Starting phenix.real_space_refine on Thu Mar 5 23:31:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mvv_24057/03_2026/7mvv_24057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mvv_24057/03_2026/7mvv_24057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mvv_24057/03_2026/7mvv_24057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mvv_24057/03_2026/7mvv_24057.map" model { file = "/net/cci-nas-00/data/ceres_data/7mvv_24057/03_2026/7mvv_24057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mvv_24057/03_2026/7mvv_24057.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.002 sd= 0.049 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: 5 Type Number sf(0) Gaussians S 67 5.16 5 C 8233 2.51 5 N 2175 2.21 5 O 2382 1.98 5 H 12907 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25764 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 24672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 24672 Classifications: {'peptide': 1542} Link IDs: {'PTRANS': 58, 'TRANS': 1483} Chain breaks: 16 Chain: "B" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 911 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 155 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Time building chain proxies: 4.58, per 1000 atoms: 0.18 Number of scatterers: 25764 At special positions: 0 Unit cell: (86.6688, 117.926, 194.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 O 2382 8.00 N 2175 7.00 C 8233 6.00 H 12907 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 2 sheets defined 76.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.767A pdb=" N THR A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.953A pdb=" N ALA A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.560A pdb=" N ARG A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.845A pdb=" N ASN A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 116 through 144 removed outlier: 3.535A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 122 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 removed outlier: 3.540A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 212 removed outlier: 3.777A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.639A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.641A pdb=" N ILE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.720A pdb=" N ARG A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.688A pdb=" N GLY A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 371 Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.538A pdb=" N LYS A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.968A pdb=" N LEU A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 Processing helix chain 'A' and resid 437 through 455 removed outlier: 3.580A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.308A pdb=" N ASP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'A' and resid 551 through 568 Processing helix chain 'A' and resid 592 through 613 Processing helix chain 'A' and resid 614 through 621 removed outlier: 3.537A pdb=" N ILE A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.836A pdb=" N ARG A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.708A pdb=" N ASN A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.792A pdb=" N GLU A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 730 Processing helix chain 'A' and resid 758 through 772 removed outlier: 3.808A pdb=" N VAL A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 798 Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 820 through 831 Processing helix chain 'A' and resid 832 through 841 removed outlier: 3.580A pdb=" N PHE A 841 " --> pdb=" O MET A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 854 removed outlier: 3.580A pdb=" N ILE A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 863 removed outlier: 3.949A pdb=" N LEU A 860 " --> pdb=" O ASP A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 894 removed outlier: 5.115A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 919 through 925 removed outlier: 4.220A pdb=" N GLY A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 removed outlier: 4.112A pdb=" N VAL A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 942 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 987 through 1002 removed outlier: 3.510A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1031 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.703A pdb=" N GLN A1041 " --> pdb=" O THR A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1076 Processing helix chain 'A' and resid 1088 through 1107 removed outlier: 3.532A pdb=" N SER A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1148 through 1153 removed outlier: 4.190A pdb=" N LEU A1152 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1183 removed outlier: 3.738A pdb=" N ALA A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1198 removed outlier: 4.077A pdb=" N LYS A1189 " --> pdb=" O ILE A1185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A1190 " --> pdb=" O PRO A1186 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN A1191 " --> pdb=" O SER A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1217 Processing helix chain 'A' and resid 1258 through 1276 removed outlier: 3.693A pdb=" N ILE A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A1276 " --> pdb=" O TYR A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1327 removed outlier: 3.512A pdb=" N VAL A1286 " --> pdb=" O PHE A1282 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A1295 " --> pdb=" O LYS A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1353 Proline residue: A1348 - end of helix Processing helix chain 'A' and resid 1359 through 1374 removed outlier: 4.003A pdb=" N GLU A1363 " --> pdb=" O ASP A1359 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A1368 " --> pdb=" O LEU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1414 removed outlier: 3.584A pdb=" N LEU A1406 " --> pdb=" O GLN A1402 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS A1407 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1434 removed outlier: 3.621A pdb=" N TYR A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A1425 " --> pdb=" O ARG A1421 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A1426 " --> pdb=" O SER A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1472 removed outlier: 3.527A pdb=" N ALA A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A1468 " --> pdb=" O THR A1464 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A1471 " --> pdb=" O ALA A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1483 removed outlier: 3.556A pdb=" N LEU A1476 " --> pdb=" O GLY A1472 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A1478 " --> pdb=" O ARG A1474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A1483 " --> pdb=" O ILE A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1508 removed outlier: 3.755A pdb=" N THR A1492 " --> pdb=" O THR A1488 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A1499 " --> pdb=" O MET A1495 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A1500 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A1507 " --> pdb=" O HIS A1503 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A1508 " --> pdb=" O THR A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1529 removed outlier: 3.625A pdb=" N ASP A1524 " --> pdb=" O CYS A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1539 removed outlier: 3.626A pdb=" N LEU A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1546 removed outlier: 3.828A pdb=" N GLU A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1587 Processing helix chain 'A' and resid 1589 through 1598 removed outlier: 3.901A pdb=" N ALA A1593 " --> pdb=" O THR A1589 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS A1594 " --> pdb=" O ARG A1590 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A1595 " --> pdb=" O GLN A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1608 removed outlier: 3.652A pdb=" N ALA A1604 " --> pdb=" O ASN A1600 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A1606 " --> pdb=" O PHE A1602 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A1607 " --> pdb=" O ARG A1603 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A1608 " --> pdb=" O ALA A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1654 removed outlier: 3.534A pdb=" N THR A1651 " --> pdb=" O GLY A1647 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A1653 " --> pdb=" O ALA A1649 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A1654 " --> pdb=" O VAL A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1668 removed outlier: 3.768A pdb=" N LYS A1663 " --> pdb=" O VAL A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1680 removed outlier: 3.555A pdb=" N VAL A1675 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A1679 " --> pdb=" O VAL A1675 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A1680 " --> pdb=" O LEU A1676 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1734 Processing helix chain 'A' and resid 1734 through 1739 removed outlier: 3.913A pdb=" N TYR A1738 " --> pdb=" O GLY A1734 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 284 removed outlier: 3.657A pdb=" N LEU B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 4.036A pdb=" N TYR B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 1199 through 1200 818 hydrogen bonds defined for protein. 2436 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: 6.23 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12875 1.03 - 1.23: 35 1.23 - 1.42: 5401 1.42 - 1.62: 7594 1.62 - 1.81: 102 Bond restraints: 26007 Sorted by residual: bond pdb=" N ALA A 721 " pdb=" CA ALA A 721 " ideal model delta sigma weight residual 1.458 1.392 0.067 1.26e-02 6.30e+03 2.81e+01 bond pdb=" CA ALA A 721 " pdb=" C ALA A 721 " ideal model delta sigma weight residual 1.524 1.458 0.065 1.32e-02 5.74e+03 2.46e+01 bond pdb=" C ILE A 723 " pdb=" O ILE A 723 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.12e-02 7.97e+03 2.41e+01 bond pdb=" CA ALA A 721 " pdb=" CB ALA A 721 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.62e-02 3.81e+03 1.67e+01 bond pdb=" C PHE A 722 " pdb=" O PHE A 722 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.26e-02 6.30e+03 1.41e+01 ... (remaining 26002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 45945 1.23 - 2.47: 1065 2.47 - 3.70: 48 3.70 - 4.93: 16 4.93 - 6.16: 6 Bond angle restraints: 47080 Sorted by residual: angle pdb=" CA ASN A 720 " pdb=" C ASN A 720 " pdb=" N ALA A 721 " ideal model delta sigma weight residual 117.63 111.47 6.16 1.25e+00 6.40e-01 2.43e+01 angle pdb=" O ASN A 720 " pdb=" C ASN A 720 " pdb=" N ALA A 721 " ideal model delta sigma weight residual 122.22 127.58 -5.36 1.17e+00 7.31e-01 2.10e+01 angle pdb=" C ILE A 723 " pdb=" N GLN A 724 " pdb=" CA GLN A 724 " ideal model delta sigma weight residual 120.28 125.69 -5.41 1.34e+00 5.57e-01 1.63e+01 angle pdb=" CA ILE A 723 " pdb=" C ILE A 723 " pdb=" N GLN A 724 " ideal model delta sigma weight residual 117.02 121.29 -4.27 1.11e+00 8.12e-01 1.48e+01 angle pdb=" CA ILE A 723 " pdb=" C ILE A 723 " pdb=" O ILE A 723 " ideal model delta sigma weight residual 121.05 117.89 3.16 1.11e+00 8.12e-01 8.12e+00 ... (remaining 47075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.89: 11422 11.89 - 23.79: 490 23.79 - 35.68: 104 35.68 - 47.57: 63 47.57 - 59.46: 59 Dihedral angle restraints: 12138 sinusoidal: 6616 harmonic: 5522 Sorted by residual: dihedral pdb=" CA ILE A1185 " pdb=" CB ILE A1185 " pdb=" CG1 ILE A1185 " pdb=" CD1 ILE A1185 " ideal model delta sinusoidal sigma weight residual 60.00 113.82 -53.82 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" C ILE A 723 " pdb=" N ILE A 723 " pdb=" CA ILE A 723 " pdb=" CB ILE A 723 " ideal model delta harmonic sigma weight residual -122.00 -129.27 7.27 0 2.50e+00 1.60e-01 8.47e+00 dihedral pdb=" CA ILE A1294 " pdb=" CB ILE A1294 " pdb=" CG1 ILE A1294 " pdb=" CD1 ILE A1294 " ideal model delta sinusoidal sigma weight residual 60.00 99.96 -39.96 3 1.50e+01 4.44e-03 7.10e+00 ... (remaining 12135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1805 0.050 - 0.101: 209 0.101 - 0.151: 21 0.151 - 0.201: 0 0.201 - 0.251: 3 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CA PHE A 722 " pdb=" N PHE A 722 " pdb=" C PHE A 722 " pdb=" CB PHE A 722 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ILE A 723 " pdb=" N ILE A 723 " pdb=" C ILE A 723 " pdb=" CB ILE A 723 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ALA A 721 " pdb=" N ALA A 721 " pdb=" C ALA A 721 " pdb=" CB ALA A 721 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2035 not shown) Planarity restraints: 3791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 720 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ASN A 720 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN A 720 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 721 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 723 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" N GLN A 724 " -0.030 2.00e-02 2.50e+03 pdb=" CA GLN A 724 " 0.008 2.00e-02 2.50e+03 pdb=" H GLN A 724 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 759 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 760 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.019 5.00e-02 4.00e+02 ... (remaining 3788 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1357 2.22 - 2.81: 55112 2.81 - 3.41: 67673 3.41 - 4.00: 83710 4.00 - 4.60: 133691 Nonbonded interactions: 341543 Sorted by model distance: nonbonded pdb=" O GLU A 161 " pdb=" H ILE A 167 " model vdw 1.621 2.450 nonbonded pdb=" O ASN A1122 " pdb=" HD1 HIS A1126 " model vdw 1.638 2.450 nonbonded pdb=" O SER A 421 " pdb=" HD1 HIS A 425 " model vdw 1.643 2.450 nonbonded pdb=" OE1 GLN A 460 " pdb=" H GLN A 460 " model vdw 1.648 2.450 nonbonded pdb=" OE1 GLU A1013 " pdb=" H GLU A1013 " model vdw 1.653 2.450 ... (remaining 341538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.570 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: 0.160 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.002 0.067 13100 Z= 0.136 Angle : 0.355 6.164 17731 Z= 0.203 Chirality : 0.032 0.251 2038 Planarity : 0.002 0.035 2260 Dihedral : 6.426 53.817 4846 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1569 helix: 0.28 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -2.18 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 478 TYR 0.012 0.000 TYR A1089 PHE 0.021 0.001 PHE A 722 TRP 0.005 0.000 TRP A1296 HIS 0.001 0.000 HIS A1068 Details of bonding type rmsd covalent geometry : bond 0.00205 (13100) covalent geometry : angle 0.35535 (17731) hydrogen bonds : bond 0.18190 ( 818) hydrogen bonds : angle 5.08478 ( 2436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7742 (tm-30) cc_final: 0.6803 (mm-30) REVERT: A 471 ILE cc_start: 0.8263 (mt) cc_final: 0.7703 (mt) REVERT: A 1404 PHE cc_start: 0.8916 (t80) cc_final: 0.8690 (t80) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.3443 time to fit residues: 85.6833 Evaluate side-chains 112 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 457 ASN A1063 GLN A1402 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.083519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.065092 restraints weight = 197442.405| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 5.34 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13100 Z= 0.149 Angle : 0.522 6.139 17731 Z= 0.272 Chirality : 0.035 0.141 2038 Planarity : 0.004 0.062 2260 Dihedral : 2.549 14.981 1720 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.57 % Allowed : 5.43 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1569 helix: 1.68 (0.15), residues: 1157 sheet: None (None), residues: 0 loop : -1.89 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 270 TYR 0.011 0.001 TYR A1636 PHE 0.021 0.001 PHE A 467 TRP 0.006 0.001 TRP A 118 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00315 (13100) covalent geometry : angle 0.52206 (17731) hydrogen bonds : bond 0.04357 ( 818) hydrogen bonds : angle 3.76027 ( 2436) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6595 (mm-30) REVERT: A 1023 ASP cc_start: 0.9036 (m-30) cc_final: 0.8754 (m-30) REVERT: A 1086 MET cc_start: 0.9282 (mmp) cc_final: 0.8965 (mmp) REVERT: A 1402 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9057 (tt0) REVERT: A 1718 ARG cc_start: 0.8799 (mmt-90) cc_final: 0.8496 (mmm-85) REVERT: B 247 ASP cc_start: 0.7672 (t0) cc_final: 0.7283 (t0) outliers start: 8 outliers final: 5 residues processed: 115 average time/residue: 0.3566 time to fit residues: 54.2342 Evaluate side-chains 101 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1402 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 298 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 67 optimal weight: 0.0770 chunk 146 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 overall best weight: 1.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 224 ASN A 677 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.078193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.059494 restraints weight = 202477.660| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 5.05 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13100 Z= 0.171 Angle : 0.501 6.276 17731 Z= 0.265 Chirality : 0.034 0.151 2038 Planarity : 0.003 0.032 2260 Dihedral : 2.865 18.409 1720 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.50 % Allowed : 5.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1569 helix: 2.12 (0.15), residues: 1163 sheet: None (None), residues: 0 loop : -1.56 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1644 TYR 0.012 0.001 TYR A 901 PHE 0.022 0.001 PHE A1338 TRP 0.009 0.001 TRP A 331 HIS 0.008 0.001 HIS A1674 Details of bonding type rmsd covalent geometry : bond 0.00365 (13100) covalent geometry : angle 0.50103 (17731) hydrogen bonds : bond 0.04232 ( 818) hydrogen bonds : angle 3.74681 ( 2436) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1023 ASP cc_start: 0.8974 (m-30) cc_final: 0.8699 (m-30) outliers start: 7 outliers final: 4 residues processed: 101 average time/residue: 0.3380 time to fit residues: 46.0377 Evaluate side-chains 89 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.078250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.059092 restraints weight = 203392.149| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 5.15 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13100 Z= 0.125 Angle : 0.459 6.194 17731 Z= 0.238 Chirality : 0.033 0.158 2038 Planarity : 0.003 0.026 2260 Dihedral : 2.824 16.579 1720 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.79 % Allowed : 6.29 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.22), residues: 1569 helix: 2.53 (0.15), residues: 1163 sheet: None (None), residues: 0 loop : -1.43 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1430 TYR 0.012 0.001 TYR A1089 PHE 0.014 0.001 PHE A1404 TRP 0.005 0.001 TRP A 674 HIS 0.002 0.001 HIS A1674 Details of bonding type rmsd covalent geometry : bond 0.00264 (13100) covalent geometry : angle 0.45865 (17731) hydrogen bonds : bond 0.03416 ( 818) hydrogen bonds : angle 3.47992 ( 2436) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8368 (mmp) cc_final: 0.7916 (mmp) REVERT: A 1023 ASP cc_start: 0.8993 (m-30) cc_final: 0.8726 (m-30) REVERT: A 1336 MET cc_start: 0.8336 (ttm) cc_final: 0.8114 (ttm) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.3167 time to fit residues: 42.0035 Evaluate side-chains 90 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1182 GLN ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.076661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.058138 restraints weight = 198494.260| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.90 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13100 Z= 0.139 Angle : 0.476 6.603 17731 Z= 0.248 Chirality : 0.033 0.157 2038 Planarity : 0.003 0.025 2260 Dihedral : 2.975 16.119 1720 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.64 % Allowed : 6.00 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.22), residues: 1569 helix: 2.66 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.41 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1634 TYR 0.013 0.001 TYR A1089 PHE 0.011 0.001 PHE A 745 TRP 0.019 0.001 TRP A1546 HIS 0.007 0.001 HIS A1674 Details of bonding type rmsd covalent geometry : bond 0.00297 (13100) covalent geometry : angle 0.47650 (17731) hydrogen bonds : bond 0.03539 ( 818) hydrogen bonds : angle 3.53038 ( 2436) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8459 (mmp) cc_final: 0.8065 (mmp) REVERT: A 1115 MET cc_start: 0.9233 (mmm) cc_final: 0.8998 (mmm) REVERT: A 1419 GLU cc_start: 0.9186 (pm20) cc_final: 0.8937 (pm20) REVERT: B 269 GLU cc_start: 0.9303 (tm-30) cc_final: 0.9036 (pp20) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.3136 time to fit residues: 39.2412 Evaluate side-chains 82 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 2 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1344 GLN ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.075325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.056773 restraints weight = 199770.839| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 4.82 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13100 Z= 0.170 Angle : 0.494 6.338 17731 Z= 0.261 Chirality : 0.034 0.205 2038 Planarity : 0.003 0.026 2260 Dihedral : 3.139 16.640 1720 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.79 % Allowed : 5.93 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.22), residues: 1569 helix: 2.59 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1430 TYR 0.014 0.001 TYR A1089 PHE 0.013 0.001 PHE A 745 TRP 0.007 0.001 TRP A 331 HIS 0.009 0.001 HIS A1674 Details of bonding type rmsd covalent geometry : bond 0.00362 (13100) covalent geometry : angle 0.49415 (17731) hydrogen bonds : bond 0.03782 ( 818) hydrogen bonds : angle 3.70987 ( 2436) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8476 (mmp) cc_final: 0.8083 (mmp) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.3196 time to fit residues: 37.6628 Evaluate side-chains 82 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 122 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.076003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.057536 restraints weight = 196747.515| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.81 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13100 Z= 0.102 Angle : 0.453 7.247 17731 Z= 0.231 Chirality : 0.033 0.137 2038 Planarity : 0.003 0.024 2260 Dihedral : 3.012 16.523 1720 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.57 % Allowed : 6.07 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.22), residues: 1569 helix: 2.88 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1421 TYR 0.015 0.001 TYR A1089 PHE 0.010 0.001 PHE A1531 TRP 0.008 0.001 TRP A1296 HIS 0.005 0.001 HIS A1674 Details of bonding type rmsd covalent geometry : bond 0.00219 (13100) covalent geometry : angle 0.45310 (17731) hydrogen bonds : bond 0.03247 ( 818) hydrogen bonds : angle 3.41318 ( 2436) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8436 (mmp) cc_final: 0.8014 (mmp) REVERT: A 1115 MET cc_start: 0.9283 (mmm) cc_final: 0.9058 (mmm) outliers start: 8 outliers final: 7 residues processed: 83 average time/residue: 0.3247 time to fit residues: 37.2422 Evaluate side-chains 80 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 52 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1221 ASN ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.074630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.056149 restraints weight = 199381.602| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.76 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13100 Z= 0.154 Angle : 0.488 6.843 17731 Z= 0.256 Chirality : 0.034 0.214 2038 Planarity : 0.003 0.028 2260 Dihedral : 3.154 17.149 1720 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.57 % Allowed : 5.93 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.22), residues: 1569 helix: 2.73 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1184 TYR 0.013 0.001 TYR A1089 PHE 0.012 0.001 PHE A 745 TRP 0.006 0.001 TRP A 332 HIS 0.009 0.001 HIS A1674 Details of bonding type rmsd covalent geometry : bond 0.00329 (13100) covalent geometry : angle 0.48783 (17731) hydrogen bonds : bond 0.03685 ( 818) hydrogen bonds : angle 3.62635 ( 2436) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8748 (mmm) cc_final: 0.8289 (mmm) REVERT: A 1115 MET cc_start: 0.9247 (mmm) cc_final: 0.8999 (mmm) REVERT: B 263 MET cc_start: 0.8711 (tmm) cc_final: 0.8311 (tmm) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 0.3222 time to fit residues: 36.0301 Evaluate side-chains 78 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.074103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.055607 restraints weight = 200057.949| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.74 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13100 Z= 0.189 Angle : 0.531 8.382 17731 Z= 0.281 Chirality : 0.035 0.152 2038 Planarity : 0.003 0.032 2260 Dihedral : 3.413 17.657 1720 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.57 % Allowed : 6.21 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.22), residues: 1569 helix: 2.49 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.55 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 985 TYR 0.014 0.001 TYR A1089 PHE 0.013 0.001 PHE A 745 TRP 0.008 0.001 TRP A 331 HIS 0.012 0.001 HIS A1674 Details of bonding type rmsd covalent geometry : bond 0.00403 (13100) covalent geometry : angle 0.53058 (17731) hydrogen bonds : bond 0.04057 ( 818) hydrogen bonds : angle 3.85142 ( 2436) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8523 (mmp) cc_final: 0.8093 (mmp) REVERT: A 483 MET cc_start: 0.8814 (mmm) cc_final: 0.8439 (mmm) REVERT: A 1115 MET cc_start: 0.9296 (mmm) cc_final: 0.9067 (mmm) REVERT: A 1233 HIS cc_start: 0.8736 (p-80) cc_final: 0.8356 (p90) REVERT: A 1336 MET cc_start: 0.8139 (tpp) cc_final: 0.7902 (mmt) REVERT: A 1338 PHE cc_start: 0.8124 (m-80) cc_final: 0.7463 (t80) REVERT: B 251 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7649 (t80) outliers start: 8 outliers final: 7 residues processed: 80 average time/residue: 0.3023 time to fit residues: 34.0976 Evaluate side-chains 78 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.074239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.055933 restraints weight = 197873.475| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 4.73 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13100 Z= 0.147 Angle : 0.501 9.316 17731 Z= 0.260 Chirality : 0.034 0.142 2038 Planarity : 0.003 0.058 2260 Dihedral : 3.343 18.610 1720 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.64 % Allowed : 6.43 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.22), residues: 1569 helix: 2.60 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 985 TYR 0.014 0.001 TYR A1089 PHE 0.010 0.001 PHE A 745 TRP 0.008 0.001 TRP A1296 HIS 0.012 0.001 HIS A1656 Details of bonding type rmsd covalent geometry : bond 0.00313 (13100) covalent geometry : angle 0.50053 (17731) hydrogen bonds : bond 0.03755 ( 818) hydrogen bonds : angle 3.68934 ( 2436) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8829 (mmm) cc_final: 0.8381 (mmm) REVERT: A 1233 HIS cc_start: 0.8692 (p-80) cc_final: 0.8380 (p90) REVERT: A 1338 PHE cc_start: 0.8086 (m-80) cc_final: 0.7466 (t80) REVERT: B 251 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7679 (t80) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.2989 time to fit residues: 33.3571 Evaluate side-chains 78 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.074592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.056318 restraints weight = 197994.371| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.74 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13100 Z= 0.113 Angle : 0.478 9.226 17731 Z= 0.245 Chirality : 0.033 0.130 2038 Planarity : 0.003 0.029 2260 Dihedral : 3.233 18.416 1720 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.71 % Allowed : 6.29 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.22), residues: 1569 helix: 2.82 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.37 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 669 TYR 0.014 0.001 TYR A1089 PHE 0.010 0.001 PHE B 275 TRP 0.009 0.001 TRP A1296 HIS 0.007 0.001 HIS A1674 Details of bonding type rmsd covalent geometry : bond 0.00245 (13100) covalent geometry : angle 0.47844 (17731) hydrogen bonds : bond 0.03381 ( 818) hydrogen bonds : angle 3.51684 ( 2436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4700.71 seconds wall clock time: 80 minutes 27.44 seconds (4827.44 seconds total)