Starting phenix.real_space_refine on Thu Jun 12 05:11:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7f_32343/06_2025/7w7f_32343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7f_32343/06_2025/7w7f_32343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w7f_32343/06_2025/7w7f_32343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7f_32343/06_2025/7w7f_32343.map" model { file = "/net/cci-nas-00/data/ceres_data/7w7f_32343/06_2025/7w7f_32343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7f_32343/06_2025/7w7f_32343.cif" } resolution = 3.35 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= 0.007 sd= 1.504 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 974 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 100 5.16 5 C 7931 2.51 5 N 1840 2.21 5 O 2113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11987 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 1004 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 992 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 122, 992 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 998 Chain: "D" Number of atoms: 9057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9057 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 29, 'TRANS': 1099} Chain breaks: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 387 Unusual residues: {'6OU': 17, '8DE': 1, '9Z9': 1, 'NAG': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'6OU:plan-1': 15, '6OU:plan-2': 12, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 114 Time building chain proxies: 8.00, per 1000 atoms: 0.67 Number of scatterers: 11987 At special positions: 0 Unit cell: (134.16, 136.24, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 3 15.00 O 2113 8.00 N 1840 7.00 C 7931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS D 911 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 913 " - pdb=" SG CYS D 919 " distance=2.04 Simple disulfide: pdb=" SG CYS D 951 " - pdb=" SG CYS D 960 " distance=2.03 Simple disulfide: pdb=" SG CYS D1364 " - pdb=" SG CYS D1384 " distance=2.03 Simple disulfide: pdb=" SG CYS D1726 " - pdb=" SG CYS D1741 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG D2101 " - " ASN D1366 " " NAG E 1 " - " ASN D 339 " " NAG F 1 " - " ASN D1380 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 62.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 153 through 190 removed outlier: 3.733A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.605A pdb=" N LYS C 107 " --> pdb=" O ASN C 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR C 108 " --> pdb=" O PRO C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 108' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.712A pdb=" N LYS D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 146 removed outlier: 3.505A pdb=" N SER D 131 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 174 removed outlier: 3.657A pdb=" N VAL D 157 " --> pdb=" O TRP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.529A pdb=" N LEU D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR D 202 " --> pdb=" O ILE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 217 Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.528A pdb=" N ARG D 222 " --> pdb=" O PHE D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.538A pdb=" N SER D 228 " --> pdb=" O LYS D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 247 through 269 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.832A pdb=" N ASP D 321 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP D 322 " --> pdb=" O ILE D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 322' Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 384 through 397 removed outlier: 4.024A pdb=" N LEU D 388 " --> pdb=" O TYR D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 411 removed outlier: 4.076A pdb=" N PHE D 404 " --> pdb=" O TYR D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 438 removed outlier: 3.690A pdb=" N ALA D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 754 removed outlier: 3.699A pdb=" N LEU D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 779 Processing helix chain 'D' and resid 788 through 811 Processing helix chain 'D' and resid 823 through 842 Processing helix chain 'D' and resid 847 through 864 Processing helix chain 'D' and resid 865 through 880 Processing helix chain 'D' and resid 882 through 911 removed outlier: 6.189A pdb=" N LYS D 906 " --> pdb=" O GLN D 902 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER D 907 " --> pdb=" O LEU D 903 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 916 removed outlier: 3.924A pdb=" N ASN D 916 " --> pdb=" O CYS D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 942 Processing helix chain 'D' and resid 944 through 955 removed outlier: 3.780A pdb=" N ASP D 950 " --> pdb=" O GLU D 946 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 985 removed outlier: 4.075A pdb=" N CYS D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN D 972 " --> pdb=" O MET D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 1191 through 1205 removed outlier: 3.538A pdb=" N THR D1198 " --> pdb=" O ASN D1194 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1225 removed outlier: 3.849A pdb=" N LEU D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA D1224 " --> pdb=" O SER D1220 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D1225 " --> pdb=" O GLY D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1235 through 1263 removed outlier: 3.549A pdb=" N LYS D1245 " --> pdb=" O GLU D1241 " (cutoff:3.500A) Processing helix chain 'D' and resid 1263 through 1269 Processing helix chain 'D' and resid 1270 through 1293 Processing helix chain 'D' and resid 1297 through 1305 removed outlier: 3.669A pdb=" N THR D1305 " --> pdb=" O LYS D1301 " (cutoff:3.500A) Processing helix chain 'D' and resid 1306 through 1312 Proline residue: D1311 - end of helix Processing helix chain 'D' and resid 1313 through 1318 removed outlier: 3.954A pdb=" N ARG D1317 " --> pdb=" O ARG D1313 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1357 Proline residue: D1333 - end of helix Processing helix chain 'D' and resid 1380 through 1386 Processing helix chain 'D' and resid 1402 through 1415 Processing helix chain 'D' and resid 1418 through 1429 removed outlier: 4.111A pdb=" N ILE D1422 " --> pdb=" O GLY D1418 " (cutoff:3.500A) Processing helix chain 'D' and resid 1441 through 1443 No H-bonds generated for 'chain 'D' and resid 1441 through 1443' Processing helix chain 'D' and resid 1444 through 1455 removed outlier: 3.585A pdb=" N PHE D1448 " --> pdb=" O MET D1444 " (cutoff:3.500A) Processing helix chain 'D' and resid 1458 through 1477 Processing helix chain 'D' and resid 1486 through 1501 removed outlier: 3.693A pdb=" N SER D1501 " --> pdb=" O LYS D1497 " (cutoff:3.500A) Processing helix chain 'D' and resid 1515 through 1524 removed outlier: 3.592A pdb=" N THR D1524 " --> pdb=" O PHE D1520 " (cutoff:3.500A) Processing helix chain 'D' and resid 1525 through 1546 removed outlier: 3.725A pdb=" N ASP D1529 " --> pdb=" O ARG D1525 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU D1546 " --> pdb=" O THR D1542 " (cutoff:3.500A) Processing helix chain 'D' and resid 1551 through 1580 removed outlier: 4.213A pdb=" N GLU D1572 " --> pdb=" O LEU D1568 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU D1575 " --> pdb=" O GLY D1571 " (cutoff:3.500A) Processing helix chain 'D' and resid 1587 through 1612 removed outlier: 3.597A pdb=" N ILE D1591 " --> pdb=" O ILE D1587 " (cutoff:3.500A) Processing helix chain 'D' and resid 1616 through 1624 removed outlier: 3.936A pdb=" N VAL D1622 " --> pdb=" O THR D1618 " (cutoff:3.500A) Processing helix chain 'D' and resid 1625 through 1633 removed outlier: 3.862A pdb=" N GLY D1629 " --> pdb=" O LEU D1625 " (cutoff:3.500A) Processing helix chain 'D' and resid 1634 through 1637 removed outlier: 3.594A pdb=" N GLY D1637 " --> pdb=" O LEU D1634 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1634 through 1637' Processing helix chain 'D' and resid 1640 through 1678 Proline residue: D1653 - end of helix removed outlier: 3.782A pdb=" N ALA D1678 " --> pdb=" O MET D1674 " (cutoff:3.500A) Processing helix chain 'D' and resid 1694 through 1707 removed outlier: 3.999A pdb=" N THR D1707 " --> pdb=" O PHE D1703 " (cutoff:3.500A) Processing helix chain 'D' and resid 1710 through 1719 Proline residue: D1717 - end of helix Processing helix chain 'D' and resid 1743 through 1778 Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'B' and resid 78 through 80 removed outlier: 5.843A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.575A pdb=" N VAL C 112 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.515A pdb=" N GLN C 70 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 124 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 275 through 279 673 hydrogen bonds defined for protein. 1941 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: 3.97 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.17: 6 1.17 - 1.35: 3575 1.35 - 1.54: 8288 1.54 - 1.72: 216 1.72 - 1.91: 166 Bond restraints: 12251 Sorted by residual: bond pdb=" C73 9Z9 D2113 " pdb=" O72 9Z9 D2113 " ideal model delta sigma weight residual 1.406 0.985 0.421 2.00e-02 2.50e+03 4.42e+02 bond pdb=" C73 9Z9 D2113 " pdb=" C76 9Z9 D2113 " ideal model delta sigma weight residual 1.522 1.102 0.420 2.00e-02 2.50e+03 4.41e+02 bond pdb=" C78 9Z9 D2113 " pdb=" C79 9Z9 D2113 " ideal model delta sigma weight residual 1.521 1.127 0.394 2.00e-02 2.50e+03 3.89e+02 bond pdb=" C78 9Z9 D2113 " pdb=" C81 9Z9 D2113 " ideal model delta sigma weight residual 1.522 1.907 -0.385 2.00e-02 2.50e+03 3.71e+02 bond pdb=" C03 9Z9 D2113 " pdb=" C74 9Z9 D2113 " ideal model delta sigma weight residual 1.534 1.158 0.376 2.00e-02 2.50e+03 3.53e+02 ... (remaining 12246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 16335 4.28 - 8.56: 166 8.56 - 12.83: 21 12.83 - 17.11: 3 17.11 - 21.39: 2 Bond angle restraints: 16527 Sorted by residual: angle pdb=" O06 8DE D2103 " pdb=" S05 8DE D2103 " pdb=" O07 8DE D2103 " ideal model delta sigma weight residual 121.45 100.06 21.39 3.00e+00 1.11e-01 5.08e+01 angle pdb=" C01 8DE D2103 " pdb=" S02 8DE D2103 " pdb=" C03 8DE D2103 " ideal model delta sigma weight residual 88.55 107.75 -19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" C GLN C 82 " pdb=" N PHE C 83 " pdb=" CA PHE C 83 " ideal model delta sigma weight residual 121.54 131.91 -10.37 1.91e+00 2.74e-01 2.95e+01 angle pdb=" O22 6OU D2108 " pdb=" P23 6OU D2108 " pdb=" O26 6OU D2108 " ideal model delta sigma weight residual 93.95 109.89 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" O22 6OU D2105 " pdb=" P23 6OU D2105 " pdb=" O26 6OU D2105 " ideal model delta sigma weight residual 93.95 109.68 -15.73 3.00e+00 1.11e-01 2.75e+01 ... (remaining 16522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 7189 32.98 - 65.96: 254 65.96 - 98.94: 29 98.94 - 131.93: 16 131.93 - 164.91: 9 Dihedral angle restraints: 7497 sinusoidal: 3320 harmonic: 4177 Sorted by residual: dihedral pdb=" CB CYS D 913 " pdb=" SG CYS D 913 " pdb=" SG CYS D 919 " pdb=" CB CYS D 919 " ideal model delta sinusoidal sigma weight residual -86.00 -6.88 -79.12 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CB CYS D1364 " pdb=" SG CYS D1364 " pdb=" SG CYS D1384 " pdb=" CB CYS D1384 " ideal model delta sinusoidal sigma weight residual -86.00 -154.51 68.51 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS D1726 " pdb=" SG CYS D1726 " pdb=" SG CYS D1741 " pdb=" CB CYS D1741 " ideal model delta sinusoidal sigma weight residual 93.00 37.57 55.43 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 7494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.284: 1888 0.284 - 0.567: 4 0.567 - 0.851: 2 0.851 - 1.135: 0 1.135 - 1.419: 2 Chirality restraints: 1896 Sorted by residual: chirality pdb=" C07 9Z9 D2113 " pdb=" C06 9Z9 D2113 " pdb=" C08 9Z9 D2113 " pdb=" C15 9Z9 D2113 " both_signs ideal model delta sigma weight residual False -2.70 -1.28 -1.42 2.00e-01 2.50e+01 5.03e+01 chirality pdb=" C73 9Z9 D2113 " pdb=" C76 9Z9 D2113 " pdb=" O72 9Z9 D2113 " pdb=" O80 9Z9 D2113 " both_signs ideal model delta sigma weight residual False 2.26 0.90 1.36 2.00e-01 2.50e+01 4.64e+01 chirality pdb=" C02 9Z9 D2113 " pdb=" C03 9Z9 D2113 " pdb=" C06 9Z9 D2113 " pdb=" C10 9Z9 D2113 " both_signs ideal model delta sigma weight residual False 2.92 2.14 0.78 2.00e-01 2.50e+01 1.52e+01 ... (remaining 1893 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D2101 " 0.226 2.00e-02 2.50e+03 1.93e-01 4.66e+02 pdb=" C7 NAG D2101 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG D2101 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG D2101 " -0.317 2.00e-02 2.50e+03 pdb=" O7 NAG D2101 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D1364 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C CYS D1364 " -0.048 2.00e-02 2.50e+03 pdb=" O CYS D1364 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL D1365 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D1722 " -0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO D1723 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D1723 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D1723 " -0.037 5.00e-02 4.00e+02 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 304 2.69 - 3.25: 12615 3.25 - 3.80: 18567 3.80 - 4.35: 24155 4.35 - 4.90: 39433 Nonbonded interactions: 95074 Sorted by model distance: nonbonded pdb=" O GLY D 163 " pdb=" OG1 THR D 166 " model vdw 2.144 3.040 nonbonded pdb=" O ASN B 93 " pdb=" OG SER B 105 " model vdw 2.152 3.040 nonbonded pdb=" O TYR D1262 " pdb=" OG1 THR D1266 " model vdw 2.176 3.040 nonbonded pdb=" OD2 ASP D 383 " pdb=" N TRP D 944 " model vdw 2.199 3.120 nonbonded pdb=" O ASP D 367 " pdb=" OG1 THR D 368 " model vdw 2.220 3.040 ... (remaining 95069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.980 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.017 0.882 12271 Z= 1.086 Angle : 1.041 21.391 16575 Z= 0.467 Chirality : 0.072 1.419 1896 Planarity : 0.007 0.193 1995 Dihedral : 18.832 164.907 4774 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.09 % Favored : 91.63 % Rotamer: Outliers : 0.31 % Allowed : 0.79 % Favored : 98.90 % 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: -1.42 (0.22), residues: 1414 helix: 0.19 (0.18), residues: 834 sheet: -2.60 (0.45), residues: 107 loop : -2.55 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 944 HIS 0.005 0.001 HIS B 134 PHE 0.018 0.001 PHE D 195 TYR 0.020 0.002 TYR D1294 ARG 0.010 0.001 ARG D 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 3.27811 ( 21) link_BETA1-4 : bond 0.01562 ( 3) link_BETA1-4 : angle 4.78699 ( 9) hydrogen bonds : bond 0.12045 ( 673) hydrogen bonds : angle 6.04900 ( 1941) SS BOND : bond 0.00402 ( 9) SS BOND : angle 1.29827 ( 18) covalent geometry : bond 0.01484 (12251) covalent geometry : angle 1.02851 (16527) Misc. bond : bond 0.88170 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 221 LEU cc_start: 0.8307 (mt) cc_final: 0.8084 (mt) REVERT: D 1348 ILE cc_start: 0.8663 (mt) cc_final: 0.8422 (mt) REVERT: D 1420 MET cc_start: 0.7083 (mmm) cc_final: 0.6881 (mmm) REVERT: D 1441 ASN cc_start: 0.8965 (t0) cc_final: 0.8703 (t0) REVERT: D 1539 ASN cc_start: 0.7229 (t0) cc_final: 0.7009 (t0) REVERT: D 1651 SER cc_start: 0.8662 (t) cc_final: 0.8428 (t) outliers start: 3 outliers final: 2 residues processed: 301 average time/residue: 0.2654 time to fit residues: 121.8305 Evaluate side-chains 251 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 GLN D 773 ASN D 972 ASN D1385 GLN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1550 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.188102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153156 restraints weight = 42992.178| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.96 r_work: 0.3660 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12271 Z= 0.180 Angle : 0.713 9.676 16575 Z= 0.360 Chirality : 0.044 0.276 1896 Planarity : 0.005 0.058 1995 Dihedral : 16.250 149.994 2112 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.09 % Favored : 91.63 % Rotamer: Outliers : 1.89 % Allowed : 10.13 % Favored : 87.98 % 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: -1.10 (0.22), residues: 1414 helix: 0.48 (0.18), residues: 839 sheet: -2.64 (0.43), residues: 113 loop : -2.45 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1419 HIS 0.004 0.001 HIS B 115 PHE 0.017 0.002 PHE C 80 TYR 0.020 0.002 TYR D 389 ARG 0.007 0.001 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 7) link_NAG-ASN : angle 2.55488 ( 21) link_BETA1-4 : bond 0.01640 ( 3) link_BETA1-4 : angle 4.61416 ( 9) hydrogen bonds : bond 0.04534 ( 673) hydrogen bonds : angle 4.90920 ( 1941) SS BOND : bond 0.00419 ( 9) SS BOND : angle 1.13132 ( 18) covalent geometry : bond 0.00416 (12251) covalent geometry : angle 0.69942 (16527) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 149 ASN cc_start: 0.6968 (t0) cc_final: 0.6521 (t0) REVERT: D 857 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7418 (mtm180) REVERT: D 916 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8332 (m-40) REVERT: D 1294 TYR cc_start: 0.7229 (m-10) cc_final: 0.6942 (m-10) REVERT: D 1321 MET cc_start: 0.8308 (mtm) cc_final: 0.7856 (mtm) REVERT: D 1348 ILE cc_start: 0.8729 (mt) cc_final: 0.8523 (mt) REVERT: D 1441 ASN cc_start: 0.9186 (t0) cc_final: 0.8795 (t0) REVERT: D 1620 PHE cc_start: 0.7790 (t80) cc_final: 0.7378 (t80) REVERT: D 1651 SER cc_start: 0.8836 (t) cc_final: 0.8606 (t) outliers start: 23 outliers final: 13 residues processed: 285 average time/residue: 0.2156 time to fit residues: 92.2164 Evaluate side-chains 271 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 257 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 916 ASN Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1288 VAL Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 1 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 115 optimal weight: 0.0870 chunk 113 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 overall best weight: 5.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1385 GLN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1539 ASN D1732 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.182864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148379 restraints weight = 38828.549| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.43 r_work: 0.3610 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12271 Z= 0.248 Angle : 0.759 11.672 16575 Z= 0.382 Chirality : 0.046 0.288 1896 Planarity : 0.005 0.057 1995 Dihedral : 14.841 147.355 2112 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.58 % Favored : 91.13 % Rotamer: Outliers : 3.14 % Allowed : 14.69 % Favored : 82.17 % 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: -1.11 (0.22), residues: 1414 helix: 0.49 (0.18), residues: 836 sheet: -2.82 (0.41), residues: 118 loop : -2.41 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1419 HIS 0.004 0.001 HIS D 781 PHE 0.020 0.002 PHE D1345 TYR 0.019 0.002 TYR B 119 ARG 0.005 0.001 ARG D1317 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 7) link_NAG-ASN : angle 2.54751 ( 21) link_BETA1-4 : bond 0.01479 ( 3) link_BETA1-4 : angle 4.64886 ( 9) hydrogen bonds : bond 0.04537 ( 673) hydrogen bonds : angle 4.87824 ( 1941) SS BOND : bond 0.00518 ( 9) SS BOND : angle 1.48610 ( 18) covalent geometry : bond 0.00583 (12251) covalent geometry : angle 0.74531 (16527) Misc. bond : bond 0.00424 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLN cc_start: 0.6898 (mp10) cc_final: 0.6548 (pm20) REVERT: D 139 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8609 (mp) REVERT: D 149 ASN cc_start: 0.7079 (t0) cc_final: 0.6683 (t0) REVERT: D 1240 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8144 (mm) REVERT: D 1321 MET cc_start: 0.8390 (mtm) cc_final: 0.7695 (mtm) REVERT: D 1387 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7497 (tm) REVERT: D 1441 ASN cc_start: 0.9208 (t0) cc_final: 0.8778 (t0) REVERT: D 1493 TYR cc_start: 0.8631 (t80) cc_final: 0.7945 (t80) REVERT: D 1620 PHE cc_start: 0.7858 (t80) cc_final: 0.7410 (t80) REVERT: D 1650 MET cc_start: 0.8352 (mmt) cc_final: 0.7735 (mmm) REVERT: D 1651 SER cc_start: 0.8860 (t) cc_final: 0.8632 (t) outliers start: 39 outliers final: 27 residues processed: 288 average time/residue: 0.2022 time to fit residues: 89.1622 Evaluate side-chains 282 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 802 ILE Chi-restraints excluded: chain D residue 814 MET Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 872 ILE Chi-restraints excluded: chain D residue 916 ASN Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1240 LEU Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1643 THR Chi-restraints excluded: chain D residue 1706 THR Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 843 ASN D1385 GLN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.182226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152210 restraints weight = 33147.008| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 4.63 r_work: 0.3539 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12271 Z= 0.165 Angle : 0.692 12.658 16575 Z= 0.349 Chirality : 0.043 0.281 1896 Planarity : 0.004 0.056 1995 Dihedral : 13.965 146.273 2112 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.16 % Favored : 91.56 % Rotamer: Outliers : 2.91 % Allowed : 17.05 % Favored : 80.05 % 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: -0.96 (0.22), residues: 1414 helix: 0.58 (0.18), residues: 838 sheet: -2.69 (0.42), residues: 118 loop : -2.32 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1419 HIS 0.003 0.001 HIS B 134 PHE 0.015 0.001 PHE D 185 TYR 0.023 0.002 TYR D 389 ARG 0.005 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 7) link_NAG-ASN : angle 2.28392 ( 21) link_BETA1-4 : bond 0.01483 ( 3) link_BETA1-4 : angle 4.15841 ( 9) hydrogen bonds : bond 0.04222 ( 673) hydrogen bonds : angle 4.73032 ( 1941) SS BOND : bond 0.00544 ( 9) SS BOND : angle 1.06334 ( 18) covalent geometry : bond 0.00380 (12251) covalent geometry : angle 0.68043 (16527) Misc. bond : bond 0.00216 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLN cc_start: 0.6754 (mp10) cc_final: 0.6479 (pm20) REVERT: D 139 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8542 (mp) REVERT: D 149 ASN cc_start: 0.7044 (t0) cc_final: 0.6652 (t0) REVERT: D 418 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8565 (mp) REVERT: D 1321 MET cc_start: 0.8499 (mtm) cc_final: 0.7856 (mtm) REVERT: D 1387 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7614 (tm) REVERT: D 1441 ASN cc_start: 0.9172 (t0) cc_final: 0.8667 (t0) REVERT: D 1493 TYR cc_start: 0.8634 (t80) cc_final: 0.7968 (t80) REVERT: D 1572 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7967 (tm-30) REVERT: D 1620 PHE cc_start: 0.7930 (t80) cc_final: 0.7451 (t80) REVERT: D 1650 MET cc_start: 0.8388 (mmt) cc_final: 0.7749 (mmm) REVERT: D 1651 SER cc_start: 0.8890 (t) cc_final: 0.8668 (t) REVERT: D 1679 TYR cc_start: 0.8242 (m-80) cc_final: 0.7965 (m-80) REVERT: D 1731 ILE cc_start: 0.8732 (tp) cc_final: 0.8529 (tp) outliers start: 36 outliers final: 29 residues processed: 296 average time/residue: 0.2117 time to fit residues: 95.5345 Evaluate side-chains 287 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 872 ILE Chi-restraints excluded: chain D residue 916 ASN Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1287 LEU Chi-restraints excluded: chain D residue 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1706 THR Chi-restraints excluded: chain D residue 1773 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 5 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 843 ASN D 916 ASN D1385 GLN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.181511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145238 restraints weight = 37993.836| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.58 r_work: 0.3560 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12271 Z= 0.195 Angle : 0.708 10.717 16575 Z= 0.356 Chirality : 0.044 0.286 1896 Planarity : 0.004 0.055 1995 Dihedral : 13.518 145.686 2112 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.51 % Favored : 91.21 % Rotamer: Outliers : 3.46 % Allowed : 18.62 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.22), residues: 1414 helix: 0.53 (0.18), residues: 844 sheet: -2.70 (0.42), residues: 118 loop : -2.36 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1419 HIS 0.003 0.001 HIS B 134 PHE 0.014 0.002 PHE D1750 TYR 0.022 0.002 TYR D 389 ARG 0.006 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 7) link_NAG-ASN : angle 2.29987 ( 21) link_BETA1-4 : bond 0.01364 ( 3) link_BETA1-4 : angle 4.22206 ( 9) hydrogen bonds : bond 0.04194 ( 673) hydrogen bonds : angle 4.71483 ( 1941) SS BOND : bond 0.00447 ( 9) SS BOND : angle 1.33332 ( 18) covalent geometry : bond 0.00456 (12251) covalent geometry : angle 0.69592 (16527) Misc. bond : bond 0.00177 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 139 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8491 (mp) REVERT: D 149 ASN cc_start: 0.7021 (t0) cc_final: 0.6708 (t0) REVERT: D 418 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8599 (mp) REVERT: D 1387 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7796 (tm) REVERT: D 1441 ASN cc_start: 0.9163 (t0) cc_final: 0.8689 (t0) REVERT: D 1493 TYR cc_start: 0.8636 (t80) cc_final: 0.7962 (t80) REVERT: D 1572 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7964 (tm-30) REVERT: D 1620 PHE cc_start: 0.7934 (t80) cc_final: 0.7458 (t80) REVERT: D 1650 MET cc_start: 0.8395 (mmt) cc_final: 0.7736 (mmm) REVERT: D 1651 SER cc_start: 0.8891 (t) cc_final: 0.8650 (t) REVERT: D 1679 TYR cc_start: 0.8265 (m-80) cc_final: 0.7997 (m-80) REVERT: D 1731 ILE cc_start: 0.8717 (tp) cc_final: 0.8494 (tp) outliers start: 43 outliers final: 33 residues processed: 278 average time/residue: 0.2089 time to fit residues: 88.2363 Evaluate side-chains 288 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 872 ILE Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 916 ASN Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1287 LEU Chi-restraints excluded: chain D residue 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1549 ASP Chi-restraints excluded: chain D residue 1643 THR Chi-restraints excluded: chain D residue 1706 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 86 optimal weight: 0.0980 chunk 123 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 843 ASN D1385 GLN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.182903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146392 restraints weight = 25921.070| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.78 r_work: 0.3632 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12271 Z= 0.167 Angle : 0.688 10.183 16575 Z= 0.347 Chirality : 0.043 0.280 1896 Planarity : 0.004 0.056 1995 Dihedral : 12.893 144.327 2112 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.09 % Favored : 91.63 % Rotamer: Outliers : 4.08 % Allowed : 18.93 % Favored : 76.98 % 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: -0.92 (0.22), residues: 1414 helix: 0.62 (0.18), residues: 842 sheet: -2.64 (0.42), residues: 116 loop : -2.35 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D1419 HIS 0.003 0.001 HIS B 115 PHE 0.015 0.001 PHE D 803 TYR 0.019 0.002 TYR D 389 ARG 0.006 0.000 ARG D1317 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 7) link_NAG-ASN : angle 2.18726 ( 21) link_BETA1-4 : bond 0.01427 ( 3) link_BETA1-4 : angle 4.00289 ( 9) hydrogen bonds : bond 0.04080 ( 673) hydrogen bonds : angle 4.65073 ( 1941) SS BOND : bond 0.00418 ( 9) SS BOND : angle 1.29811 ( 18) covalent geometry : bond 0.00386 (12251) covalent geometry : angle 0.67641 (16527) Misc. bond : bond 0.00246 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 GLN cc_start: 0.7276 (mp10) cc_final: 0.6840 (mp10) REVERT: B 133 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8479 (mm-30) REVERT: D 139 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8451 (mp) REVERT: D 149 ASN cc_start: 0.6971 (t0) cc_final: 0.6688 (t0) REVERT: D 176 ARG cc_start: 0.7239 (mtt-85) cc_final: 0.4579 (mmt180) REVERT: D 195 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7236 (t80) REVERT: D 418 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8583 (mp) REVERT: D 1387 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7905 (tm) REVERT: D 1407 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7082 (m-10) REVERT: D 1441 ASN cc_start: 0.9084 (t0) cc_final: 0.8610 (t0) REVERT: D 1493 TYR cc_start: 0.8596 (t80) cc_final: 0.7908 (t80) REVERT: D 1558 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7276 (mm) REVERT: D 1572 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7888 (tm-30) REVERT: D 1620 PHE cc_start: 0.8071 (t80) cc_final: 0.7603 (t80) REVERT: D 1650 MET cc_start: 0.8362 (mmt) cc_final: 0.7698 (mmm) REVERT: D 1651 SER cc_start: 0.8847 (t) cc_final: 0.8588 (t) REVERT: D 1731 ILE cc_start: 0.8713 (tp) cc_final: 0.8484 (tp) outliers start: 51 outliers final: 30 residues processed: 305 average time/residue: 0.2158 time to fit residues: 100.0379 Evaluate side-chains 291 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1287 LEU Chi-restraints excluded: chain D residue 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1407 TYR Chi-restraints excluded: chain D residue 1558 LEU Chi-restraints excluded: chain D residue 1643 THR Chi-restraints excluded: chain D residue 1706 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 916 ASN D1385 GLN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1732 HIS D1773 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.181355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152788 restraints weight = 34301.792| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 4.91 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12271 Z= 0.190 Angle : 0.715 10.487 16575 Z= 0.360 Chirality : 0.044 0.287 1896 Planarity : 0.004 0.057 1995 Dihedral : 12.569 143.871 2112 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.51 % Favored : 91.21 % Rotamer: Outliers : 3.69 % Allowed : 19.32 % Favored : 76.98 % 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: -0.97 (0.22), residues: 1414 helix: 0.58 (0.18), residues: 845 sheet: -2.66 (0.42), residues: 116 loop : -2.39 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1711 HIS 0.011 0.001 HIS D1732 PHE 0.015 0.002 PHE D 803 TYR 0.022 0.002 TYR B 119 ARG 0.006 0.001 ARG D1317 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 7) link_NAG-ASN : angle 2.77127 ( 21) link_BETA1-4 : bond 0.01184 ( 3) link_BETA1-4 : angle 4.03316 ( 9) hydrogen bonds : bond 0.04121 ( 673) hydrogen bonds : angle 4.67312 ( 1941) SS BOND : bond 0.00379 ( 9) SS BOND : angle 1.18734 ( 18) covalent geometry : bond 0.00446 (12251) covalent geometry : angle 0.70172 (16527) Misc. bond : bond 0.00219 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 262 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8481 (mm-30) REVERT: D 139 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8504 (mp) REVERT: D 149 ASN cc_start: 0.6972 (t0) cc_final: 0.6714 (t0) REVERT: D 176 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.4765 (mmt180) REVERT: D 195 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7052 (t80) REVERT: D 418 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8556 (mp) REVERT: D 1321 MET cc_start: 0.7935 (mtm) cc_final: 0.7347 (mtm) REVERT: D 1387 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7948 (tm) REVERT: D 1407 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: D 1420 MET cc_start: 0.7408 (mmm) cc_final: 0.7105 (mmm) REVERT: D 1441 ASN cc_start: 0.8829 (t0) cc_final: 0.8444 (t0) REVERT: D 1493 TYR cc_start: 0.8613 (t80) cc_final: 0.8232 (t80) REVERT: D 1558 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7208 (mm) REVERT: D 1572 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7650 (tm-30) REVERT: D 1620 PHE cc_start: 0.8082 (t80) cc_final: 0.7616 (t80) REVERT: D 1650 MET cc_start: 0.8319 (mmt) cc_final: 0.7997 (mmm) REVERT: D 1651 SER cc_start: 0.8970 (t) cc_final: 0.8722 (t) REVERT: D 1729 ASP cc_start: 0.7054 (p0) cc_final: 0.6826 (p0) REVERT: D 1731 ILE cc_start: 0.8627 (tp) cc_final: 0.8380 (tp) outliers start: 46 outliers final: 35 residues processed: 291 average time/residue: 0.2086 time to fit residues: 91.6154 Evaluate side-chains 292 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1287 LEU Chi-restraints excluded: chain D residue 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1407 TYR Chi-restraints excluded: chain D residue 1464 ILE Chi-restraints excluded: chain D residue 1549 ASP Chi-restraints excluded: chain D residue 1558 LEU Chi-restraints excluded: chain D residue 1643 THR Chi-restraints excluded: chain D residue 1706 THR Chi-restraints excluded: chain D residue 1773 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 21 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 95 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 916 ASN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** 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 = 0.4171 r_free = 0.4171 target = 0.182435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147380 restraints weight = 44630.479| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 4.04 r_work: 0.3578 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12271 Z= 0.167 Angle : 0.728 12.724 16575 Z= 0.360 Chirality : 0.044 0.297 1896 Planarity : 0.004 0.057 1995 Dihedral : 12.221 142.846 2112 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.01 % Favored : 91.84 % Rotamer: Outliers : 3.77 % Allowed : 19.56 % Favored : 76.67 % 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: -0.91 (0.22), residues: 1414 helix: 0.62 (0.18), residues: 845 sheet: -2.42 (0.43), residues: 116 loop : -2.43 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1419 HIS 0.003 0.001 HIS B 115 PHE 0.015 0.001 PHE D 413 TYR 0.018 0.002 TYR B 119 ARG 0.006 0.000 ARG D1317 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 7) link_NAG-ASN : angle 3.66032 ( 21) link_BETA1-4 : bond 0.01328 ( 3) link_BETA1-4 : angle 3.87707 ( 9) hydrogen bonds : bond 0.04069 ( 673) hydrogen bonds : angle 4.65159 ( 1941) SS BOND : bond 0.00317 ( 9) SS BOND : angle 1.07905 ( 18) covalent geometry : bond 0.00388 (12251) covalent geometry : angle 0.71056 (16527) Misc. bond : bond 0.00388 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 GLN cc_start: 0.7240 (mp10) cc_final: 0.6930 (mp10) REVERT: B 133 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8560 (mm-30) REVERT: D 139 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 149 ASN cc_start: 0.7010 (t0) cc_final: 0.6699 (t0) REVERT: D 176 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.4597 (mmt180) REVERT: D 195 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7317 (t80) REVERT: D 418 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8623 (mp) REVERT: D 827 PHE cc_start: 0.7002 (t80) cc_final: 0.6785 (t80) REVERT: D 1321 MET cc_start: 0.8352 (mtm) cc_final: 0.7765 (mtm) REVERT: D 1373 PHE cc_start: 0.8074 (m-80) cc_final: 0.7794 (m-80) REVERT: D 1387 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7971 (tm) REVERT: D 1407 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7106 (m-10) REVERT: D 1419 TRP cc_start: 0.7231 (p-90) cc_final: 0.6815 (p-90) REVERT: D 1420 MET cc_start: 0.7980 (mmm) cc_final: 0.7742 (mmm) REVERT: D 1441 ASN cc_start: 0.9105 (t0) cc_final: 0.8648 (t0) REVERT: D 1493 TYR cc_start: 0.8599 (t80) cc_final: 0.7883 (t80) REVERT: D 1558 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7274 (mm) REVERT: D 1572 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7966 (tm-30) REVERT: D 1620 PHE cc_start: 0.8104 (t80) cc_final: 0.7631 (t80) REVERT: D 1650 MET cc_start: 0.8422 (mmt) cc_final: 0.8033 (mmm) REVERT: D 1651 SER cc_start: 0.8857 (t) cc_final: 0.8593 (t) outliers start: 47 outliers final: 36 residues processed: 306 average time/residue: 0.2116 time to fit residues: 97.0055 Evaluate side-chains 296 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1287 LEU Chi-restraints excluded: chain D residue 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1407 TYR Chi-restraints excluded: chain D residue 1464 ILE Chi-restraints excluded: chain D residue 1471 PHE Chi-restraints excluded: chain D residue 1523 VAL Chi-restraints excluded: chain D residue 1558 LEU Chi-restraints excluded: chain D residue 1643 THR Chi-restraints excluded: chain D residue 1706 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 79 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 75 optimal weight: 0.6980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1385 GLN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.188198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152433 restraints weight = 25771.754| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.80 r_work: 0.3700 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12271 Z= 0.134 Angle : 0.723 13.517 16575 Z= 0.355 Chirality : 0.043 0.257 1896 Planarity : 0.004 0.058 1995 Dihedral : 11.453 139.805 2112 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.27 % Rotamer: Outliers : 2.51 % Allowed : 21.29 % Favored : 76.20 % 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: -0.72 (0.22), residues: 1414 helix: 0.79 (0.18), residues: 843 sheet: -2.17 (0.44), residues: 118 loop : -2.41 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1419 HIS 0.005 0.001 HIS B 115 PHE 0.016 0.001 PHE D1463 TYR 0.022 0.001 TYR D 363 ARG 0.006 0.001 ARG D1317 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 7) link_NAG-ASN : angle 4.40317 ( 21) link_BETA1-4 : bond 0.01370 ( 3) link_BETA1-4 : angle 3.48653 ( 9) hydrogen bonds : bond 0.03865 ( 673) hydrogen bonds : angle 4.53757 ( 1941) SS BOND : bond 0.00274 ( 9) SS BOND : angle 1.69110 ( 18) covalent geometry : bond 0.00292 (12251) covalent geometry : angle 0.70000 (16527) Misc. bond : bond 0.00447 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8545 (mm-30) REVERT: C 62 GLN cc_start: 0.6337 (pm20) cc_final: 0.6052 (pm20) REVERT: D 139 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8489 (mp) REVERT: D 149 ASN cc_start: 0.7121 (t0) cc_final: 0.6819 (t0) REVERT: D 167 PHE cc_start: 0.6766 (m-10) cc_final: 0.6412 (m-10) REVERT: D 176 ARG cc_start: 0.7342 (mtt-85) cc_final: 0.4722 (mmt180) REVERT: D 418 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8541 (mp) REVERT: D 810 LYS cc_start: 0.6890 (mttm) cc_final: 0.6513 (mtmt) REVERT: D 857 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7696 (mtm110) REVERT: D 1387 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8001 (tm) REVERT: D 1441 ASN cc_start: 0.8956 (t0) cc_final: 0.8538 (t0) REVERT: D 1490 LYS cc_start: 0.8735 (tppt) cc_final: 0.8529 (mttt) REVERT: D 1493 TYR cc_start: 0.8532 (t80) cc_final: 0.8168 (t80) REVERT: D 1572 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7871 (tm-30) REVERT: D 1650 MET cc_start: 0.8340 (mmt) cc_final: 0.8021 (mmm) REVERT: D 1729 ASP cc_start: 0.7096 (p0) cc_final: 0.6891 (p0) outliers start: 31 outliers final: 21 residues processed: 311 average time/residue: 0.2141 time to fit residues: 99.6617 Evaluate side-chains 287 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1287 LEU Chi-restraints excluded: chain D residue 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1773 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 21 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1205 HIS ** D1461 ASN ** 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 = 0.4151 r_free = 0.4151 target = 0.180458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145339 restraints weight = 43176.318| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.85 r_work: 0.3545 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12271 Z= 0.248 Angle : 0.820 12.304 16575 Z= 0.405 Chirality : 0.048 0.461 1896 Planarity : 0.005 0.057 1995 Dihedral : 11.817 141.376 2112 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.37 % Favored : 91.49 % Rotamer: Outliers : 2.20 % Allowed : 22.47 % Favored : 75.33 % 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: -1.00 (0.22), residues: 1414 helix: 0.57 (0.18), residues: 844 sheet: -2.32 (0.44), residues: 116 loop : -2.54 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1346 HIS 0.004 0.001 HIS C 136 PHE 0.047 0.002 PHE D 827 TYR 0.022 0.002 TYR D 389 ARG 0.006 0.001 ARG D1430 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 7) link_NAG-ASN : angle 4.03384 ( 21) link_BETA1-4 : bond 0.01283 ( 3) link_BETA1-4 : angle 4.03196 ( 9) hydrogen bonds : bond 0.04252 ( 673) hydrogen bonds : angle 4.67706 ( 1941) SS BOND : bond 0.00704 ( 9) SS BOND : angle 2.82660 ( 18) covalent geometry : bond 0.00585 (12251) covalent geometry : angle 0.79797 (16527) Misc. bond : bond 0.00424 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8601 (mm-30) REVERT: D 149 ASN cc_start: 0.7114 (t0) cc_final: 0.6811 (t0) REVERT: D 176 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.4640 (mmt180) REVERT: D 418 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8597 (mp) REVERT: D 901 MET cc_start: 0.7521 (tpp) cc_final: 0.7111 (ttt) REVERT: D 1387 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8026 (tm) REVERT: D 1407 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: D 1441 ASN cc_start: 0.9206 (t0) cc_final: 0.8715 (t0) REVERT: D 1493 TYR cc_start: 0.8593 (t80) cc_final: 0.7872 (t80) REVERT: D 1572 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7943 (tm-30) REVERT: D 1650 MET cc_start: 0.8454 (mmt) cc_final: 0.8013 (mmm) REVERT: D 1651 SER cc_start: 0.8785 (t) cc_final: 0.8527 (t) REVERT: D 1693 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8522 (mt-10) REVERT: D 1729 ASP cc_start: 0.7251 (p0) cc_final: 0.7045 (p0) outliers start: 27 outliers final: 19 residues processed: 275 average time/residue: 0.2126 time to fit residues: 90.1155 Evaluate side-chains 270 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1274 TRP Chi-restraints excluded: chain D residue 1287 LEU Chi-restraints excluded: chain D residue 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1407 TYR Chi-restraints excluded: chain D residue 1464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 1 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1205 HIS ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1461 ASN ** 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 = 0.4180 r_free = 0.4180 target = 0.183283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148717 restraints weight = 38263.048| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.54 r_work: 0.3600 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12271 Z= 0.168 Angle : 0.770 12.094 16575 Z= 0.378 Chirality : 0.046 0.368 1896 Planarity : 0.004 0.058 1995 Dihedral : 11.512 140.820 2112 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.73 % Favored : 92.13 % Rotamer: Outliers : 2.28 % Allowed : 22.86 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1414 helix: 0.68 (0.18), residues: 841 sheet: -2.20 (0.44), residues: 116 loop : -2.41 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1419 HIS 0.004 0.001 HIS B 134 PHE 0.021 0.001 PHE D1620 TYR 0.025 0.002 TYR D1249 ARG 0.005 0.000 ARG D1317 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 7) link_NAG-ASN : angle 3.45837 ( 21) link_BETA1-4 : bond 0.01341 ( 3) link_BETA1-4 : angle 3.64665 ( 9) hydrogen bonds : bond 0.04036 ( 673) hydrogen bonds : angle 4.60429 ( 1941) SS BOND : bond 0.00553 ( 9) SS BOND : angle 2.07145 ( 18) covalent geometry : bond 0.00390 (12251) covalent geometry : angle 0.75317 (16527) Misc. bond : bond 0.00521 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6856.87 seconds wall clock time: 118 minutes 24.19 seconds (7104.19 seconds total)