Starting phenix.real_space_refine on Thu Sep 26 15:08:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/09_2024/7b52_12017.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/09_2024/7b52_12017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/09_2024/7b52_12017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/09_2024/7b52_12017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/09_2024/7b52_12017.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/09_2024/7b52_12017.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.065 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 87 5.16 5 C 8294 2.51 5 N 2229 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13186 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13186 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1638, 13185 Classifications: {'peptide': 1638} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 65} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 1589} Chain breaks: 19 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 132 Conformer: "B" Number of residues, atoms: 1638, 13185 Classifications: {'peptide': 1638} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 65} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 1589} Chain breaks: 19 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 132 bond proxies already assigned to first conformer: 13455 Time building chain proxies: 14.22, per 1000 atoms: 1.08 Number of scatterers: 13186 At special positions: 0 Unit cell: (104.58, 134.46, 144.42, 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 87 16.00 O 2576 8.00 N 2229 7.00 C 8294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 228 " distance=2.02 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 322 " distance=2.04 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A 771 " - pdb=" SG CYS A 910 " distance=2.04 Simple disulfide: pdb=" SG CYS A 785 " - pdb=" SG CYS A 803 " distance=2.03 Simple disulfide: pdb=" SG CYS A 799 " - pdb=" SG CYS A 966 " distance=2.03 Simple disulfide: pdb=" SG CYS A 807 " - pdb=" SG CYS A 964 " distance=2.03 Simple disulfide: pdb=" SG CYS A 975 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A1005 " distance=2.03 Simple disulfide: pdb=" SG CYS A1149 " - pdb=" SG CYS A1180 " distance=2.03 Simple disulfide: pdb=" SG ACYS A1219 " - pdb=" SG CYS A1418 " distance=2.03 Simple disulfide: pdb=" SG CYS A1230 " - pdb=" SG CYS A1273 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1264 " distance=2.03 Simple disulfide: pdb=" SG CYS A1344 " - pdb=" SG CYS A1437 " distance=2.02 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG BCYS A1219 " distance=2.03 Simple disulfide: pdb=" SG CYS A1462 " - pdb=" SG CYS A1546 " distance=2.02 Simple disulfide: pdb=" SG CYS A1476 " - pdb=" SG CYS A1501 " distance=2.03 Simple disulfide: pdb=" SG CYS A1486 " - pdb=" SG CYS A1576 " distance=2.03 Simple disulfide: pdb=" SG CYS A1505 " - pdb=" SG CYS A1574 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1632 " distance=2.03 Simple disulfide: pdb=" SG CYS A1688 " - pdb=" SG CYS A1782 " distance=2.03 Simple disulfide: pdb=" SG CYS A1689 " - pdb=" SG CYS A1906 " distance=2.03 Simple disulfide: pdb=" SG CYS A1807 " - pdb=" SG CYS A1909 " distance=2.03 Simple disulfide: pdb=" SG CYS A1821 " - pdb=" SG CYS A1838 " distance=2.03 Simple disulfide: pdb=" SG CYS A1842 " - pdb=" SG CYS A1961 " distance=2.03 Simple disulfide: pdb=" SG CYS A1896 " - pdb=" SG CYS A1907 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 54.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 4.060A pdb=" N TYR A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 29 removed outlier: 3.990A pdb=" N LEU A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.578A pdb=" N GLU A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 120 through 141 removed outlier: 4.075A pdb=" N PHE A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 168 Processing helix chain 'A' and resid 176 through 194 removed outlier: 4.010A pdb=" N ASN A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 206 through 227 removed outlier: 5.447A pdb=" N GLN A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 298 Processing helix chain 'A' and resid 319 through 349 removed outlier: 4.234A pdb=" N LYS A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.853A pdb=" N ASN A 354 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.892A pdb=" N PHE A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 3.812A pdb=" N LYS A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 391 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 575 removed outlier: 3.850A pdb=" N ALA A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 575' Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 642 through 659 removed outlier: 3.661A pdb=" N LYS A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 684 removed outlier: 3.663A pdb=" N LYS A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 714 removed outlier: 4.719A pdb=" N TRP A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 725 Processing helix chain 'A' and resid 757 through 780 removed outlier: 4.626A pdb=" N TRP A 766 " --> pdb=" O PHE A 762 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 803 through 816 Processing helix chain 'A' and resid 830 through 851 removed outlier: 3.546A pdb=" N ARG A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 896 through 905 removed outlier: 3.616A pdb=" N TYR A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 977 removed outlier: 3.665A pdb=" N THR A 974 " --> pdb=" O THR A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1053 removed outlier: 3.992A pdb=" N THR A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1049 " --> pdb=" O GLN A1045 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A1053 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1126 removed outlier: 3.550A pdb=" N LYS A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1157 removed outlier: 3.550A pdb=" N PHE A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A1153 " --> pdb=" O CYS A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1180 removed outlier: 3.760A pdb=" N PHE A1175 " --> pdb=" O ASP A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1200 removed outlier: 3.960A pdb=" N SER A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'A' and resid 1274 through 1278 removed outlier: 3.560A pdb=" N LEU A1277 " --> pdb=" O VAL A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1317 Processing helix chain 'A' and resid 1342 through 1359 removed outlier: 3.625A pdb=" N LEU A1359 " --> pdb=" O LYS A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1381 removed outlier: 3.785A pdb=" N LEU A1372 " --> pdb=" O HIS A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1427 removed outlier: 4.435A pdb=" N ARG A1410 " --> pdb=" O LYS A1406 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1447 Processing helix chain 'A' and resid 1448 through 1476 Processing helix chain 'A' and resid 1499 through 1530 removed outlier: 4.116A pdb=" N GLN A1517 " --> pdb=" O SER A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1543 Processing helix chain 'A' and resid 1559 through 1564 Processing helix chain 'A' and resid 1567 through 1572 removed outlier: 3.657A pdb=" N SER A1572 " --> pdb=" O ASP A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1630 Processing helix chain 'A' and resid 1635 through 1644 removed outlier: 4.407A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1674 removed outlier: 4.050A pdb=" N GLU A1653 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1703 Processing helix chain 'A' and resid 1710 through 1725 removed outlier: 3.990A pdb=" N TYR A1715 " --> pdb=" O GLU A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1741 Processing helix chain 'A' and resid 1755 through 1776 removed outlier: 4.987A pdb=" N TRP A1761 " --> pdb=" O ARG A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1821 removed outlier: 3.635A pdb=" N GLU A1815 " --> pdb=" O THR A1811 " (cutoff:3.500A) Processing helix chain 'A' and resid 1838 through 1867 Proline residue: A1851 - end of helix removed outlier: 3.733A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A1855 " --> pdb=" O PRO A1851 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A1856 " --> pdb=" O LYS A1852 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1894 Processing helix chain 'A' and resid 1941 through 1948 removed outlier: 4.283A pdb=" N ASN A1948 " --> pdb=" O ASN A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1984 removed outlier: 3.629A pdb=" N ALA A1956 " --> pdb=" O LYS A1952 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS A1957 " --> pdb=" O LYS A1953 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET A1959 " --> pdb=" O SER A1955 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 569 through 570 Processing sheet with id=AA2, first strand: chain 'A' and resid 923 through 925 614 hydrogen bonds defined for protein. 1800 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: 4.04 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4294 1.35 - 1.47: 3298 1.47 - 1.59: 5760 1.59 - 1.72: 0 1.72 - 1.84: 105 Bond restraints: 13457 Sorted by residual: bond pdb=" C LEU A 236 " pdb=" N ILE A 237 " ideal model delta sigma weight residual 1.329 1.301 0.028 1.69e-02 3.50e+03 2.76e+00 bond pdb=" N ASP A 31 " pdb=" CA ASP A 31 " ideal model delta sigma weight residual 1.456 1.434 0.021 1.48e-02 4.57e+03 2.05e+00 bond pdb=" C SER A 951 " pdb=" N PRO A 952 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.97e+00 bond pdb=" CB TYR A 655 " pdb=" CG TYR A 655 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.20e-02 2.07e+03 1.75e+00 bond pdb=" N ASP A 891 " pdb=" CA ASP A 891 " ideal model delta sigma weight residual 1.460 1.484 -0.023 1.83e-02 2.99e+03 1.62e+00 ... (remaining 13452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17472 1.97 - 3.94: 551 3.94 - 5.90: 91 5.90 - 7.87: 10 7.87 - 9.84: 9 Bond angle restraints: 18133 Sorted by residual: angle pdb=" N GLN A1758 " pdb=" CA GLN A1758 " pdb=" C GLN A1758 " ideal model delta sigma weight residual 113.18 106.45 6.73 1.33e+00 5.65e-01 2.56e+01 angle pdb=" C THR A 146 " pdb=" N ASN A 147 " pdb=" CA ASN A 147 " ideal model delta sigma weight residual 121.70 129.19 -7.49 1.80e+00 3.09e-01 1.73e+01 angle pdb=" N GLU A 504 " pdb=" CA GLU A 504 " pdb=" C GLU A 504 " ideal model delta sigma weight residual 110.53 115.74 -5.21 1.32e+00 5.74e-01 1.55e+01 angle pdb=" N GLY A1621 " pdb=" CA GLY A1621 " pdb=" C GLY A1621 " ideal model delta sigma weight residual 115.08 109.05 6.03 1.54e+00 4.22e-01 1.54e+01 angle pdb=" N TYR A1366 " pdb=" CA TYR A1366 " pdb=" C TYR A1366 " ideal model delta sigma weight residual 110.80 102.48 8.32 2.13e+00 2.20e-01 1.53e+01 ... (remaining 18128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7367 17.90 - 35.80: 684 35.80 - 53.70: 96 53.70 - 71.60: 26 71.60 - 89.50: 21 Dihedral angle restraints: 8194 sinusoidal: 3384 harmonic: 4810 Sorted by residual: dihedral pdb=" CB CYS A 771 " pdb=" SG CYS A 771 " pdb=" SG CYS A 910 " pdb=" CB CYS A 910 " ideal model delta sinusoidal sigma weight residual 93.00 11.65 81.35 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS A1149 " pdb=" SG CYS A1149 " pdb=" SG CYS A1180 " pdb=" CB CYS A1180 " ideal model delta sinusoidal sigma weight residual 93.00 170.90 -77.90 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CA GLN A 965 " pdb=" C GLN A 965 " pdb=" N CYS A 966 " pdb=" CA CYS A 966 " ideal model delta harmonic sigma weight residual -180.00 -137.00 -43.00 0 5.00e+00 4.00e-02 7.40e+01 ... (remaining 8191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1441 0.050 - 0.101: 393 0.101 - 0.151: 46 0.151 - 0.202: 3 0.202 - 0.252: 1 Chirality restraints: 1884 Sorted by residual: chirality pdb=" CA SER A 951 " pdb=" N SER A 951 " pdb=" C SER A 951 " pdb=" CB SER A 951 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA GLU A1541 " pdb=" N GLU A1541 " pdb=" C GLU A1541 " pdb=" CB GLU A1541 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB ILE A1165 " pdb=" CA ILE A1165 " pdb=" CG1 ILE A1165 " pdb=" CG2 ILE A1165 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 1881 not shown) Planarity restraints: 2343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 560 " -0.027 2.00e-02 2.50e+03 2.72e-02 1.86e+01 pdb=" CG TRP A 560 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 560 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 560 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 560 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 560 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 560 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 560 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 560 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 560 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 766 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C TRP A 766 " -0.067 2.00e-02 2.50e+03 pdb=" O TRP A 766 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL A 767 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 890 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C ILE A 890 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 890 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A 891 " -0.016 2.00e-02 2.50e+03 ... (remaining 2340 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 300 2.61 - 3.18: 13719 3.18 - 3.75: 22258 3.75 - 4.33: 29935 4.33 - 4.90: 45762 Nonbonded interactions: 111974 Sorted by model distance: nonbonded pdb=" O TYR A 688 " pdb=" OG SER A 702 " model vdw 2.035 3.040 nonbonded pdb=" O THR A 895 " pdb=" OG SER A 899 " model vdw 2.057 3.040 nonbonded pdb=" OH TYR A 842 " pdb=" O LEU A 894 " model vdw 2.058 3.040 nonbonded pdb=" O GLU A 573 " pdb=" NH2 ARG A 841 " model vdw 2.098 3.120 nonbonded pdb=" O ASN A1027 " pdb=" OG1 THR A1030 " model vdw 2.115 3.040 ... (remaining 111969 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=0.50 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: 4.320 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.040 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.090 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13457 Z= 0.255 Angle : 0.845 9.840 18133 Z= 0.496 Chirality : 0.043 0.252 1884 Planarity : 0.005 0.062 2343 Dihedral : 14.200 89.497 5015 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.40 % Favored : 83.42 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -2.23 (0.20), residues: 1598 helix: 0.15 (0.18), residues: 820 sheet: -4.87 (1.00), residues: 10 loop : -3.45 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP A 560 HIS 0.006 0.002 HIS A1709 PHE 0.020 0.002 PHE A 373 TYR 0.028 0.002 TYR A 655 ARG 0.014 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9081 (mpp) cc_final: 0.8819 (mpp) REVERT: A 1783 MET cc_start: 0.8976 (tpp) cc_final: 0.8675 (tpp) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.2679 time to fit residues: 12.5244 Evaluate side-chains 22 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 9.9990 chunk 123 optimal weight: 0.0670 chunk 68 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 182 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A 903 ASN A1039 ASN A1048 GLN A1143 ASN A1498 GLN ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1674 ASN A1857 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13457 Z= 0.230 Angle : 0.775 10.162 18133 Z= 0.412 Chirality : 0.044 0.206 1884 Planarity : 0.005 0.082 2343 Dihedral : 6.513 41.171 1761 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.71 % Favored : 85.04 % Rotamer: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.96 (0.21), residues: 1598 helix: 0.31 (0.18), residues: 829 sheet: -4.59 (1.08), residues: 10 loop : -3.28 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 283 HIS 0.006 0.001 HIS A 888 PHE 0.015 0.002 PHE A1031 TYR 0.024 0.002 TYR A 351 ARG 0.006 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 186 MET cc_start: 0.9034 (mpp) cc_final: 0.8712 (mpp) REVERT: A 1764 MET cc_start: 0.9552 (mmm) cc_final: 0.9259 (mmt) REVERT: A 1783 MET cc_start: 0.9025 (tpp) cc_final: 0.8653 (tpp) REVERT: A 1943 MET cc_start: 0.9370 (tpp) cc_final: 0.9122 (mtm) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.2426 time to fit residues: 12.1662 Evaluate side-chains 24 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1601 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 chunk 40 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 HIS ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13457 Z= 0.188 Angle : 0.716 9.852 18133 Z= 0.378 Chirality : 0.042 0.183 1884 Planarity : 0.004 0.049 2343 Dihedral : 6.168 40.487 1761 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.14 % Favored : 85.73 % Rotamer: Outliers : 0.42 % Allowed : 6.36 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.76 (0.21), residues: 1598 helix: 0.51 (0.18), residues: 820 sheet: -4.39 (1.04), residues: 10 loop : -3.20 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 283 HIS 0.005 0.001 HIS A 888 PHE 0.013 0.002 PHE A1031 TYR 0.018 0.001 TYR A 351 ARG 0.006 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1783 MET cc_start: 0.8934 (tpp) cc_final: 0.8650 (tpp) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.2386 time to fit residues: 13.2709 Evaluate side-chains 25 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1445 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 76 optimal weight: 0.0060 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 HIS A 903 ASN A1542 ASN ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13457 Z= 0.185 Angle : 0.702 10.218 18133 Z= 0.367 Chirality : 0.042 0.173 1884 Planarity : 0.004 0.050 2343 Dihedral : 5.954 39.931 1761 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.95 % Favored : 85.98 % Rotamer: Outliers : 0.49 % Allowed : 8.06 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.67 (0.21), residues: 1598 helix: 0.67 (0.18), residues: 815 sheet: -4.32 (1.04), residues: 10 loop : -3.23 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 283 HIS 0.005 0.001 HIS A 888 PHE 0.013 0.002 PHE A1031 TYR 0.015 0.001 TYR A 981 ARG 0.004 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1698 LEU cc_start: 0.9810 (OUTLIER) cc_final: 0.9573 (pp) REVERT: A 1783 MET cc_start: 0.8909 (tpp) cc_final: 0.8647 (tpp) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.2347 time to fit residues: 13.7894 Evaluate side-chains 29 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 193 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN A 955 ASN A1143 ASN ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13457 Z= 0.277 Angle : 0.724 10.889 18133 Z= 0.384 Chirality : 0.042 0.188 1884 Planarity : 0.004 0.049 2343 Dihedral : 6.001 39.760 1761 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.46 % Favored : 85.48 % Rotamer: Outliers : 0.64 % Allowed : 9.19 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.64 (0.21), residues: 1598 helix: 0.67 (0.18), residues: 825 sheet: -4.40 (1.05), residues: 10 loop : -3.25 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 283 HIS 0.006 0.001 HIS A1709 PHE 0.017 0.002 PHE A1031 TYR 0.014 0.001 TYR A1715 ARG 0.007 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: A 1445 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8819 (p0) REVERT: A 1698 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9578 (pp) REVERT: A 1783 MET cc_start: 0.8898 (tpp) cc_final: 0.8610 (tpp) REVERT: A 1943 MET cc_start: 0.8525 (ptp) cc_final: 0.8308 (mpp) outliers start: 7 outliers final: 1 residues processed: 31 average time/residue: 0.2487 time to fit residues: 13.8750 Evaluate side-chains 26 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 903 ASN A1143 ASN ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1847 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13457 Z= 0.176 Angle : 0.694 10.101 18133 Z= 0.363 Chirality : 0.042 0.169 1884 Planarity : 0.004 0.052 2343 Dihedral : 5.864 39.733 1761 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.39 % Favored : 86.55 % Rotamer: Outliers : 0.92 % Allowed : 8.90 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.59 (0.21), residues: 1598 helix: 0.74 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -3.22 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 560 HIS 0.004 0.001 HIS A 888 PHE 0.018 0.002 PHE A 276 TYR 0.015 0.001 TYR A 981 ARG 0.010 0.001 ARG A 834 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9236 (tptp) REVERT: A 706 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8752 (mt-10) REVERT: A 1445 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8759 (p0) REVERT: A 1698 LEU cc_start: 0.9796 (OUTLIER) cc_final: 0.9558 (pp) REVERT: A 1783 MET cc_start: 0.8876 (tpp) cc_final: 0.8612 (tpp) outliers start: 11 outliers final: 3 residues processed: 35 average time/residue: 0.2158 time to fit residues: 13.4458 Evaluate side-chains 30 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 97 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1143 ASN ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13457 Z= 0.188 Angle : 0.681 11.400 18133 Z= 0.358 Chirality : 0.042 0.276 1884 Planarity : 0.004 0.051 2343 Dihedral : 5.757 39.244 1761 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.08 % Favored : 86.86 % Rotamer: Outliers : 0.71 % Allowed : 9.33 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1598 helix: 0.79 (0.18), residues: 814 sheet: -4.20 (0.99), residues: 10 loop : -3.20 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 560 HIS 0.004 0.001 HIS A1709 PHE 0.012 0.001 PHE A1031 TYR 0.012 0.001 TYR A 981 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 23 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9229 (tptp) REVERT: A 1445 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8715 (p0) REVERT: A 1698 LEU cc_start: 0.9799 (OUTLIER) cc_final: 0.9561 (pp) outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.2250 time to fit residues: 12.3830 Evaluate side-chains 31 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 23 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.0670 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1857 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13457 Z= 0.179 Angle : 0.668 9.318 18133 Z= 0.351 Chirality : 0.041 0.264 1884 Planarity : 0.004 0.051 2343 Dihedral : 5.634 39.421 1761 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.45 % Favored : 86.48 % Rotamer: Outliers : 0.99 % Allowed : 9.19 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.47 (0.21), residues: 1598 helix: 0.86 (0.18), residues: 815 sheet: -4.06 (0.99), residues: 10 loop : -3.16 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 560 HIS 0.003 0.001 HIS A1709 PHE 0.011 0.001 PHE A1031 TYR 0.013 0.001 TYR A 351 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 23 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9230 (tptp) REVERT: A 1357 MET cc_start: 0.9726 (tmm) cc_final: 0.9448 (tmm) REVERT: A 1445 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8625 (p0) REVERT: A 1698 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9545 (pp) outliers start: 12 outliers final: 5 residues processed: 34 average time/residue: 0.2156 time to fit residues: 13.2037 Evaluate side-chains 31 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 23 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0030 chunk 146 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 132 optimal weight: 0.0980 chunk 138 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1601 ASN ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13457 Z= 0.167 Angle : 0.680 11.631 18133 Z= 0.353 Chirality : 0.042 0.255 1884 Planarity : 0.004 0.051 2343 Dihedral : 5.529 38.899 1761 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.70 % Favored : 87.23 % Rotamer: Outliers : 0.78 % Allowed : 9.33 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.51 (0.21), residues: 1598 helix: 0.78 (0.18), residues: 816 sheet: -4.03 (0.97), residues: 10 loop : -3.13 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 283 HIS 0.003 0.001 HIS A 888 PHE 0.012 0.001 PHE A 159 TYR 0.012 0.001 TYR A 981 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9510 (tmmt) cc_final: 0.9219 (tptp) REVERT: A 1011 ASP cc_start: 0.9275 (m-30) cc_final: 0.9005 (t70) REVERT: A 1445 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8585 (p0) REVERT: A 1698 LEU cc_start: 0.9785 (OUTLIER) cc_final: 0.9552 (pp) REVERT: A 1941 ASP cc_start: 0.9004 (p0) cc_final: 0.8712 (p0) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.2255 time to fit residues: 13.9999 Evaluate side-chains 34 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1574 CYS Chi-restraints excluded: chain A residue 1601 ASN Chi-restraints excluded: chain A residue 1698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13457 Z= 0.165 Angle : 0.681 12.338 18133 Z= 0.353 Chirality : 0.042 0.251 1884 Planarity : 0.004 0.052 2343 Dihedral : 5.441 38.890 1761 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.83 % Favored : 87.11 % Rotamer: Outliers : 0.78 % Allowed : 9.61 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.44 (0.21), residues: 1598 helix: 0.86 (0.18), residues: 816 sheet: -4.09 (0.97), residues: 10 loop : -3.12 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 283 HIS 0.003 0.001 HIS A 888 PHE 0.010 0.001 PHE A 159 TYR 0.011 0.001 TYR A 351 ARG 0.003 0.000 ARG A 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9504 (tmmt) cc_final: 0.9205 (tptp) REVERT: A 1011 ASP cc_start: 0.9251 (m-30) cc_final: 0.8988 (t0) REVERT: A 1445 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8608 (p0) REVERT: A 1941 ASP cc_start: 0.8992 (p0) cc_final: 0.8712 (p0) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.3150 time to fit residues: 17.9490 Evaluate side-chains 33 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1574 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 54 optimal weight: 0.0870 chunk 132 optimal weight: 0.0070 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1601 ASN ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.033543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.026149 restraints weight = 166385.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.026900 restraints weight = 104976.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.027431 restraints weight = 76224.333| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13457 Z= 0.170 Angle : 0.671 11.030 18133 Z= 0.351 Chirality : 0.041 0.246 1884 Planarity : 0.004 0.051 2343 Dihedral : 5.393 38.764 1761 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.64 % Favored : 87.30 % Rotamer: Outliers : 0.85 % Allowed : 9.82 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.41 (0.21), residues: 1598 helix: 0.89 (0.18), residues: 822 sheet: -4.11 (0.96), residues: 10 loop : -3.16 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 283 HIS 0.003 0.001 HIS A1709 PHE 0.010 0.001 PHE A 159 TYR 0.011 0.001 TYR A 351 ARG 0.003 0.000 ARG A 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.96 seconds wall clock time: 41 minutes 56.60 seconds (2516.60 seconds total)