Starting phenix.real_space_refine on Sat Aug 23 17:13:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7f_32343/08_2025/7w7f_32343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7f_32343/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7w7f_32343/08_2025/7w7f_32343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7f_32343/08_2025/7w7f_32343.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w7f_32343/08_2025/7w7f_32343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7f_32343/08_2025/7w7f_32343.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.78, per 1000 atoms: 0.23 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: 1.06 Conformation dependent library (CDL) restraints added in 550.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.25 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: 1.63 Time building geometry restraints manager: 1.48 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.870 ------------------------------------------------------------------------------- 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 : 13.74 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG D 394 TYR 0.020 0.002 TYR D1294 PHE 0.018 0.001 PHE D 195 TRP 0.027 0.001 TRP D 944 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.01484 (12251) covalent geometry : angle 1.02851 (16527) SS BOND : bond 0.00402 ( 9) SS BOND : angle 1.29827 ( 18) hydrogen bonds : bond 0.12045 ( 673) hydrogen bonds : angle 6.04900 ( 1941) Misc. bond : bond 0.88170 ( 1) link_BETA1-4 : bond 0.01562 ( 3) link_BETA1-4 : angle 4.78699 ( 9) link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 3.27811 ( 21) *********************** 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 : 0.411 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: 0.0834 time to fit residues: 38.3758 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 : 0.417 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** D1539 ASN D1732 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.184841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149861 restraints weight = 42911.292| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.96 r_work: 0.3612 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12271 Z= 0.251 Angle : 0.767 11.046 16575 Z= 0.387 Chirality : 0.046 0.295 1896 Planarity : 0.005 0.059 1995 Dihedral : 16.451 149.830 2112 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.58 % Favored : 91.13 % Rotamer: Outliers : 2.20 % Allowed : 10.68 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.22), residues: 1414 helix: 0.42 (0.18), residues: 834 sheet: -2.83 (0.42), residues: 115 loop : -2.45 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 98 TYR 0.021 0.002 TYR D 389 PHE 0.017 0.002 PHE D1345 TRP 0.013 0.002 TRP D1711 HIS 0.004 0.001 HIS D 781 Details of bonding type rmsd covalent geometry : bond 0.00588 (12251) covalent geometry : angle 0.75161 (16527) SS BOND : bond 0.00497 ( 9) SS BOND : angle 1.39436 ( 18) hydrogen bonds : bond 0.04721 ( 673) hydrogen bonds : angle 5.01920 ( 1941) Misc. bond : bond 0.00003 ( 1) link_BETA1-4 : bond 0.01639 ( 3) link_BETA1-4 : angle 4.86858 ( 9) link_NAG-ASN : bond 0.00208 ( 7) link_NAG-ASN : angle 2.70793 ( 21) *********************** 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 291 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8734 (t80) cc_final: 0.7961 (t80) REVERT: D 149 ASN cc_start: 0.6959 (t0) cc_final: 0.6516 (t0) REVERT: D 857 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7496 (mtm180) REVERT: D 916 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8370 (m-40) REVERT: D 1294 TYR cc_start: 0.7194 (m-10) cc_final: 0.6973 (m-10) REVERT: D 1321 MET cc_start: 0.8337 (mtm) cc_final: 0.7897 (mtm) REVERT: D 1441 ASN cc_start: 0.9189 (t0) cc_final: 0.8774 (t0) REVERT: D 1620 PHE cc_start: 0.7827 (t80) cc_final: 0.7407 (t80) REVERT: D 1651 SER cc_start: 0.8886 (t) cc_final: 0.8670 (t) outliers start: 27 outliers final: 19 residues processed: 274 average time/residue: 0.0814 time to fit residues: 33.7976 Evaluate side-chains 270 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL 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 146 THR 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 802 ILE Chi-restraints excluded: chain D residue 849 VAL 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 41 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 50.0000 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 0.0670 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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** D1550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.186650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151942 restraints weight = 38869.255| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.58 r_work: 0.3637 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12271 Z= 0.128 Angle : 0.649 8.472 16575 Z= 0.328 Chirality : 0.042 0.255 1896 Planarity : 0.004 0.056 1995 Dihedral : 13.845 145.609 2112 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.38 % Favored : 92.34 % Rotamer: Outliers : 2.36 % Allowed : 14.22 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.22), residues: 1414 helix: 0.66 (0.18), residues: 839 sheet: -2.46 (0.43), residues: 116 loop : -2.37 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1317 TYR 0.017 0.001 TYR D 389 PHE 0.018 0.001 PHE C 80 TRP 0.023 0.001 TRP D1419 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00267 (12251) covalent geometry : angle 0.63950 (16527) SS BOND : bond 0.00509 ( 9) SS BOND : angle 0.97542 ( 18) hydrogen bonds : bond 0.04057 ( 673) hydrogen bonds : angle 4.68014 ( 1941) Misc. bond : bond 0.00243 ( 1) link_BETA1-4 : bond 0.01584 ( 3) link_BETA1-4 : angle 3.74356 ( 9) link_NAG-ASN : bond 0.00328 ( 7) link_NAG-ASN : angle 2.05199 ( 21) *********************** 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 344 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 315 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 30 MET cc_start: 0.3426 (tpt) cc_final: 0.3038 (tpp) REVERT: C 62 GLN cc_start: 0.6838 (mp10) cc_final: 0.6474 (pm20) REVERT: D 145 MET cc_start: 0.7669 (mtp) cc_final: 0.7453 (mtm) REVERT: D 149 ASN cc_start: 0.6936 (t0) cc_final: 0.6517 (t0) REVERT: D 779 MET cc_start: 0.8465 (mpp) cc_final: 0.7881 (mpp) REVERT: D 810 LYS cc_start: 0.6875 (mttm) cc_final: 0.6465 (mtmt) REVERT: D 851 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.6023 (ttm-80) REVERT: D 1321 MET cc_start: 0.8356 (mtm) cc_final: 0.7858 (mtm) REVERT: D 1441 ASN cc_start: 0.9012 (t0) cc_final: 0.8549 (t0) REVERT: D 1493 TYR cc_start: 0.8550 (t80) cc_final: 0.8156 (t80) REVERT: D 1620 PHE cc_start: 0.7859 (t80) cc_final: 0.7475 (t80) REVERT: D 1650 MET cc_start: 0.8207 (mmt) cc_final: 0.7988 (mmm) outliers start: 29 outliers final: 14 residues processed: 330 average time/residue: 0.0821 time to fit residues: 40.3318 Evaluate side-chains 284 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 269 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 D residue 133 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 851 ARG 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 1381 LEU Chi-restraints excluded: chain D residue 1387 LEU Chi-restraints excluded: chain D residue 1389 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 28 optimal weight: 50.0000 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 29 optimal weight: 0.0050 chunk 25 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.2600 ------------------------------------------------------------------------------- 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 382 GLN ** 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** D1732 HIS D1773 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.184470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.155299 restraints weight = 32567.580| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.48 r_work: 0.3581 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12271 Z= 0.151 Angle : 0.686 11.875 16575 Z= 0.342 Chirality : 0.043 0.263 1896 Planarity : 0.004 0.056 1995 Dihedral : 13.070 142.072 2112 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.87 % Favored : 91.84 % Rotamer: Outliers : 2.67 % Allowed : 16.89 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.22), residues: 1414 helix: 0.73 (0.18), residues: 842 sheet: -2.30 (0.44), residues: 114 loop : -2.35 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 98 TYR 0.023 0.002 TYR D 389 PHE 0.022 0.001 PHE D1594 TRP 0.021 0.001 TRP D1419 HIS 0.003 0.001 HIS D1732 Details of bonding type rmsd covalent geometry : bond 0.00345 (12251) covalent geometry : angle 0.67545 (16527) SS BOND : bond 0.00333 ( 9) SS BOND : angle 1.14398 ( 18) hydrogen bonds : bond 0.04039 ( 673) hydrogen bonds : angle 4.55512 ( 1941) Misc. bond : bond 0.00224 ( 1) link_BETA1-4 : bond 0.01436 ( 3) link_BETA1-4 : angle 4.01010 ( 9) link_NAG-ASN : bond 0.00361 ( 7) link_NAG-ASN : angle 2.17360 ( 21) *********************** 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 308 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 GLN cc_start: 0.7261 (mp10) cc_final: 0.6801 (mp10) REVERT: C 62 GLN cc_start: 0.6888 (mp10) cc_final: 0.6631 (pm20) REVERT: D 139 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8009 (tp) REVERT: D 145 MET cc_start: 0.7788 (mtp) cc_final: 0.7547 (mtm) REVERT: D 149 ASN cc_start: 0.7057 (t0) cc_final: 0.6737 (t0) REVERT: D 176 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.4753 (mmt180) REVERT: D 418 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8500 (mp) REVERT: D 810 LYS cc_start: 0.7075 (mttm) cc_final: 0.6725 (mtmt) REVERT: D 1321 MET cc_start: 0.8419 (mtm) cc_final: 0.7783 (mtm) REVERT: D 1387 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7465 (tm) REVERT: D 1441 ASN cc_start: 0.9162 (t0) cc_final: 0.8693 (t0) REVERT: D 1493 TYR cc_start: 0.8600 (t80) cc_final: 0.7947 (t80) REVERT: D 1620 PHE cc_start: 0.7893 (t80) cc_final: 0.7459 (t80) REVERT: D 1650 MET cc_start: 0.8313 (mmt) cc_final: 0.7660 (mmm) REVERT: D 1651 SER cc_start: 0.8841 (t) cc_final: 0.8595 (t) outliers start: 33 outliers final: 23 residues processed: 289 average time/residue: 0.0749 time to fit residues: 32.9192 Evaluate side-chains 284 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 235 THR Chi-restraints excluded: chain D residue 243 SER 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 916 ASN 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 1339 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 1773 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 27 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 64 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.183730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147452 restraints weight = 41942.815| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.98 r_work: 0.3588 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1813 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= 0.181 Angle : 0.704 15.099 16575 Z= 0.350 Chirality : 0.043 0.266 1896 Planarity : 0.004 0.055 1995 Dihedral : 12.734 140.585 2112 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.73 % Favored : 91.99 % Rotamer: Outliers : 2.75 % Allowed : 18.77 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.22), residues: 1414 helix: 0.70 (0.18), residues: 843 sheet: -2.33 (0.43), residues: 116 loop : -2.35 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1317 TYR 0.021 0.002 TYR D 389 PHE 0.018 0.002 PHE D1594 TRP 0.017 0.001 TRP D1419 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00421 (12251) covalent geometry : angle 0.69191 (16527) SS BOND : bond 0.00377 ( 9) SS BOND : angle 1.10863 ( 18) hydrogen bonds : bond 0.04086 ( 673) hydrogen bonds : angle 4.57811 ( 1941) Misc. bond : bond 0.00252 ( 1) link_BETA1-4 : bond 0.01331 ( 3) link_BETA1-4 : angle 4.04099 ( 9) link_NAG-ASN : bond 0.00279 ( 7) link_NAG-ASN : angle 2.60135 ( 21) *********************** 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 299 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 GLN cc_start: 0.7324 (mp10) cc_final: 0.7112 (mp10) REVERT: D 139 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8372 (mp) REVERT: D 149 ASN cc_start: 0.7098 (t0) cc_final: 0.6767 (t0) REVERT: D 176 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.4745 (mmt180) REVERT: D 418 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 810 LYS cc_start: 0.7044 (mttm) cc_final: 0.6672 (mtmt) REVERT: D 827 PHE cc_start: 0.7035 (t80) cc_final: 0.6792 (t80) REVERT: D 1287 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6831 (mp) REVERT: D 1387 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7491 (tm) REVERT: D 1441 ASN cc_start: 0.9123 (t0) cc_final: 0.8652 (t0) REVERT: D 1620 PHE cc_start: 0.7897 (t80) cc_final: 0.7442 (t80) REVERT: D 1650 MET cc_start: 0.8329 (mmt) cc_final: 0.7666 (mmm) REVERT: D 1651 SER cc_start: 0.8868 (t) cc_final: 0.8622 (t) outliers start: 34 outliers final: 22 residues processed: 283 average time/residue: 0.0762 time to fit residues: 33.1389 Evaluate side-chains 280 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 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 1339 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 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 63 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.184062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149476 restraints weight = 38234.393| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.52 r_work: 0.3604 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 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 = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1934 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= 0.152 Angle : 0.706 16.624 16575 Z= 0.347 Chirality : 0.043 0.262 1896 Planarity : 0.004 0.056 1995 Dihedral : 12.105 138.524 2112 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.59 % Favored : 92.13 % Rotamer: Outliers : 3.46 % Allowed : 18.54 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.22), residues: 1414 helix: 0.75 (0.18), residues: 844 sheet: -2.17 (0.44), residues: 116 loop : -2.37 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1317 TYR 0.019 0.002 TYR D 389 PHE 0.018 0.001 PHE D1451 TRP 0.019 0.001 TRP D1419 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00350 (12251) covalent geometry : angle 0.67566 (16527) SS BOND : bond 0.00281 ( 9) SS BOND : angle 1.08396 ( 18) hydrogen bonds : bond 0.04017 ( 673) hydrogen bonds : angle 4.52853 ( 1941) Misc. bond : bond 0.00366 ( 1) link_BETA1-4 : bond 0.01378 ( 3) link_BETA1-4 : angle 3.77326 ( 9) link_NAG-ASN : bond 0.00379 ( 7) link_NAG-ASN : angle 5.18852 ( 21) *********************** 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 312 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 GLN cc_start: 0.7392 (mp10) cc_final: 0.6763 (mp10) REVERT: D 149 ASN cc_start: 0.7073 (t0) cc_final: 0.6756 (t0) REVERT: D 176 ARG cc_start: 0.7302 (mtt-85) cc_final: 0.4690 (mmt180) REVERT: D 195 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7217 (t80) REVERT: D 418 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 810 LYS cc_start: 0.7159 (mttm) cc_final: 0.6763 (mtmt) REVERT: D 827 PHE cc_start: 0.7016 (t80) cc_final: 0.6782 (t80) REVERT: D 1387 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7684 (tm) REVERT: D 1441 ASN cc_start: 0.9087 (t0) cc_final: 0.8606 (t0) REVERT: D 1490 LYS cc_start: 0.8744 (tppt) cc_final: 0.8510 (mttp) REVERT: D 1533 MET cc_start: 0.7844 (mmm) cc_final: 0.7619 (mmm) REVERT: D 1620 PHE cc_start: 0.8040 (t80) cc_final: 0.7633 (t80) REVERT: D 1650 MET cc_start: 0.8292 (mmt) cc_final: 0.8009 (mmm) REVERT: D 1729 ASP cc_start: 0.7264 (p0) cc_final: 0.7049 (p0) outliers start: 43 outliers final: 27 residues processed: 291 average time/residue: 0.0772 time to fit residues: 33.7303 Evaluate side-chains 283 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ASN 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 146 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 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 1339 LEU Chi-restraints excluded: chain D residue 1341 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 1.9990 chunk 25 optimal weight: 40.0000 chunk 99 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.184144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.149922 restraints weight = 38684.142| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.57 r_work: 0.3619 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2085 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= 0.155 Angle : 0.712 13.069 16575 Z= 0.348 Chirality : 0.045 0.485 1896 Planarity : 0.004 0.056 1995 Dihedral : 11.755 138.026 2112 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.59 % Favored : 92.20 % Rotamer: Outliers : 2.99 % Allowed : 20.42 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.22), residues: 1414 helix: 0.79 (0.18), residues: 843 sheet: -2.12 (0.43), residues: 116 loop : -2.39 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1430 TYR 0.018 0.001 TYR D 389 PHE 0.018 0.001 PHE D1451 TRP 0.023 0.001 TRP D1419 HIS 0.005 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00357 (12251) covalent geometry : angle 0.68704 (16527) SS BOND : bond 0.00480 ( 9) SS BOND : angle 1.22762 ( 18) hydrogen bonds : bond 0.03932 ( 673) hydrogen bonds : angle 4.53181 ( 1941) Misc. bond : bond 0.00283 ( 1) link_BETA1-4 : bond 0.01381 ( 3) link_BETA1-4 : angle 3.72837 ( 9) link_NAG-ASN : bond 0.00453 ( 7) link_NAG-ASN : angle 4.65677 ( 21) *********************** 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 305 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 GLN cc_start: 0.7426 (mp10) cc_final: 0.6803 (mp10) REVERT: B 133 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8471 (mm-30) REVERT: D 149 ASN cc_start: 0.7061 (t0) cc_final: 0.6752 (t0) REVERT: D 176 ARG cc_start: 0.7296 (mtt-85) cc_final: 0.4698 (mmt180) REVERT: D 251 MET cc_start: 0.8235 (tpp) cc_final: 0.8026 (mmt) REVERT: D 418 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8548 (mp) REVERT: D 810 LYS cc_start: 0.7117 (mttm) cc_final: 0.6709 (mtmt) REVERT: D 827 PHE cc_start: 0.6973 (t80) cc_final: 0.6771 (t80) REVERT: D 1387 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7844 (tm) REVERT: D 1441 ASN cc_start: 0.9079 (t0) cc_final: 0.8640 (t0) REVERT: D 1490 LYS cc_start: 0.8737 (tppt) cc_final: 0.8536 (mttp) REVERT: D 1533 MET cc_start: 0.7778 (mmm) cc_final: 0.7569 (mmm) REVERT: D 1650 MET cc_start: 0.8279 (mmt) cc_final: 0.7974 (mmm) REVERT: D 1729 ASP cc_start: 0.7222 (p0) cc_final: 0.7017 (p0) outliers start: 37 outliers final: 27 residues processed: 291 average time/residue: 0.0728 time to fit residues: 32.6371 Evaluate side-chains 279 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 110 ASN 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 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 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 1341 VAL 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 1467 ILE Chi-restraints excluded: chain D residue 1549 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 73 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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** ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.183304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.155388 restraints weight = 34949.805| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 5.19 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2151 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= 0.171 Angle : 0.723 12.029 16575 Z= 0.356 Chirality : 0.045 0.495 1896 Planarity : 0.004 0.056 1995 Dihedral : 11.585 138.188 2112 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.94 % Favored : 91.84 % Rotamer: Outliers : 3.30 % Allowed : 20.19 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.22), residues: 1414 helix: 0.79 (0.18), residues: 843 sheet: -2.16 (0.43), residues: 116 loop : -2.46 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1430 TYR 0.019 0.002 TYR B 119 PHE 0.021 0.001 PHE D1451 TRP 0.015 0.001 TRP D1419 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00398 (12251) covalent geometry : angle 0.70366 (16527) SS BOND : bond 0.00387 ( 9) SS BOND : angle 1.08293 ( 18) hydrogen bonds : bond 0.03993 ( 673) hydrogen bonds : angle 4.54522 ( 1941) Misc. bond : bond 0.00655 ( 1) link_BETA1-4 : bond 0.01241 ( 3) link_BETA1-4 : angle 3.74784 ( 9) link_NAG-ASN : bond 0.00419 ( 7) link_NAG-ASN : angle 3.96244 ( 21) *********************** 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 306 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8734 (m) REVERT: B 79 GLN cc_start: 0.7361 (mp10) cc_final: 0.6792 (mp10) REVERT: B 133 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8472 (mm-30) REVERT: D 149 ASN cc_start: 0.7061 (t0) cc_final: 0.6790 (t0) REVERT: D 176 ARG cc_start: 0.7399 (mtt-85) cc_final: 0.4880 (mmt180) REVERT: D 195 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6957 (t80) REVERT: D 418 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8484 (mp) REVERT: D 810 LYS cc_start: 0.7206 (mttm) cc_final: 0.6820 (mtmt) REVERT: D 1387 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7981 (tm) REVERT: D 1407 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.6663 (m-10) REVERT: D 1441 ASN cc_start: 0.8750 (t0) cc_final: 0.8369 (t0) REVERT: D 1490 LYS cc_start: 0.8747 (tppt) cc_final: 0.8485 (mttp) REVERT: D 1650 MET cc_start: 0.8204 (mmt) cc_final: 0.7877 (mmm) REVERT: D 1651 SER cc_start: 0.8905 (t) cc_final: 0.8644 (t) outliers start: 41 outliers final: 28 residues processed: 290 average time/residue: 0.0799 time to fit residues: 34.9091 Evaluate side-chains 291 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 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 200 MET 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 851 ARG 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 1523 VAL Chi-restraints excluded: chain D residue 1549 ASP 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 75 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1385 GLN ** D1441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145501 restraints weight = 41229.825| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.64 r_work: 0.3562 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 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 = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12271 Z= 0.235 Angle : 0.813 14.939 16575 Z= 0.397 Chirality : 0.053 1.150 1896 Planarity : 0.005 0.055 1995 Dihedral : 11.858 141.026 2112 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.01 % Favored : 90.78 % Rotamer: Outliers : 3.38 % Allowed : 20.27 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.22), residues: 1414 helix: 0.60 (0.18), residues: 843 sheet: -2.28 (0.43), residues: 114 loop : -2.60 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1430 TYR 0.027 0.002 TYR D1249 PHE 0.039 0.002 PHE D 827 TRP 0.016 0.002 TRP D1259 HIS 0.004 0.001 HIS D1363 Details of bonding type rmsd covalent geometry : bond 0.00553 (12251) covalent geometry : angle 0.78424 (16527) SS BOND : bond 0.00476 ( 9) SS BOND : angle 2.74352 ( 18) hydrogen bonds : bond 0.04265 ( 673) hydrogen bonds : angle 4.68009 ( 1941) Misc. bond : bond 0.00495 ( 1) link_BETA1-4 : bond 0.01211 ( 3) link_BETA1-4 : angle 4.00467 ( 9) link_NAG-ASN : bond 0.00498 ( 7) link_NAG-ASN : angle 4.90303 ( 21) *********************** 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 305 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8821 (m) REVERT: B 79 GLN cc_start: 0.7588 (mp10) cc_final: 0.6909 (mp10) REVERT: B 133 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8494 (mm-30) REVERT: D 149 ASN cc_start: 0.7097 (t0) cc_final: 0.6787 (t0) REVERT: D 176 ARG cc_start: 0.7320 (mtt-85) cc_final: 0.4703 (mmt180) REVERT: D 195 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7295 (t80) REVERT: D 418 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8612 (mp) REVERT: D 1226 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7938 (mt-10) REVERT: D 1321 MET cc_start: 0.8368 (mtm) cc_final: 0.7824 (mtm) REVERT: D 1387 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8060 (tm) REVERT: D 1407 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7194 (m-10) REVERT: D 1441 ASN cc_start: 0.9188 (t0) cc_final: 0.8690 (t0) REVERT: D 1533 MET cc_start: 0.7894 (mmm) cc_final: 0.7674 (mmm) REVERT: D 1650 MET cc_start: 0.8382 (mmt) cc_final: 0.8065 (mmm) REVERT: D 1651 SER cc_start: 0.8912 (t) cc_final: 0.8663 (t) outliers start: 42 outliers final: 32 residues processed: 289 average time/residue: 0.0781 time to fit residues: 34.4391 Evaluate side-chains 291 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 200 MET 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 851 ARG 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 1274 TRP Chi-restraints excluded: chain D residue 1287 LEU Chi-restraints excluded: chain D residue 1355 ASN 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 1523 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.7045 > 50: distance: 4 - 9: 29.043 distance: 9 - 10: 16.397 distance: 10 - 13: 32.923 distance: 11 - 12: 11.517 distance: 11 - 14: 8.614 distance: 14 - 15: 9.387 distance: 15 - 16: 36.246 distance: 15 - 18: 22.157 distance: 16 - 17: 40.183 distance: 16 - 21: 21.630 distance: 18 - 20: 40.221 distance: 21 - 22: 43.410 distance: 22 - 23: 45.105 distance: 22 - 25: 12.669 distance: 23 - 24: 20.464 distance: 23 - 29: 37.997 distance: 25 - 26: 8.285 distance: 26 - 27: 50.986 distance: 26 - 28: 28.955 distance: 29 - 30: 8.073 distance: 30 - 31: 16.823 distance: 30 - 33: 30.193 distance: 31 - 32: 18.951 distance: 31 - 37: 14.176 distance: 33 - 34: 32.367 distance: 34 - 35: 28.526 distance: 34 - 36: 37.097 distance: 37 - 38: 18.460 distance: 38 - 39: 4.980 distance: 38 - 41: 24.032 distance: 39 - 40: 18.019 distance: 39 - 44: 27.612 distance: 41 - 42: 5.332 distance: 41 - 43: 34.508 distance: 44 - 45: 15.887 distance: 45 - 46: 14.336 distance: 45 - 48: 11.233 distance: 46 - 47: 27.251 distance: 46 - 52: 53.018 distance: 48 - 49: 15.861 distance: 49 - 50: 12.039 distance: 49 - 51: 18.279 distance: 53 - 54: 5.213 distance: 53 - 56: 21.536 distance: 54 - 55: 10.882 distance: 54 - 60: 24.180 distance: 56 - 57: 11.075 distance: 57 - 58: 8.428 distance: 57 - 59: 23.563 distance: 60 - 61: 9.933 distance: 61 - 62: 51.819 distance: 62 - 63: 41.021 distance: 62 - 64: 12.810 distance: 64 - 67: 5.722 distance: 64 - 70: 42.260 distance: 65 - 66: 9.370 distance: 65 - 67: 46.488 distance: 65 - 70: 15.782 distance: 65 - 73: 31.685 distance: 67 - 68: 51.468 distance: 68 - 69: 16.989 distance: 70 - 71: 49.118 distance: 71 - 72: 43.459 distance: 73 - 74: 43.707 distance: 74 - 75: 13.990 distance: 74 - 77: 23.952 distance: 75 - 81: 27.375 distance: 77 - 78: 28.534 distance: 78 - 79: 22.112 distance: 78 - 80: 22.896