Starting phenix.real_space_refine on Sat Dec 9 19:25:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw3_33490/12_2023/7xw3_33490.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw3_33490/12_2023/7xw3_33490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw3_33490/12_2023/7xw3_33490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw3_33490/12_2023/7xw3_33490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw3_33490/12_2023/7xw3_33490.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw3_33490/12_2023/7xw3_33490.pdb" } resolution = 4.04 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= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 7694 2.51 5 N 2060 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 732": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 824": "OE1" <-> "OE2" Residue "A GLU 866": "OE1" <-> "OE2" Residue "A GLU 898": "OE1" <-> "OE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 1018": "OE1" <-> "OE2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A ASP 1088": "OD1" <-> "OD2" Residue "A TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1444": "OE1" <-> "OE2" Residue "A GLU 1448": "OE1" <-> "OE2" Residue "A ASP 1454": "OD1" <-> "OD2" Residue "A GLU 1600": "OE1" <-> "OE2" Residue "A ASP 1654": "OD1" <-> "OD2" Residue "A GLU 1670": "OE1" <-> "OE2" Residue "A GLU 1705": "OE1" <-> "OE2" Residue "A TYR 1752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1764": "OE1" <-> "OE2" Residue "A GLU 1781": "OE1" <-> "OE2" Residue "A ASP 1786": "OD1" <-> "OD2" Residue "A GLU 1788": "OE1" <-> "OE2" Residue "A GLU 1794": "OE1" <-> "OE2" Residue "A GLU 1796": "OE1" <-> "OE2" Residue "A GLU 1797": "OE1" <-> "OE2" Residue "A GLU 1813": "OE1" <-> "OE2" Residue "A TYR 1820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1822": "OD1" <-> "OD2" Residue "A GLU 1828": "OE1" <-> "OE2" Residue "A GLU 1871": "OE1" <-> "OE2" Residue "A ASP 1875": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12081 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1502, 12081 Classifications: {'peptide': 1502} Link IDs: {'PTRANS': 89, 'TRANS': 1412} Chain breaks: 5 Time building chain proxies: 6.72, per 1000 atoms: 0.56 Number of scatterers: 12081 At special positions: 0 Unit cell: (101.384, 106.894, 160.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 2260 8.00 N 2060 7.00 C 7694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 2.3 seconds 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2878 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 43.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 removed outlier: 4.268A pdb=" N GLU A 50 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 58 removed outlier: 4.271A pdb=" N ALA A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 4.912A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 5.387A pdb=" N TYR A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 84 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.698A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.873A pdb=" N TRP A 133 " --> pdb=" O ASN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.544A pdb=" N LEU A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.338A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 Processing helix chain 'A' and resid 266 through 282 Processing helix chain 'A' and resid 295 through 313 Processing helix chain 'A' and resid 314 through 336 removed outlier: 3.969A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 363 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.748A pdb=" N ILE A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 468 through 473 removed outlier: 3.625A pdb=" N TYR A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 510 removed outlier: 3.669A pdb=" N ALA A 510 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 567 through 588 removed outlier: 4.429A pdb=" N SER A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.770A pdb=" N ILE A 631 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 705 Processing helix chain 'A' and resid 754 through 758 Processing helix chain 'A' and resid 839 through 857 Processing helix chain 'A' and resid 893 through 903 removed outlier: 3.745A pdb=" N MET A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 903 " --> pdb=" O ASP A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 974 removed outlier: 3.598A pdb=" N TYR A 971 " --> pdb=" O THR A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1036 No H-bonds generated for 'chain 'A' and resid 1034 through 1036' Processing helix chain 'A' and resid 1044 through 1053 removed outlier: 3.963A pdb=" N CYS A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1078 Processing helix chain 'A' and resid 1293 through 1302 removed outlier: 3.748A pdb=" N ILE A1297 " --> pdb=" O ASN A1293 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A1299 " --> pdb=" O GLY A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1333 removed outlier: 3.894A pdb=" N MET A1317 " --> pdb=" O GLU A1313 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1351 removed outlier: 5.487A pdb=" N LYS A1349 " --> pdb=" O TYR A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1361 removed outlier: 3.777A pdb=" N ARG A1358 " --> pdb=" O CYS A1354 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1359 " --> pdb=" O ASN A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1369 removed outlier: 3.595A pdb=" N MET A1369 " --> pdb=" O PRO A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1380 removed outlier: 3.502A pdb=" N ASN A1379 " --> pdb=" O ASP A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1452 removed outlier: 4.120A pdb=" N ILE A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1587 removed outlier: 4.234A pdb=" N ALA A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY A1568 " --> pdb=" O GLU A1564 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N GLU A1576 " --> pdb=" O THR A1572 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N ARG A1577 " --> pdb=" O SER A1573 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A1578 " --> pdb=" O CYS A1574 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1586 " --> pdb=" O PHE A1582 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A1587 " --> pdb=" O LEU A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1601 removed outlier: 3.533A pdb=" N ARG A1599 " --> pdb=" O LYS A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1668 removed outlier: 4.418A pdb=" N ASN A1668 " --> pdb=" O SER A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1688 removed outlier: 4.344A pdb=" N PHE A1687 " --> pdb=" O LEU A1683 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1722 removed outlier: 3.759A pdb=" N ALA A1710 " --> pdb=" O PHE A1706 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1752 Processing helix chain 'A' and resid 1762 through 1778 removed outlier: 3.955A pdb=" N PHE A1766 " --> pdb=" O SER A1762 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1801 Processing helix chain 'A' and resid 1807 through 1823 removed outlier: 3.564A pdb=" N ILE A1811 " --> pdb=" O ALA A1807 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER A1823 " --> pdb=" O ILE A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1846 removed outlier: 3.981A pdb=" N VAL A1830 " --> pdb=" O SER A1826 " (cutoff:3.500A) Proline residue: A1836 - end of helix Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1852 through 1861 Processing helix chain 'A' and resid 1896 through 1916 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.685A pdb=" N THR A 60 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 204 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 203 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 removed outlier: 5.514A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 256 removed outlier: 5.844A pdb=" N SER A 558 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS A 251 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 560 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 253 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 562 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 534 " --> pdb=" O ASN A 559 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 563 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 445 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY A 444 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA A 518 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE A 446 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 589 through 590 Processing sheet with id=AA5, first strand: chain 'A' and resid 652 through 657 Processing sheet with id=AA6, first strand: chain 'A' and resid 746 through 750 removed outlier: 4.133A pdb=" N GLN A 747 " --> pdb=" O ILE A1554 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A1554 " --> pdb=" O GLN A 747 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 805 through 806 removed outlier: 3.617A pdb=" N THR A 806 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 836 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 770 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER A 834 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL A 772 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS A 832 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 777 removed outlier: 3.673A pdb=" N VAL A 776 " --> pdb=" O THR A 826 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 823 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 820 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 801 through 802 Processing sheet with id=AB1, first strand: chain 'A' and resid 865 through 867 removed outlier: 3.711A pdb=" N GLU A 866 " --> pdb=" O VAL A1386 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A1386 " --> pdb=" O GLU A 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 988 through 991 removed outlier: 5.702A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 947 " --> pdb=" O ASP A 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 945 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL A 931 " --> pdb=" O HIS A1041 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1878 through 1881 removed outlier: 3.611A pdb=" N VAL A1878 " --> pdb=" O GLY A1894 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A1894 " --> pdb=" O VAL A1878 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A1892 " --> pdb=" O VAL A1880 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2063 1.32 - 1.44: 3116 1.44 - 1.57: 7070 1.57 - 1.69: 0 1.69 - 1.82: 95 Bond restraints: 12344 Sorted by residual: bond pdb=" N ARG A 763 " pdb=" CA ARG A 763 " ideal model delta sigma weight residual 1.455 1.485 -0.030 7.00e-03 2.04e+04 1.88e+01 bond pdb=" C VAL A 129 " pdb=" O VAL A 129 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.23e-02 6.61e+03 1.28e+01 bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" N ILE A 813 " pdb=" CA ILE A 813 " ideal model delta sigma weight residual 1.461 1.491 -0.031 9.10e-03 1.21e+04 1.13e+01 bond pdb=" N GLN A 488 " pdb=" CA GLN A 488 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.04e-02 9.25e+03 1.12e+01 ... (remaining 12339 not shown) Histogram of bond angle deviations from ideal: 96.67 - 104.29: 267 104.29 - 111.90: 5682 111.90 - 119.52: 4923 119.52 - 127.13: 5741 127.13 - 134.74: 99 Bond angle restraints: 16712 Sorted by residual: angle pdb=" N ILE A 73 " pdb=" CA ILE A 73 " pdb=" C ILE A 73 " ideal model delta sigma weight residual 113.43 103.09 10.34 1.09e+00 8.42e-01 9.00e+01 angle pdb=" N PRO A1376 " pdb=" CA PRO A1376 " pdb=" C PRO A1376 " ideal model delta sigma weight residual 110.70 121.51 -10.81 1.22e+00 6.72e-01 7.85e+01 angle pdb=" N THR A 71 " pdb=" CA THR A 71 " pdb=" C THR A 71 " ideal model delta sigma weight residual 111.28 103.06 8.22 1.09e+00 8.42e-01 5.69e+01 angle pdb=" N MET A1346 " pdb=" CA MET A1346 " pdb=" C MET A1346 " ideal model delta sigma weight residual 112.72 103.16 9.56 1.28e+00 6.10e-01 5.58e+01 angle pdb=" N ASN A1455 " pdb=" CA ASN A1455 " pdb=" C ASN A1455 " ideal model delta sigma weight residual 112.87 105.22 7.65 1.20e+00 6.94e-01 4.07e+01 ... (remaining 16707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6709 17.66 - 35.32: 681 35.32 - 52.98: 124 52.98 - 70.64: 53 70.64 - 88.29: 27 Dihedral angle restraints: 7594 sinusoidal: 3153 harmonic: 4441 Sorted by residual: dihedral pdb=" C ASP A1753 " pdb=" N ASP A1753 " pdb=" CA ASP A1753 " pdb=" CB ASP A1753 " ideal model delta harmonic sigma weight residual -122.60 -141.23 18.63 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" N ASP A1753 " pdb=" C ASP A1753 " pdb=" CA ASP A1753 " pdb=" CB ASP A1753 " ideal model delta harmonic sigma weight residual 122.80 139.98 -17.18 0 2.50e+00 1.60e-01 4.72e+01 dihedral pdb=" C TYR A1752 " pdb=" N TYR A1752 " pdb=" CA TYR A1752 " pdb=" CB TYR A1752 " ideal model delta harmonic sigma weight residual -122.60 -135.92 13.32 0 2.50e+00 1.60e-01 2.84e+01 ... (remaining 7591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1754 0.139 - 0.279: 103 0.279 - 0.418: 7 0.418 - 0.558: 1 0.558 - 0.697: 1 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CA ASP A1753 " pdb=" N ASP A1753 " pdb=" C ASP A1753 " pdb=" CB ASP A1753 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA PHE A 72 " pdb=" N PHE A 72 " pdb=" C PHE A 72 " pdb=" CB PHE A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA TYR A1752 " pdb=" N TYR A1752 " pdb=" C TYR A1752 " pdb=" CB TYR A1752 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 1863 not shown) Planarity restraints: 2158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 553 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ALA A 553 " 0.075 2.00e-02 2.50e+03 pdb=" O ALA A 553 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG A 554 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1667 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C GLU A1667 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU A1667 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN A1668 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1778 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLU A1778 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU A1778 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS A1779 " -0.020 2.00e-02 2.50e+03 ... (remaining 2155 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1908 2.75 - 3.29: 12432 3.29 - 3.83: 19617 3.83 - 4.36: 23741 4.36 - 4.90: 38336 Nonbonded interactions: 96034 Sorted by model distance: nonbonded pdb=" OD2 ASP A 319 " pdb=" NZ LYS A 320 " model vdw 2.218 2.520 nonbonded pdb=" O HIS A 145 " pdb=" NE2 GLN A 146 " model vdw 2.219 2.520 nonbonded pdb=" O HIS A 856 " pdb=" NH2 ARG A 944 " model vdw 2.244 2.520 nonbonded pdb=" N GLU A 188 " pdb=" OE1 GLU A 188 " model vdw 2.248 2.520 nonbonded pdb=" O SER A1287 " pdb=" OG SER A1287 " model vdw 2.256 2.440 ... (remaining 96029 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=0.00 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.290 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.720 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 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 : 0.009 0.119 12344 Z= 0.620 Angle : 1.242 11.914 16712 Z= 0.820 Chirality : 0.074 0.697 1866 Planarity : 0.007 0.078 2158 Dihedral : 16.199 88.294 4716 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.39 % Favored : 91.54 % Rotamer: Outliers : 2.51 % Allowed : 10.78 % Favored : 86.71 % Cbeta Deviations : 0.28 % 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: -4.09 (0.18), residues: 1490 helix: -2.80 (0.16), residues: 615 sheet: -3.97 (0.38), residues: 120 loop : -2.36 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 133 HIS 0.014 0.003 HIS A1325 PHE 0.055 0.003 PHE A1812 TYR 0.031 0.003 TYR A1546 ARG 0.010 0.001 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 1.395 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 outliers start: 34 outliers final: 11 residues processed: 179 average time/residue: 0.2826 time to fit residues: 72.1935 Evaluate side-chains 117 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2156 time to fit residues: 7.0407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 65 ASN A 84 GLN ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 249 GLN A 362 HIS A 588 ASN A 628 ASN A 885 ASN A1004 HIS A1028 GLN A1041 HIS A1339 HIS A1355 ASN A1660 ASN A1668 ASN A1727 HIS A1780 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12344 Z= 0.183 Angle : 0.629 6.075 16712 Z= 0.338 Chirality : 0.044 0.168 1866 Planarity : 0.005 0.046 2158 Dihedral : 6.069 26.203 1653 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 0.30 % Allowed : 3.32 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.20), residues: 1490 helix: -1.08 (0.20), residues: 632 sheet: -3.41 (0.42), residues: 123 loop : -2.00 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1831 HIS 0.006 0.001 HIS A 511 PHE 0.017 0.002 PHE A 98 TYR 0.026 0.002 TYR A 560 ARG 0.016 0.000 ARG A1049 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 158 average time/residue: 0.2705 time to fit residues: 61.6951 Evaluate side-chains 96 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1231 time to fit residues: 2.5112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.0070 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 0.0770 chunk 147 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN A 493 GLN A1031 GLN A1388 ASN A1660 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12344 Z= 0.169 Angle : 0.584 6.296 16712 Z= 0.308 Chirality : 0.042 0.154 1866 Planarity : 0.005 0.047 2158 Dihedral : 5.384 29.565 1653 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 0.22 % Allowed : 4.14 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.21), residues: 1490 helix: -0.28 (0.21), residues: 624 sheet: -3.04 (0.45), residues: 108 loop : -1.72 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1831 HIS 0.007 0.001 HIS A 145 PHE 0.019 0.002 PHE A 347 TYR 0.022 0.002 TYR A 560 ARG 0.004 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 145 average time/residue: 0.2213 time to fit residues: 49.0595 Evaluate side-chains 92 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.511 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1188 time to fit residues: 2.3641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 0.2980 chunk 144 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 129 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 488 GLN A 493 GLN A 532 ASN A 850 HIS A1031 GLN A1742 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12344 Z= 0.241 Angle : 0.620 8.004 16712 Z= 0.324 Chirality : 0.044 0.217 1866 Planarity : 0.005 0.049 2158 Dihedral : 5.478 32.955 1653 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.03 % Favored : 94.90 % Rotamer: Outliers : 0.22 % Allowed : 4.14 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1490 helix: -0.17 (0.21), residues: 624 sheet: -2.91 (0.45), residues: 114 loop : -1.77 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1831 HIS 0.011 0.002 HIS A1449 PHE 0.032 0.002 PHE A1812 TYR 0.025 0.002 TYR A 186 ARG 0.004 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 133 average time/residue: 0.2287 time to fit residues: 46.9228 Evaluate side-chains 96 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.3980 chunk 130 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 488 GLN A 532 ASN A1449 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12344 Z= 0.154 Angle : 0.552 6.631 16712 Z= 0.286 Chirality : 0.041 0.172 1866 Planarity : 0.005 0.052 2158 Dihedral : 4.984 26.772 1653 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -1.34 (0.21), residues: 1490 helix: 0.28 (0.21), residues: 624 sheet: -2.64 (0.48), residues: 94 loop : -1.66 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1048 HIS 0.005 0.001 HIS A 356 PHE 0.013 0.001 PHE A1812 TYR 0.016 0.001 TYR A 186 ARG 0.010 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2325 time to fit residues: 48.5989 Evaluate side-chains 93 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 139 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 488 GLN A 532 ASN A1580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12344 Z= 0.150 Angle : 0.554 8.100 16712 Z= 0.284 Chirality : 0.041 0.158 1866 Planarity : 0.005 0.049 2158 Dihedral : 4.792 26.022 1653 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -1.12 (0.22), residues: 1490 helix: 0.46 (0.22), residues: 626 sheet: -2.57 (0.48), residues: 95 loop : -1.54 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1048 HIS 0.004 0.001 HIS A 356 PHE 0.026 0.001 PHE A 280 TYR 0.035 0.001 TYR A 927 ARG 0.010 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2133 time to fit residues: 42.6550 Evaluate side-chains 90 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.513 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 488 GLN A 532 ASN A1660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12344 Z= 0.156 Angle : 0.560 7.193 16712 Z= 0.288 Chirality : 0.042 0.156 1866 Planarity : 0.005 0.049 2158 Dihedral : 4.650 25.179 1653 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -1.05 (0.22), residues: 1490 helix: 0.47 (0.22), residues: 633 sheet: -2.40 (0.46), residues: 105 loop : -1.47 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1831 HIS 0.004 0.001 HIS A 356 PHE 0.020 0.001 PHE A 347 TYR 0.022 0.001 TYR A 927 ARG 0.012 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.412 Fit side-chains 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: 137 average time/residue: 0.2642 time to fit residues: 53.1283 Evaluate side-chains 92 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 chunk 138 optimal weight: 0.5980 chunk 126 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 488 GLN A 532 ASN A1767 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12344 Z= 0.146 Angle : 0.551 7.523 16712 Z= 0.281 Chirality : 0.041 0.228 1866 Planarity : 0.004 0.050 2158 Dihedral : 4.514 23.703 1653 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -0.90 (0.22), residues: 1490 helix: 0.55 (0.21), residues: 629 sheet: -2.46 (0.51), residues: 85 loop : -1.35 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1048 HIS 0.004 0.001 HIS A1727 PHE 0.021 0.001 PHE A 347 TYR 0.019 0.001 TYR A 927 ARG 0.012 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2384 time to fit residues: 47.8467 Evaluate side-chains 91 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 0.0010 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 0.0000 chunk 142 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN A 532 ASN A1353 ASN A1767 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12344 Z= 0.143 Angle : 0.550 7.728 16712 Z= 0.280 Chirality : 0.041 0.210 1866 Planarity : 0.004 0.048 2158 Dihedral : 4.374 22.334 1653 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -0.73 (0.22), residues: 1490 helix: 0.69 (0.22), residues: 631 sheet: -2.61 (0.47), residues: 97 loop : -1.19 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1048 HIS 0.005 0.001 HIS A1661 PHE 0.020 0.001 PHE A 347 TYR 0.019 0.001 TYR A 927 ARG 0.004 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2396 time to fit residues: 46.6912 Evaluate side-chains 93 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.0010 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 overall best weight: 2.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN A 532 ASN A 982 ASN A1767 HIS A1776 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12344 Z= 0.319 Angle : 0.721 11.631 16712 Z= 0.367 Chirality : 0.047 0.250 1866 Planarity : 0.005 0.050 2158 Dihedral : 5.261 39.335 1653 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.22), residues: 1490 helix: 0.05 (0.21), residues: 623 sheet: -3.07 (0.50), residues: 88 loop : -1.33 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1831 HIS 0.012 0.002 HIS A1325 PHE 0.026 0.003 PHE A1812 TYR 0.033 0.002 TYR A1570 ARG 0.012 0.001 ARG A 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2345 time to fit residues: 41.5515 Evaluate side-chains 83 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 0.0770 chunk 15 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 104 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN A 532 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.186493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.157475 restraints weight = 31678.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.156260 restraints weight = 39744.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.157673 restraints weight = 34750.828| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12344 Z= 0.152 Angle : 0.588 8.624 16712 Z= 0.301 Chirality : 0.042 0.197 1866 Planarity : 0.005 0.068 2158 Dihedral : 4.670 28.430 1653 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % 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: -0.93 (0.22), residues: 1490 helix: 0.46 (0.21), residues: 619 sheet: -2.81 (0.45), residues: 107 loop : -1.16 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1048 HIS 0.005 0.001 HIS A1661 PHE 0.024 0.001 PHE A 347 TYR 0.023 0.001 TYR A 186 ARG 0.013 0.000 ARG A 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.50 seconds wall clock time: 45 minutes 12.17 seconds (2712.17 seconds total)