb=" CB GLU D 136 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ARG B1639 " pdb=" N ARG B1639 " pdb=" C ARG B1639 " pdb=" CB ARG B1639 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" CA GLU B1513 " pdb=" N GLU B1513 " pdb=" C GLU B1513 " pdb=" CB GLU B1513 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 2183 not shown) Planarity restraints: 2386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 669 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO A 670 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 67 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C GLN C 67 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN C 67 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU C 68 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 148 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO D 149 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " 0.021 5.00e-02 4.00e+02 ... (remaining 2383 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 176 2.66 - 3.22: 13487 3.22 - 3.78: 21777 3.78 - 4.34: 29896 4.34 - 4.90: 48636 Nonbonded interactions: 113972 Sorted by model distance: nonbonded pdb=" OG1 THR C 148 " pdb=" OG SER C 151 " model vdw 2.095 2.440 nonbonded pdb=" OD2 ASP A1206 " pdb=" OG1 THR A1222 " model vdw 2.119 2.440 nonbonded pdb=" O ASP A 508 " pdb=" OG SER A 512 " model vdw 2.140 2.440 nonbonded pdb=" OE1 GLU A1311 " pdb=" OG SER A1503 " model vdw 2.160 2.440 nonbonded pdb=" O ILE A 511 " pdb=" OH TYR A 675 " model vdw 2.176 2.440 ... (remaining 113967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 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: 2.270 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: 8.620 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.910 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 0.047 13760 Z= 0.289 Angle : 0.729 10.315 18582 Z= 0.439 Chirality : 0.041 0.203 2186 Planarity : 0.004 0.054 2386 Dihedral : 15.876 89.804 5281 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -2.72 (0.17), residues: 1704 helix: -1.44 (0.13), residues: 1221 sheet: None (None), residues: 0 loop : -2.35 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1500 HIS 0.005 0.001 HIS A1376 PHE 0.012 0.001 PHE A1453 TYR 0.010 0.001 TYR D 193 ARG 0.002 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 1.618 Fit side-chains REVERT: A 1217 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7839 (tp40) REVERT: A 1259 ILE cc_start: 0.8804 (tp) cc_final: 0.8559 (tp) REVERT: A 1483 MET cc_start: 0.8347 (mpp) cc_final: 0.7976 (mpt) REVERT: B 1513 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: B 1514 PRO cc_start: 0.8866 (Cg_exo) cc_final: 0.8394 (Cg_endo) REVERT: C 78 MET cc_start: 0.8123 (tpt) cc_final: 0.7902 (tpt) REVERT: C 233 ARG cc_start: 0.8674 (ttm170) cc_final: 0.8387 (mtt90) REVERT: D 78 MET cc_start: 0.8476 (ptm) cc_final: 0.8258 (pp-130) REVERT: D 236 LEU cc_start: 0.6454 (tt) cc_final: 0.6006 (mt) outliers start: 4 outliers final: 1 residues processed: 220 average time/residue: 1.3088 time to fit residues: 313.7596 Evaluate side-chains 140 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1513 GLU Chi-restraints excluded: chain C residue 94 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 430 GLN A 455 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN A 636 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN A 797 HIS A 823 GLN A 917 GLN A 951 GLN A 962 GLN ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 HIS ** A1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS A1440 GLN A1463 HIS A1482 GLN A1510 ASN C 74 ASN C 85 GLN C 137 GLN C 152 GLN C 219 GLN C 228 GLN D 118 ASN D 137 GLN D 174 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13760 Z= 0.333 Angle : 0.664 11.559 18582 Z= 0.328 Chirality : 0.041 0.163 2186 Planarity : 0.004 0.055 2386 Dihedral : 5.483 74.295 1816 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.46 % Allowed : 12.10 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -1.04 (0.19), residues: 1704 helix: -0.16 (0.14), residues: 1222 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1532 HIS 0.004 0.001 HIS A1363 PHE 0.014 0.002 PHE A1533 TYR 0.013 0.002 TYR A 739 ARG 0.007 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 867 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.7930 (ptp) REVERT: A 1217 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7815 (tp40) REVERT: A 1259 ILE cc_start: 0.8832 (tp) cc_final: 0.8569 (tp) REVERT: A 1483 MET cc_start: 0.8472 (mpp) cc_final: 0.7844 (mpt) REVERT: B 1606 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: C 68 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8460 (tp30) REVERT: C 78 MET cc_start: 0.7991 (tpt) cc_final: 0.7731 (tpt) REVERT: C 136 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7922 (mm-30) REVERT: C 241 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 72 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8006 (mtm-85) REVERT: D 78 MET cc_start: 0.8500 (ptm) cc_final: 0.8295 (pp-130) REVERT: D 89 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8092 (pp20) REVERT: D 236 LEU cc_start: 0.6388 (tt) cc_final: 0.5961 (mt) outliers start: 38 outliers final: 8 residues processed: 167 average time/residue: 1.1250 time to fit residues: 207.6960 Evaluate side-chains 141 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1583 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13760 Z= 0.356 Angle : 0.639 11.357 18582 Z= 0.315 Chirality : 0.041 0.145 2186 Planarity : 0.004 0.055 2386 Dihedral : 4.849 20.896 1811 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.85 % Allowed : 14.42 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.25 (0.20), residues: 1704 helix: 0.40 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : -1.46 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1532 HIS 0.004 0.001 HIS A1363 PHE 0.013 0.001 PHE B1597 TYR 0.013 0.001 TYR D 239 ARG 0.006 0.000 ARG A1402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 1.750 Fit side-chains revert: symmetry clash REVERT: A 426 ASP cc_start: 0.7492 (t0) cc_final: 0.7129 (p0) REVERT: A 867 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.7930 (ptp) REVERT: A 1217 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7833 (tp40) REVERT: A 1402 ARG cc_start: 0.7987 (mtp85) cc_final: 0.6945 (mmm-85) REVERT: A 1483 MET cc_start: 0.8472 (mpp) cc_final: 0.7689 (mpt) REVERT: B 1606 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: C 136 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7943 (mm-30) REVERT: C 241 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8275 (tm-30) REVERT: D 78 MET cc_start: 0.8508 (ptm) cc_final: 0.8290 (pp-130) REVERT: D 89 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8147 (pp20) REVERT: D 206 ASP cc_start: 0.8017 (m-30) cc_final: 0.7774 (m-30) REVERT: D 236 LEU cc_start: 0.6371 (tt) cc_final: 0.6001 (mt) outliers start: 44 outliers final: 16 residues processed: 170 average time/residue: 1.1196 time to fit residues: 211.4561 Evaluate side-chains 150 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1054 ASP Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1491 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1583 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 10.0000 chunk 116 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 HIS A1336 ASN B1507 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13760 Z= 0.185 Angle : 0.573 10.639 18582 Z= 0.280 Chirality : 0.037 0.149 2186 Planarity : 0.004 0.051 2386 Dihedral : 4.577 19.417 1811 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.10 % Allowed : 15.78 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.45 (0.20), residues: 1704 helix: 0.93 (0.15), residues: 1218 sheet: None (None), residues: 0 loop : -1.22 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1532 HIS 0.004 0.001 HIS A1376 PHE 0.012 0.001 PHE A1573 TYR 0.016 0.001 TYR D 239 ARG 0.007 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7630 (t) REVERT: A 426 ASP cc_start: 0.7372 (t0) cc_final: 0.6979 (p0) REVERT: A 522 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7280 (ptp-110) REVERT: A 831 TYR cc_start: 0.7738 (t80) cc_final: 0.7495 (t80) REVERT: A 867 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.7713 (ptp) REVERT: A 1217 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7808 (tp40) REVERT: A 1259 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8503 (tp) REVERT: A 1402 ARG cc_start: 0.7875 (mtp85) cc_final: 0.6880 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8468 (tptt) cc_final: 0.8234 (tptt) REVERT: A 1483 MET cc_start: 0.8491 (mpp) cc_final: 0.7708 (mpt) REVERT: B 1606 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: C 136 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7980 (mm-30) REVERT: C 241 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8204 (tm-30) REVERT: D 78 MET cc_start: 0.8507 (ptm) cc_final: 0.8280 (pp-130) REVERT: D 163 MET cc_start: 0.8226 (tpp) cc_final: 0.8010 (tpt) REVERT: D 206 ASP cc_start: 0.7907 (m-30) cc_final: 0.7658 (m-30) REVERT: D 236 LEU cc_start: 0.6391 (tt) cc_final: 0.6023 (mt) outliers start: 48 outliers final: 10 residues processed: 180 average time/residue: 1.0702 time to fit residues: 214.2277 Evaluate side-chains 146 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain A residue 1549 LYS Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 10.0000 chunk 93 optimal weight: 0.0020 chunk 2 optimal weight: 0.3980 chunk 122 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 overall best weight: 0.8910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13760 Z= 0.219 Angle : 0.582 11.136 18582 Z= 0.282 Chirality : 0.038 0.190 2186 Planarity : 0.003 0.050 2386 Dihedral : 4.424 18.622 1811 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.98 % Allowed : 17.46 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.84 (0.20), residues: 1704 helix: 1.22 (0.15), residues: 1219 sheet: None (None), residues: 0 loop : -1.07 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1532 HIS 0.003 0.001 HIS A1376 PHE 0.011 0.001 PHE A 738 TYR 0.018 0.001 TYR D 239 ARG 0.007 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7546 (t) REVERT: A 426 ASP cc_start: 0.7298 (t0) cc_final: 0.6953 (p0) REVERT: A 522 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7259 (ptp-110) REVERT: A 831 TYR cc_start: 0.7756 (t80) cc_final: 0.7511 (t80) REVERT: A 867 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.7771 (ptp) REVERT: A 1217 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7795 (tp40) REVERT: A 1259 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 1402 ARG cc_start: 0.7785 (mtp85) cc_final: 0.6820 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8495 (tptt) cc_final: 0.8197 (tptt) REVERT: A 1483 MET cc_start: 0.8535 (mpp) cc_final: 0.7777 (mpt) REVERT: B 1606 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: C 136 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7917 (mm-30) REVERT: C 241 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 78 MET cc_start: 0.8500 (ptm) cc_final: 0.8291 (pp-130) REVERT: D 108 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8660 (tp) REVERT: D 163 MET cc_start: 0.8313 (tpp) cc_final: 0.8042 (tpt) REVERT: D 206 ASP cc_start: 0.7929 (m-30) cc_final: 0.7696 (m-30) REVERT: D 236 LEU cc_start: 0.6325 (tt) cc_final: 0.5958 (mt) outliers start: 46 outliers final: 18 residues processed: 177 average time/residue: 1.1236 time to fit residues: 220.5587 Evaluate side-chains 160 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1365 LYS Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1583 SER Chi-restraints excluded: chain B residue 1586 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13760 Z= 0.180 Angle : 0.581 12.635 18582 Z= 0.278 Chirality : 0.037 0.167 2186 Planarity : 0.003 0.047 2386 Dihedral : 4.287 18.277 1811 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 18.63 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.11 (0.21), residues: 1704 helix: 1.42 (0.15), residues: 1221 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1532 HIS 0.003 0.001 HIS A1376 PHE 0.017 0.001 PHE A1573 TYR 0.020 0.001 TYR D 239 ARG 0.012 0.000 ARG B1551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7336 (t) REVERT: A 426 ASP cc_start: 0.7230 (t0) cc_final: 0.6936 (p0) REVERT: A 522 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7201 (ptp-110) REVERT: A 831 TYR cc_start: 0.7728 (t80) cc_final: 0.7496 (t80) REVERT: A 867 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.7691 (ptp) REVERT: A 1217 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7787 (tp40) REVERT: A 1259 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8476 (tp) REVERT: A 1402 ARG cc_start: 0.7745 (mtp85) cc_final: 0.6843 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8501 (tptt) cc_final: 0.8242 (tptt) REVERT: A 1483 MET cc_start: 0.8527 (mpp) cc_final: 0.7742 (mpt) REVERT: A 1548 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7565 (t) REVERT: C 136 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7968 (mm-30) REVERT: C 241 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 78 MET cc_start: 0.8512 (ptm) cc_final: 0.8302 (pp-130) REVERT: D 108 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8652 (tp) REVERT: D 112 MET cc_start: 0.8414 (mmp) cc_final: 0.7982 (mmp) REVERT: D 163 MET cc_start: 0.8372 (tpp) cc_final: 0.8027 (tpt) REVERT: D 206 ASP cc_start: 0.7905 (m-30) cc_final: 0.7681 (m-30) REVERT: D 236 LEU cc_start: 0.6329 (tt) cc_final: 0.5954 (mt) outliers start: 38 outliers final: 15 residues processed: 179 average time/residue: 1.1988 time to fit residues: 235.7557 Evaluate side-chains 160 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1365 LYS Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1518 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 0.0270 chunk 120 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13760 Z= 0.191 Angle : 0.579 13.134 18582 Z= 0.279 Chirality : 0.038 0.184 2186 Planarity : 0.003 0.046 2386 Dihedral : 4.223 18.111 1811 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.33 % Allowed : 19.15 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.30 (0.21), residues: 1704 helix: 1.55 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : -0.87 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1532 HIS 0.003 0.001 HIS A1363 PHE 0.010 0.001 PHE A 738 TYR 0.011 0.001 TYR A 914 ARG 0.010 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 420 LEU cc_start: 0.8747 (pp) cc_final: 0.8403 (pt) REVERT: A 423 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7223 (t) REVERT: A 426 ASP cc_start: 0.7177 (t0) cc_final: 0.6952 (p0) REVERT: A 831 TYR cc_start: 0.7744 (t80) cc_final: 0.7515 (t80) REVERT: A 867 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.7677 (ptp) REVERT: A 1217 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7790 (tp40) REVERT: A 1259 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 1402 ARG cc_start: 0.7782 (mtp85) cc_final: 0.6874 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8532 (tptt) cc_final: 0.8304 (tptt) REVERT: A 1483 MET cc_start: 0.8532 (mpp) cc_final: 0.7755 (mpt) REVERT: A 1548 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7604 (t) REVERT: C 136 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7965 (mm-30) REVERT: C 241 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8149 (tm-30) REVERT: D 78 MET cc_start: 0.8494 (ptm) cc_final: 0.8278 (pp-130) REVERT: D 108 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8641 (tp) REVERT: D 206 ASP cc_start: 0.7905 (m-30) cc_final: 0.7672 (m-30) REVERT: D 236 LEU cc_start: 0.6333 (tt) cc_final: 0.5955 (mt) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 1.2356 time to fit residues: 227.2290 Evaluate side-chains 158 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1518 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1583 SER Chi-restraints excluded: chain B residue 1586 SER Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.0770 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13760 Z= 0.190 Angle : 0.586 14.024 18582 Z= 0.280 Chirality : 0.037 0.179 2186 Planarity : 0.003 0.046 2386 Dihedral : 4.160 18.013 1811 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.07 % Allowed : 19.86 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.40 (0.21), residues: 1704 helix: 1.62 (0.15), residues: 1227 sheet: None (None), residues: 0 loop : -0.84 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1532 HIS 0.002 0.001 HIS A1363 PHE 0.021 0.001 PHE A1573 TYR 0.011 0.001 TYR A 914 ARG 0.014 0.001 ARG D 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 426 ASP cc_start: 0.7139 (t0) cc_final: 0.6896 (p0) REVERT: A 831 TYR cc_start: 0.7790 (t80) cc_final: 0.7587 (t80) REVERT: A 867 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.7683 (ptp) REVERT: A 1259 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8460 (tp) REVERT: A 1402 ARG cc_start: 0.7757 (mtp85) cc_final: 0.6914 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8565 (tptt) cc_final: 0.8323 (tptt) REVERT: A 1483 MET cc_start: 0.8526 (mpp) cc_final: 0.7744 (mpt) REVERT: C 72 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8352 (mtm-85) REVERT: C 136 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7994 (mm-30) REVERT: D 78 MET cc_start: 0.8492 (ptm) cc_final: 0.8273 (pp-130) REVERT: D 108 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8644 (tp) REVERT: D 206 ASP cc_start: 0.7869 (m-30) cc_final: 0.7642 (m-30) REVERT: D 233 ARG cc_start: 0.7510 (ptp-110) cc_final: 0.7200 (mtm-85) REVERT: D 236 LEU cc_start: 0.6370 (tt) cc_final: 0.6085 (tp) REVERT: D 239 TYR cc_start: 0.6692 (t80) cc_final: 0.6354 (t80) outliers start: 32 outliers final: 16 residues processed: 168 average time/residue: 1.2132 time to fit residues: 225.5922 Evaluate side-chains 155 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1518 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1583 SER Chi-restraints excluded: chain B residue 1586 SER Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 152 optimal weight: 30.0000 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.0020 chunk 46 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13760 Z= 0.213 Angle : 0.600 14.823 18582 Z= 0.287 Chirality : 0.038 0.181 2186 Planarity : 0.003 0.046 2386 Dihedral : 4.125 18.026 1811 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.62 % Allowed : 20.57 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.40 (0.21), residues: 1704 helix: 1.61 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -0.90 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1532 HIS 0.003 0.001 HIS A1363 PHE 0.012 0.001 PHE B1597 TYR 0.010 0.001 TYR A 914 ARG 0.013 0.001 ARG D 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 426 ASP cc_start: 0.7072 (t0) cc_final: 0.6871 (p0) REVERT: A 831 TYR cc_start: 0.7795 (t80) cc_final: 0.7559 (t80) REVERT: A 867 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.7708 (ptp) REVERT: A 1259 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8466 (tp) REVERT: A 1402 ARG cc_start: 0.7656 (mtp85) cc_final: 0.6872 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8574 (tptt) cc_final: 0.8323 (tptt) REVERT: A 1483 MET cc_start: 0.8551 (mpp) cc_final: 0.7803 (mpt) REVERT: C 72 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: C 136 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7972 (mm-30) REVERT: D 72 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7977 (mtm-85) REVERT: D 78 MET cc_start: 0.8480 (ptm) cc_final: 0.8263 (pp-130) REVERT: D 108 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8632 (tp) REVERT: D 206 ASP cc_start: 0.7866 (m-30) cc_final: 0.7642 (m-30) REVERT: D 236 LEU cc_start: 0.6343 (tt) cc_final: 0.6073 (tp) REVERT: D 239 TYR cc_start: 0.6738 (t80) cc_final: 0.6483 (t80) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 1.1875 time to fit residues: 208.0927 Evaluate side-chains 155 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1365 LYS Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain B residue 1518 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1583 SER Chi-restraints excluded: chain B residue 1586 SER Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 GLN C 241 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13760 Z= 0.337 Angle : 0.653 15.953 18582 Z= 0.310 Chirality : 0.040 0.178 2186 Planarity : 0.004 0.046 2386 Dihedral : 4.261 22.599 1811 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.62 % Allowed : 20.63 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.28 (0.20), residues: 1704 helix: 1.51 (0.15), residues: 1229 sheet: None (None), residues: 0 loop : -0.85 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1532 HIS 0.004 0.001 HIS A1363 PHE 0.025 0.002 PHE A1573 TYR 0.013 0.001 TYR A 531 ARG 0.013 0.001 ARG D 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.4544 (ttp) cc_final: 0.3974 (ttp) REVERT: A 423 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7359 (t) REVERT: A 426 ASP cc_start: 0.7086 (t0) cc_final: 0.6861 (p0) REVERT: A 831 TYR cc_start: 0.7837 (t80) cc_final: 0.7607 (t80) REVERT: A 867 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.7845 (ptp) REVERT: A 1259 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8527 (tp) REVERT: A 1402 ARG cc_start: 0.7696 (mtp85) cc_final: 0.6880 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8560 (tptt) cc_final: 0.8310 (tptt) REVERT: A 1483 MET cc_start: 0.8578 (mpp) cc_final: 0.7805 (mpt) REVERT: C 136 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7980 (mm-30) REVERT: D 78 MET cc_start: 0.8497 (ptm) cc_final: 0.8273 (pp-130) REVERT: D 108 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8677 (tp) REVERT: D 206 ASP cc_start: 0.7915 (m-30) cc_final: 0.7683 (m-30) REVERT: D 236 LEU cc_start: 0.6381 (tt) cc_final: 0.5961 (mt) outliers start: 25 outliers final: 15 residues processed: 156 average time/residue: 1.1838 time to fit residues: 203.6783 Evaluate side-chains 153 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1365 LYS Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1583 SER Chi-restraints excluded: chain B residue 1586 SER Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.145744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096766 restraints weight = 20045.006| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.86 r_work: 0.3252 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13760 Z= 0.214 Angle : 0.617 16.421 18582 Z= 0.293 Chirality : 0.038 0.158 2186 Planarity : 0.004 0.045 2386 Dihedral : 4.206 18.166 1811 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.55 % Allowed : 20.89 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 1.40 (0.21), residues: 1704 helix: 1.59 (0.15), residues: 1241 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1532 HIS 0.003 0.001 HIS A1363 PHE 0.012 0.001 PHE D 120 TYR 0.024 0.001 TYR D 239 ARG 0.012 0.001 ARG D 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4580.02 seconds wall clock time: 81 minutes 54.36 seconds (4914.36 seconds total)