Starting phenix.real_space_refine on Tue Mar 19 22:38:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/03_2024/7mvu_24056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/03_2024/7mvu_24056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/03_2024/7mvu_24056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/03_2024/7mvu_24056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/03_2024/7mvu_24056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/03_2024/7mvu_24056.pdb" } resolution = 3.77 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= -0.001 sd= 0.025 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 66 5.16 5 C 8190 2.51 5 N 2169 2.21 5 O 2379 1.98 5 H 12841 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 305": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 452": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 503": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 985": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1259": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1300": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1506": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25645 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 24654 Classifications: {'peptide': 1541} Link IDs: {'PTRANS': 58, 'TRANS': 1482} Chain breaks: 16 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 991 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Time building chain proxies: 10.94, per 1000 atoms: 0.43 Number of scatterers: 25645 At special positions: 0 Unit cell: (86.736, 118.428, 195.156, 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 66 16.00 O 2379 8.00 N 2169 7.00 C 8190 6.00 H 12841 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 - 3.50 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: 19.78 Conformation dependent library (CDL) restraints added in 2.5 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3076 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 2 sheets defined 77.2% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.830A pdb=" N GLU A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.887A pdb=" N ALA A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.536A pdb=" N ASN A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.245A pdb=" N THR A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 144 removed outlier: 3.632A pdb=" N ARG A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 184 through 212 removed outlier: 3.882A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 252 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.502A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.725A 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: 3.519A pdb=" N ARG A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.650A 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: 3.604A pdb=" N LYS A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.881A pdb=" N LEU A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.986A pdb=" N GLN A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 455 removed outlier: 3.565A 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: 4.576A 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: 3.534A 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: 3.909A pdb=" N ARG A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.734A pdb=" N ASN A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.790A pdb=" N GLU A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 730 Processing helix chain 'A' and resid 758 through 772 removed outlier: 3.647A pdb=" N VAL A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 799 removed outlier: 3.596A pdb=" N THR A 799 " --> pdb=" O VAL A 795 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 842 through 854 removed outlier: 3.632A pdb=" N ILE A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 863 removed outlier: 3.887A pdb=" N LEU A 860 " --> pdb=" O ASP A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 894 removed outlier: 5.136A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.858A 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 928 through 937 removed outlier: 4.073A pdb=" N VAL A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 941 removed outlier: 4.159A pdb=" N GLY A 941 " --> pdb=" O CYS A 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 938 through 941' 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 Processing helix chain 'A' and resid 1012 through 1031 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.683A 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 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: 4.201A pdb=" N LEU A1152 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1183 removed outlier: 3.688A pdb=" N ALA A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1198 removed outlier: 4.130A pdb=" N LYS A1189 " --> pdb=" O ILE A1185 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A1190 " --> pdb=" O PRO A1186 " (cutoff:3.500A) removed outlier: 4.771A 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 1257 through 1276 removed outlier: 4.196A pdb=" N ALA A1261 " --> pdb=" O ASP A1257 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A1276 " --> pdb=" O TYR A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1326 removed outlier: 3.751A pdb=" N PHE A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A1284 " --> pdb=" O PRO A1280 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR A1285 " --> pdb=" O GLU A1281 " (cutoff:3.500A) removed outlier: 4.199A 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: 3.920A pdb=" N GLU A1363 " --> pdb=" O ASP A1359 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A1368 " --> pdb=" O LEU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1413 removed outlier: 3.705A pdb=" N GLN A1405 " --> pdb=" O PHE A1401 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A1406 " --> pdb=" O GLN A1402 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A1407 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1408 " --> pdb=" O PHE A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1435 removed outlier: 3.523A pdb=" N ALA A1434 " --> pdb=" O ARG A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1472 removed outlier: 3.778A pdb=" N TYR A1471 " --> pdb=" O ALA A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1482 removed outlier: 3.770A pdb=" N LEU A1476 " --> pdb=" O GLY A1472 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A1478 " --> pdb=" O ARG A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1508 removed outlier: 3.929A pdb=" N THR A1492 " --> pdb=" O THR A1488 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1508 " --> pdb=" O THR A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1529 removed outlier: 3.728A pdb=" N ASP A1524 " --> pdb=" O CYS A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1538 removed outlier: 3.720A pdb=" N VAL A1534 " --> pdb=" O ASN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1546 removed outlier: 3.641A pdb=" N GLU A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1587 removed outlier: 3.582A pdb=" N CYS A1587 " --> pdb=" O LEU A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1599 removed outlier: 3.657A pdb=" N ALA A1593 " --> pdb=" O THR A1589 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS A1594 " --> pdb=" O ARG A1590 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A1595 " --> pdb=" O GLN A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1608 removed outlier: 3.722A pdb=" N GLN A1607 " --> pdb=" O ARG A1603 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A1608 " --> pdb=" O ALA A1604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1603 through 1608' Processing helix chain 'A' and resid 1630 through 1654 removed outlier: 4.444A pdb=" N ARG A1653 " --> pdb=" O ALA A1649 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY A1654 " --> pdb=" O VAL A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1668 Processing helix chain 'A' and resid 1670 through 1680 removed outlier: 3.533A pdb=" N VAL A1675 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A1679 " --> pdb=" O VAL A1675 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.993A pdb=" N TYR A1738 " --> pdb=" O GLY A1734 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 284 removed outlier: 3.599A pdb=" N SER B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 4.130A 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 840 hydrogen bonds defined for protein. 2502 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: 9.12 Time building geometry restraints manager: 20.68 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: 12809 1.03 - 1.23: 32 1.23 - 1.42: 5384 1.42 - 1.62: 7561 1.62 - 1.81: 100 Bond restraints: 25886 Sorted by residual: bond pdb=" N PRO A1186 " pdb=" CD PRO A1186 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET A 1 " pdb=" H MET A 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" CA GLY A 757 " pdb=" C GLY A 757 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.43e+00 bond pdb=" N GLY A 757 " pdb=" CA GLY A 757 " ideal model delta sigma weight residual 1.449 1.465 -0.016 1.45e-02 4.76e+03 1.18e+00 ... (remaining 25881 not shown) Histogram of bond angle deviations from ideal: 73.92 - 85.93: 3 85.93 - 97.94: 0 97.94 - 109.95: 21415 109.95 - 121.96: 21199 121.96 - 133.97: 4237 Bond angle restraints: 46854 Sorted by residual: angle pdb=" C SER A1187 " pdb=" CA SER A1187 " pdb=" HA SER A1187 " ideal model delta sigma weight residual 109.00 73.92 35.08 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N SER A1187 " pdb=" CA SER A1187 " pdb=" HA SER A1187 " ideal model delta sigma weight residual 110.00 75.50 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB SER A1187 " pdb=" CA SER A1187 " pdb=" HA SER A1187 " ideal model delta sigma weight residual 109.00 74.86 34.14 3.00e+00 1.11e-01 1.29e+02 angle pdb=" N LYS A 978 " pdb=" CA LYS A 978 " pdb=" C LYS A 978 " ideal model delta sigma weight residual 114.56 110.92 3.64 1.27e+00 6.20e-01 8.23e+00 angle pdb=" N LEU A1283 " pdb=" CA LEU A1283 " pdb=" C LEU A1283 " ideal model delta sigma weight residual 111.02 107.89 3.13 1.22e+00 6.72e-01 6.58e+00 ... (remaining 46849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.12: 11355 12.12 - 24.24: 515 24.24 - 36.36: 99 36.36 - 48.48: 49 48.48 - 60.60: 61 Dihedral angle restraints: 12079 sinusoidal: 6584 harmonic: 5495 Sorted by residual: dihedral pdb=" C SER A1187 " pdb=" N SER A1187 " pdb=" CA SER A1187 " pdb=" CB SER A1187 " ideal model delta harmonic sigma weight residual -122.60 -131.33 8.73 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" N SER A1187 " pdb=" C SER A1187 " pdb=" CA SER A1187 " pdb=" CB SER A1187 " ideal model delta harmonic sigma weight residual 122.80 130.62 -7.82 0 2.50e+00 1.60e-01 9.78e+00 dihedral pdb=" N LEU B 279 " pdb=" CA LEU B 279 " pdb=" CB LEU B 279 " pdb=" CG LEU B 279 " ideal model delta sinusoidal sigma weight residual -60.00 -98.85 38.85 3 1.50e+01 4.44e-03 6.86e+00 ... (remaining 12076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1907 0.067 - 0.135: 120 0.135 - 0.202: 1 0.202 - 0.269: 0 0.269 - 0.337: 1 Chirality restraints: 2029 Sorted by residual: chirality pdb=" CA SER A1187 " pdb=" N SER A1187 " pdb=" C SER A1187 " pdb=" CB SER A1187 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ILE A 167 " pdb=" N ILE A 167 " pdb=" C ILE A 167 " pdb=" CB ILE A 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 404 " pdb=" N ILE A 404 " pdb=" C ILE A 404 " pdb=" CB ILE A 404 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 2026 not shown) Planarity restraints: 3782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 759 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 760 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1307 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C LEU A1307 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A1307 " -0.006 2.00e-02 2.50e+03 pdb=" N THR A1308 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1294 " 0.005 2.00e-02 2.50e+03 9.54e-03 9.10e-01 pdb=" C ILE A1294 " -0.016 2.00e-02 2.50e+03 pdb=" O ILE A1294 " 0.006 2.00e-02 2.50e+03 pdb=" N GLU A1295 " 0.005 2.00e-02 2.50e+03 ... (remaining 3779 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1271 2.21 - 2.81: 54868 2.81 - 3.41: 68510 3.41 - 4.00: 83955 4.00 - 4.60: 135333 Nonbonded interactions: 343937 Sorted by model distance: nonbonded pdb=" HA SER A1187 " pdb=" HB3 SER A1187 " model vdw 1.618 1.952 nonbonded pdb=" OE1 GLN A 460 " pdb=" H GLN A 460 " model vdw 1.650 1.850 nonbonded pdb=" OE1 GLU A1013 " pdb=" H GLU A1013 " model vdw 1.653 1.850 nonbonded pdb=" O SER A 421 " pdb=" HD1 HIS A 425 " model vdw 1.661 1.850 nonbonded pdb=" OE1 GLN A 702 " pdb=" H GLN A 702 " model vdw 1.662 1.850 ... (remaining 343932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.360 Extract box with map and model: 2.990 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 76.980 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 0.046 13045 Z= 0.100 Angle : 0.363 5.941 17658 Z= 0.209 Chirality : 0.032 0.337 2029 Planarity : 0.002 0.037 2254 Dihedral : 6.378 60.596 4824 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1568 helix: 0.62 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -2.59 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A1296 HIS 0.001 0.000 HIS A1068 PHE 0.005 0.000 PHE A 745 TYR 0.009 0.001 TYR A1089 ARG 0.001 0.000 ARG A1430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.151 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: 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: 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 191 GLU cc_start: 0.9104 (tt0) cc_final: 0.8644 (tp30) REVERT: A 471 ILE cc_start: 0.8770 (mt) cc_final: 0.8444 (mt) REVERT: A 675 MET cc_start: 0.7012 (mmm) cc_final: 0.5909 (mmm) REVERT: A 1173 ILE cc_start: 0.9086 (mt) cc_final: 0.8789 (tp) REVERT: A 1369 LYS cc_start: 0.8446 (tttt) cc_final: 0.8092 (tppt) REVERT: A 1636 TYR cc_start: 0.9147 (m-80) cc_final: 0.8818 (m-10) REVERT: A 1727 MET cc_start: 0.7813 (ttp) cc_final: 0.7373 (tpt) REVERT: B 290 GLN cc_start: 0.8858 (tt0) cc_final: 0.8369 (tm-30) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.7006 time to fit residues: 295.1708 Evaluate side-chains 186 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN A1135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13045 Z= 0.210 Angle : 0.504 6.606 17658 Z= 0.268 Chirality : 0.034 0.342 2029 Planarity : 0.004 0.039 2254 Dihedral : 2.324 12.039 1716 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.08 % Allowed : 7.97 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1568 helix: 1.80 (0.16), residues: 1162 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 552 HIS 0.003 0.001 HIS A1126 PHE 0.016 0.001 PHE A1067 TYR 0.013 0.001 TYR A 602 ARG 0.006 0.000 ARG A1430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 2.068 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: 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: symmetry clash REVERT: A 190 MET cc_start: 0.9091 (mmm) cc_final: 0.8887 (mmm) REVERT: A 191 GLU cc_start: 0.9146 (tt0) cc_final: 0.8705 (tp30) REVERT: A 1043 LEU cc_start: 0.8717 (mt) cc_final: 0.8473 (mt) REVERT: A 1636 TYR cc_start: 0.9173 (m-80) cc_final: 0.8789 (m-10) REVERT: A 1727 MET cc_start: 0.7915 (ttp) cc_final: 0.7454 (tpt) REVERT: B 247 ASP cc_start: 0.7901 (t70) cc_final: 0.7576 (t70) outliers start: 15 outliers final: 12 residues processed: 196 average time/residue: 0.7018 time to fit residues: 186.1676 Evaluate side-chains 179 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 238 GLN A 254 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN A 771 ASN A1233 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 13045 Z= 0.332 Angle : 0.612 8.410 17658 Z= 0.335 Chirality : 0.035 0.355 2029 Planarity : 0.004 0.043 2254 Dihedral : 2.947 13.767 1716 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.87 % Allowed : 8.76 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1568 helix: 1.56 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 287 HIS 0.009 0.002 HIS A 239 PHE 0.027 0.002 PHE A1404 TYR 0.023 0.002 TYR A 602 ARG 0.004 0.001 ARG A1310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 2.267 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: 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 191 GLU cc_start: 0.9147 (tt0) cc_final: 0.8669 (tp30) REVERT: A 598 MET cc_start: 0.8096 (tmm) cc_final: 0.7536 (tmm) REVERT: A 602 TYR cc_start: 0.8222 (m-10) cc_final: 0.7943 (m-80) REVERT: A 1636 TYR cc_start: 0.9192 (m-80) cc_final: 0.8764 (m-10) REVERT: B 247 ASP cc_start: 0.8487 (t70) cc_final: 0.8214 (t70) outliers start: 26 outliers final: 19 residues processed: 172 average time/residue: 0.6848 time to fit residues: 162.0476 Evaluate side-chains 158 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1319 ASN A1574 GLN B 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13045 Z= 0.173 Angle : 0.503 6.831 17658 Z= 0.261 Chirality : 0.033 0.342 2029 Planarity : 0.004 0.035 2254 Dihedral : 2.769 13.868 1716 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.65 % Allowed : 9.91 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.21), residues: 1568 helix: 2.08 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1105 HIS 0.007 0.001 HIS A 239 PHE 0.014 0.001 PHE A1404 TYR 0.014 0.001 TYR B 251 ARG 0.003 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 2.071 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: 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 191 GLU cc_start: 0.9070 (tt0) cc_final: 0.8646 (tp30) REVERT: A 1101 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9314 (mt) REVERT: A 1372 LEU cc_start: 0.9279 (tp) cc_final: 0.9052 (tp) REVERT: A 1727 MET cc_start: 0.8187 (ttp) cc_final: 0.7802 (tpp) REVERT: B 247 ASP cc_start: 0.8424 (t70) cc_final: 0.8176 (t70) outliers start: 23 outliers final: 18 residues processed: 161 average time/residue: 0.6673 time to fit residues: 149.9790 Evaluate side-chains 161 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1122 ASN Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1574 GLN Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.0050 chunk 138 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13045 Z= 0.216 Angle : 0.513 6.366 17658 Z= 0.273 Chirality : 0.033 0.337 2029 Planarity : 0.004 0.034 2254 Dihedral : 2.869 13.850 1716 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.65 % Allowed : 10.41 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.21), residues: 1568 helix: 2.10 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.59 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 287 HIS 0.005 0.001 HIS A 239 PHE 0.018 0.001 PHE A1404 TYR 0.014 0.001 TYR B 251 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 2.670 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: 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 191 GLU cc_start: 0.9150 (tt0) cc_final: 0.8685 (tp30) REVERT: A 598 MET cc_start: 0.8407 (tmm) cc_final: 0.7117 (tmm) REVERT: A 602 TYR cc_start: 0.8195 (m-10) cc_final: 0.7592 (m-80) REVERT: A 624 GLU cc_start: 0.8067 (pm20) cc_final: 0.7569 (pm20) REVERT: A 1101 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9328 (mt) REVERT: A 1372 LEU cc_start: 0.9400 (tp) cc_final: 0.9177 (tp) REVERT: A 1495 MET cc_start: 0.8502 (mtm) cc_final: 0.8243 (ptm) REVERT: A 1727 MET cc_start: 0.7979 (ttp) cc_final: 0.7732 (tpp) REVERT: B 247 ASP cc_start: 0.8473 (t70) cc_final: 0.8259 (t70) REVERT: B 273 ARG cc_start: 0.9446 (ptm160) cc_final: 0.9100 (ptm-80) outliers start: 23 outliers final: 20 residues processed: 152 average time/residue: 0.6956 time to fit residues: 148.7057 Evaluate side-chains 157 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 ASN A1459 ASN A1607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13045 Z= 0.263 Angle : 0.573 11.340 17658 Z= 0.311 Chirality : 0.035 0.331 2029 Planarity : 0.004 0.036 2254 Dihedral : 3.258 14.549 1716 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.94 % Allowed : 10.62 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1568 helix: 1.84 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -1.56 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 287 HIS 0.007 0.001 HIS A 239 PHE 0.016 0.001 PHE A 467 TYR 0.016 0.002 TYR B 251 ARG 0.004 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 2.232 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: 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 191 GLU cc_start: 0.9257 (tt0) cc_final: 0.8827 (tp30) REVERT: A 1541 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8547 (mp0) outliers start: 27 outliers final: 21 residues processed: 158 average time/residue: 0.6368 time to fit residues: 142.4927 Evaluate side-chains 150 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 269 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13045 Z= 0.191 Angle : 0.522 11.845 17658 Z= 0.274 Chirality : 0.034 0.334 2029 Planarity : 0.004 0.039 2254 Dihedral : 3.124 13.661 1716 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.44 % Allowed : 11.49 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.21), residues: 1568 helix: 2.09 (0.15), residues: 1183 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 748 HIS 0.004 0.001 HIS A 239 PHE 0.015 0.001 PHE A 467 TYR 0.015 0.001 TYR B 251 ARG 0.008 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 2.264 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: 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 191 GLU cc_start: 0.9225 (tt0) cc_final: 0.8808 (tp30) REVERT: A 1101 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9325 (mt) REVERT: A 1495 MET cc_start: 0.8733 (mtm) cc_final: 0.8298 (ptm) REVERT: A 1541 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: A 1636 TYR cc_start: 0.9037 (m-10) cc_final: 0.8806 (m-10) REVERT: B 247 ASP cc_start: 0.8214 (t70) cc_final: 0.7702 (t0) REVERT: B 249 ASP cc_start: 0.8810 (m-30) cc_final: 0.8533 (m-30) outliers start: 20 outliers final: 16 residues processed: 152 average time/residue: 0.6213 time to fit residues: 136.0759 Evaluate side-chains 151 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 532 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13045 Z= 0.138 Angle : 0.508 11.120 17658 Z= 0.257 Chirality : 0.034 0.338 2029 Planarity : 0.003 0.032 2254 Dihedral : 2.994 14.322 1716 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.22 % Allowed : 11.92 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.22), residues: 1568 helix: 2.44 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.23 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 748 HIS 0.006 0.001 HIS A 239 PHE 0.014 0.001 PHE A 467 TYR 0.014 0.001 TYR B 251 ARG 0.005 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 2.955 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: 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 191 GLU cc_start: 0.9204 (tt0) cc_final: 0.8784 (tp30) REVERT: A 1101 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9273 (mt) REVERT: A 1541 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: B 247 ASP cc_start: 0.8135 (t70) cc_final: 0.7596 (t0) REVERT: B 249 ASP cc_start: 0.8703 (m-30) cc_final: 0.8421 (m-30) outliers start: 17 outliers final: 15 residues processed: 156 average time/residue: 0.6251 time to fit residues: 140.2079 Evaluate side-chains 149 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 532 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13045 Z= 0.164 Angle : 0.516 10.650 17658 Z= 0.266 Chirality : 0.034 0.332 2029 Planarity : 0.003 0.033 2254 Dihedral : 2.974 13.615 1716 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.44 % Allowed : 12.28 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.22), residues: 1568 helix: 2.42 (0.15), residues: 1187 sheet: None (None), residues: 0 loop : -1.19 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 748 HIS 0.005 0.001 HIS A 239 PHE 0.012 0.001 PHE A 467 TYR 0.012 0.001 TYR B 251 ARG 0.005 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.958 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: 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 191 GLU cc_start: 0.9189 (tt0) cc_final: 0.8804 (tp30) REVERT: A 1101 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9275 (mt) REVERT: A 1495 MET cc_start: 0.8720 (mtm) cc_final: 0.8296 (ptm) REVERT: A 1541 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: B 247 ASP cc_start: 0.7795 (t70) cc_final: 0.7277 (t0) REVERT: B 249 ASP cc_start: 0.8695 (m-30) cc_final: 0.8410 (m-30) REVERT: B 273 ARG cc_start: 0.9448 (ptm160) cc_final: 0.9109 (ptm160) outliers start: 20 outliers final: 16 residues processed: 150 average time/residue: 0.6587 time to fit residues: 140.5132 Evaluate side-chains 155 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 532 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 7.9990 chunk 92 optimal weight: 0.4980 chunk 72 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13045 Z= 0.147 Angle : 0.520 10.811 17658 Z= 0.262 Chirality : 0.034 0.334 2029 Planarity : 0.003 0.036 2254 Dihedral : 2.964 13.809 1716 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.08 % Allowed : 12.63 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.54 (0.22), residues: 1568 helix: 2.52 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -1.13 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 748 HIS 0.004 0.001 HIS A 239 PHE 0.012 0.001 PHE A 467 TYR 0.012 0.001 TYR B 251 ARG 0.006 0.000 ARG A1506 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 2.039 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: 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 191 GLU cc_start: 0.9174 (tt0) cc_final: 0.8801 (tp30) REVERT: A 1101 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9251 (mt) REVERT: A 1495 MET cc_start: 0.8700 (mtm) cc_final: 0.8276 (ptm) REVERT: A 1541 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8574 (mp0) REVERT: A 1596 VAL cc_start: 0.8768 (t) cc_final: 0.8556 (m) REVERT: A 1636 TYR cc_start: 0.9042 (m-10) cc_final: 0.8794 (m-10) REVERT: B 247 ASP cc_start: 0.7789 (t70) cc_final: 0.7268 (t0) REVERT: B 249 ASP cc_start: 0.8663 (m-30) cc_final: 0.8383 (m-30) REVERT: B 273 ARG cc_start: 0.9450 (ptm160) cc_final: 0.9116 (ptm160) outliers start: 15 outliers final: 13 residues processed: 152 average time/residue: 0.6310 time to fit residues: 135.6396 Evaluate side-chains 151 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 532 PHE Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.0070 chunk 130 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** 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 = 0.3618 r_free = 0.3618 target = 0.060317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.043679 restraints weight = 226160.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.045973 restraints weight = 120241.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.047541 restraints weight = 77148.664| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13045 Z= 0.136 Angle : 0.515 10.902 17658 Z= 0.257 Chirality : 0.034 0.335 2029 Planarity : 0.003 0.039 2254 Dihedral : 2.896 13.753 1716 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.36 % Allowed : 12.42 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.22), residues: 1568 helix: 2.65 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 748 HIS 0.004 0.001 HIS A 239 PHE 0.014 0.001 PHE A 467 TYR 0.012 0.001 TYR B 251 ARG 0.004 0.000 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5009.58 seconds wall clock time: 93 minutes 22.62 seconds (5602.62 seconds total)