Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 12 07:14:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/07_2023/7mvu_24056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/07_2023/7mvu_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_24056/07_2023/7mvu_24056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/07_2023/7mvu_24056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/07_2023/7mvu_24056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvu_24056/07_2023/7mvu_24056.pdb" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-1.21rc1-5013/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: 10.01, per 1000 atoms: 0.39 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: 19.91 Conformation dependent library (CDL) restraints added in 1.9 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: 0.75 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: 10.02 Time building geometry restraints manager: 20.76 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: 9923 12.12 - 24.24: 409 24.24 - 36.36: 49 36.36 - 48.48: 18 48.48 - 60.60: 1 Dihedral angle restraints: 10400 sinusoidal: 4905 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 10397 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: 0.300 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: 0.420 Extract box with map and model: 4.090 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 74.890 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.440 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.355 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 outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.7371 time to fit residues: 313.1176 Evaluate side-chains 184 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6155 ------------------------------------------------------------------------------- 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: 3.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN A1135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 13045 Z= 0.205 Angle : 0.511 7.146 17658 Z= 0.269 Chirality : 0.033 0.343 2029 Planarity : 0.003 0.039 2254 Dihedral : 2.307 11.953 1716 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 1.01 % 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: 1.81 (0.16), residues: 1165 sheet: None (None), residues: 0 loop : -2.18 (0.28), residues: 403 *********************** 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 199 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 2.001 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 outliers start: 14 outliers final: 12 residues processed: 193 average time/residue: 0.7407 time to fit residues: 194.2028 Evaluate side-chains 177 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3191 time to fit residues: 9.4659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 642 HIS A 718 GLN A 724 GLN B 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13045 Z= 0.179 Angle : 0.507 8.996 17658 Z= 0.260 Chirality : 0.033 0.364 2029 Planarity : 0.003 0.040 2254 Dihedral : 2.420 12.627 1716 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.22), residues: 1568 helix: 2.23 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 398 *********************** 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 176 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 1.887 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 outliers start: 9 outliers final: 4 residues processed: 171 average time/residue: 0.6975 time to fit residues: 163.7567 Evaluate side-chains 155 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3174 time to fit residues: 4.7738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 254 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 ASN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1459 ASN A1607 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 13045 Z= 0.318 Angle : 0.610 6.389 17658 Z= 0.333 Chirality : 0.035 0.332 2029 Planarity : 0.005 0.059 2254 Dihedral : 2.999 18.519 1716 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.72 % 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: 1.27 (0.21), residues: 1568 helix: 1.72 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.87 (0.28), residues: 398 *********************** 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 166 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 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 outliers start: 10 outliers final: 10 residues processed: 163 average time/residue: 0.6845 time to fit residues: 157.1382 Evaluate side-chains 151 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3298 time to fit residues: 8.3157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** A1221 ASN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1574 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13045 Z= 0.216 Angle : 0.527 6.925 17658 Z= 0.281 Chirality : 0.034 0.340 2029 Planarity : 0.004 0.035 2254 Dihedral : 2.941 14.171 1716 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.72 % 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: 1.71 (0.21), residues: 1568 helix: 2.01 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.65 (0.29), residues: 397 *********************** 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 150 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 2.384 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 outliers start: 10 outliers final: 7 residues processed: 145 average time/residue: 0.6632 time to fit residues: 135.7504 Evaluate side-chains 138 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 2.090 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3169 time to fit residues: 6.5319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 154 optimal weight: 0.1980 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 13045 Z= 0.151 Angle : 0.497 6.264 17658 Z= 0.257 Chirality : 0.033 0.338 2029 Planarity : 0.003 0.034 2254 Dihedral : 2.847 13.243 1716 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.22), residues: 1568 helix: 2.36 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.47 (0.30), residues: 397 *********************** 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 148 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 2.098 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 outliers start: 6 outliers final: 3 residues processed: 145 average time/residue: 0.6596 time to fit residues: 134.4632 Evaluate side-chains 138 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3505 time to fit residues: 4.5627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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** A1135 GLN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 13045 Z= 0.274 Angle : 0.569 7.224 17658 Z= 0.312 Chirality : 0.035 0.328 2029 Planarity : 0.004 0.038 2254 Dihedral : 3.184 14.360 1716 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.57 % 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: 1.66 (0.21), residues: 1568 helix: 1.92 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.55 (0.30), residues: 386 *********************** 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 149 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 2.186 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 outliers start: 8 outliers final: 7 residues processed: 143 average time/residue: 0.6936 time to fit residues: 138.4810 Evaluate side-chains 139 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3988 time to fit residues: 7.0780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.0000 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.0670 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 0.3160 ------------------------------------------------------------------------------- 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** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 13045 Z= 0.144 Angle : 0.522 7.804 17658 Z= 0.262 Chirality : 0.035 0.341 2029 Planarity : 0.003 0.033 2254 Dihedral : 2.968 13.440 1716 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.22), residues: 1568 helix: 2.52 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.26 (0.31), residues: 388 *********************** 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 148 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 2.210 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 outliers start: 5 outliers final: 3 residues processed: 145 average time/residue: 0.7117 time to fit residues: 146.7936 Evaluate side-chains 139 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 2.420 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.3570 time to fit residues: 5.0338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 13045 Z= 0.239 Angle : 0.558 8.932 17658 Z= 0.299 Chirality : 0.034 0.325 2029 Planarity : 0.004 0.039 2254 Dihedral : 3.098 13.572 1716 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.21), residues: 1568 helix: 2.22 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -1.37 (0.30), residues: 387 *********************** 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 146 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 2.073 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 outliers start: 5 outliers final: 5 residues processed: 142 average time/residue: 0.6271 time to fit residues: 126.1154 Evaluate side-chains 138 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.872 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.4172 time to fit residues: 5.6116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.3980 chunk 159 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 13045 Z= 0.142 Angle : 0.529 7.614 17658 Z= 0.269 Chirality : 0.034 0.337 2029 Planarity : 0.003 0.036 2254 Dihedral : 2.984 13.763 1716 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.07 % 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: 2.51 (0.22), residues: 1568 helix: 2.52 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -1.16 (0.31), residues: 387 ********************** 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 143 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.897 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 outliers start: 1 outliers final: 1 residues processed: 143 average time/residue: 0.6418 time to fit residues: 131.4124 Evaluate side-chains 138 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.869 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2984 time to fit residues: 3.0575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** ** A1319 ASN ** 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 = 0.3620 r_free = 0.3620 target = 0.060265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.043674 restraints weight = 229016.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.045945 restraints weight = 120042.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.047507 restraints weight = 76936.431| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 13045 Z= 0.161 Angle : 0.527 7.491 17658 Z= 0.272 Chirality : 0.034 0.330 2029 Planarity : 0.003 0.038 2254 Dihedral : 2.958 13.370 1716 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.14 % 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: 2.55 (0.22), residues: 1568 helix: 2.55 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.17 (0.31), residues: 386 =============================================================================== Job complete usr+sys time: 4864.82 seconds wall clock time: 87 minutes 22.72 seconds (5242.72 seconds total)