Starting phenix.real_space_refine on Fri Jul 3 09:28:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w77_32341/07_2026/7w77_32341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w77_32341/07_2026/7w77_32341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w77_32341/07_2026/7w77_32341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w77_32341/07_2026/7w77_32341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w77_32341/07_2026/7w77_32341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w77_32341/07_2026/7w77_32341.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w77_32341/07_2026/7w77_32341.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w77_32341/07_2026/7w77_32341.cif" } resolution = 3.3 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= 0.005 sd= 0.099 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 973 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 99 5.16 5 C 7989 2.51 5 N 1835 2.21 5 O 2125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12051 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: 1007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 995 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Conformer: "B" Number of residues, atoms: 122, 995 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} bond proxies already assigned to first conformer: 1001 Chain: "D" Number of atoms: 9051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9051 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 27, 'TRANS': 1095} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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 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 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 chiralities: 4 Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Unusual residues: {'6OU': 16, '966': 1, '9Z9': 3, 'NAG': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 383 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'6OU:plan-1': 14, '6OU:plan-2': 11, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 102 Time building chain proxies: 2.70, per 1000 atoms: 0.22 Number of scatterers: 12051 At special positions: 0 Unit cell: (135.2, 138.32, 112.32, 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 99 16.00 P 3 15.00 O 2125 8.00 N 1835 7.00 C 7989 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=2.02 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 337 " 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=2.00 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=5, 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 D2001 " - " ASN D1366 " " NAG E 1 " - " ASN D 339 " " NAG F 1 " - " ASN D1380 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 599.0 milliseconds 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: 59 helices and 7 sheets defined 63.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.507A pdb=" N PHE B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 87' Processing helix chain 'B' and resid 153 through 190 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.991A pdb=" N GLU C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.216A pdb=" N LYS D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 146 Processing helix chain 'D' and resid 153 through 174 removed outlier: 3.819A pdb=" N VAL D 157 " --> pdb=" O TRP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.626A pdb=" N TRP D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 223 removed outlier: 3.633A pdb=" N PHE D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 232 through 244 removed outlier: 3.543A pdb=" N ILE D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) 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: 3.889A pdb=" N ASP D 321 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 4.159A 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 396 removed outlier: 3.839A pdb=" N LEU D 388 " --> pdb=" O TYR D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 400 through 411 removed outlier: 4.106A pdb=" N PHE D 404 " --> pdb=" O TYR D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 438 Processing helix chain 'D' and resid 742 through 755 Processing helix chain 'D' and resid 763 through 779 removed outlier: 3.510A pdb=" N THR D 767 " --> pdb=" O ASP D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.813A pdb=" N ALA D 813 " --> pdb=" O LEU D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 842 Processing helix chain 'D' and resid 848 through 864 removed outlier: 3.627A pdb=" N ARG D 854 " --> pdb=" O ARG D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 880 removed outlier: 3.591A pdb=" N VAL D 879 " --> pdb=" O ILE D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 911 removed outlier: 5.698A pdb=" N LYS D 906 " --> pdb=" O GLN D 902 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER D 907 " --> pdb=" O LEU D 903 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 915 Processing helix chain 'D' and resid 928 through 942 Processing helix chain 'D' and resid 944 through 956 removed outlier: 4.178A pdb=" N ASP D 950 " --> pdb=" O GLU D 946 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 956 " --> pdb=" O MET D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 985 removed outlier: 3.940A pdb=" N ASN D 972 " --> pdb=" O MET D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 1191 through 1205 removed outlier: 3.518A pdb=" N THR D1198 " --> pdb=" O ASN D1194 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1222 Processing helix chain 'D' and resid 1229 through 1234 Processing helix chain 'D' and resid 1235 through 1263 removed outlier: 3.701A 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 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: 3.783A 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 1382 through 1386 Processing helix chain 'D' and resid 1402 through 1416 Processing helix chain 'D' and resid 1418 through 1429 removed outlier: 3.776A 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 1454 removed outlier: 3.788A pdb=" N PHE D1448 " --> pdb=" O MET D1444 " (cutoff:3.500A) Processing helix chain 'D' and resid 1457 through 1479 removed outlier: 3.543A pdb=" N GLY D1479 " --> pdb=" O LYS D1475 " (cutoff:3.500A) Processing helix chain 'D' and resid 1486 through 1501 removed outlier: 3.839A pdb=" N LYS D1498 " --> pdb=" O ASN D1494 " (cutoff:3.500A) Processing helix chain 'D' and resid 1515 through 1524 Processing helix chain 'D' and resid 1525 through 1545 removed outlier: 3.908A pdb=" N MET D1533 " --> pdb=" O ASP D1529 " (cutoff:3.500A) Processing helix chain 'D' and resid 1551 through 1581 Processing helix chain 'D' and resid 1587 through 1613 removed outlier: 4.044A pdb=" N ILE D1591 " --> pdb=" O ILE D1587 " (cutoff:3.500A) Processing helix chain 'D' and resid 1616 through 1624 removed outlier: 3.995A pdb=" N VAL D1622 " --> pdb=" O THR D1618 " (cutoff:3.500A) Processing helix chain 'D' and resid 1625 through 1633 removed outlier: 3.877A pdb=" N GLY D1629 " --> pdb=" O LEU D1625 " (cutoff:3.500A) Processing helix chain 'D' and resid 1634 through 1637 Processing helix chain 'D' and resid 1640 through 1677 Proline residue: D1653 - end of helix Processing helix chain 'D' and resid 1678 through 1680 No H-bonds generated for 'chain 'D' and resid 1678 through 1680' Processing helix chain 'D' and resid 1694 through 1707 removed outlier: 3.823A pdb=" N THR D1707 " --> pdb=" O PHE D1703 " (cutoff:3.500A) Processing helix chain 'D' and resid 1710 through 1716 Processing helix chain 'D' and resid 1743 through 1778 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.298A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'B' and resid 78 through 80 removed outlier: 5.695A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 33 removed outlier: 4.046A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.970A pdb=" N LEU C 38 " --> pdb=" O HIS C 143 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN C 145 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AA7, first strand: chain 'D' and resid 275 through 279 706 hydrogen bonds defined for protein. 2016 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: 1.45 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.17: 18 1.17 - 1.35: 3577 1.35 - 1.54: 8258 1.54 - 1.72: 298 1.72 - 1.91: 178 Bond restraints: 12329 Sorted by residual: bond pdb=" C73 9Z9 D2002 " pdb=" C76 9Z9 D2002 " ideal model delta sigma weight residual 1.522 1.097 0.425 2.00e-02 2.50e+03 4.52e+02 bond pdb=" C73 9Z9 D2002 " pdb=" O72 9Z9 D2002 " ideal model delta sigma weight residual 1.406 0.981 0.425 2.00e-02 2.50e+03 4.51e+02 bond pdb=" C73 9Z9 D2003 " pdb=" O72 9Z9 D2003 " ideal model delta sigma weight residual 1.406 0.983 0.423 2.00e-02 2.50e+03 4.47e+02 bond pdb=" C73 9Z9 D2003 " pdb=" C76 9Z9 D2003 " ideal model delta sigma weight residual 1.522 1.099 0.423 2.00e-02 2.50e+03 4.47e+02 bond pdb=" C73 9Z9 D2013 " pdb=" C76 9Z9 D2013 " ideal model delta sigma weight residual 1.522 1.100 0.422 2.00e-02 2.50e+03 4.45e+02 ... (remaining 12324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 16488 4.68 - 9.35: 166 9.35 - 14.03: 10 14.03 - 18.70: 5 18.70 - 23.38: 1 Bond angle restraints: 16670 Sorted by residual: angle pdb=" C CYS D1384 " pdb=" CA CYS D1384 " pdb=" CB CYS D1384 " ideal model delta sigma weight residual 110.72 95.49 15.23 1.77e+00 3.19e-01 7.41e+01 angle pdb=" C07 966 D2021 " pdb=" C05 966 D2021 " pdb=" C08 966 D2021 " ideal model delta sigma weight residual 113.79 137.17 -23.38 3.00e+00 1.11e-01 6.07e+01 angle pdb=" N GLN D1385 " pdb=" CA GLN D1385 " pdb=" C GLN D1385 " ideal model delta sigma weight residual 112.54 101.41 11.13 1.51e+00 4.39e-01 5.43e+01 angle pdb=" N LEU D1387 " pdb=" CA LEU D1387 " pdb=" C LEU D1387 " ideal model delta sigma weight residual 111.14 103.72 7.42 1.08e+00 8.57e-01 4.72e+01 angle pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" CD PRO C 132 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.13e+01 ... (remaining 16665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 7050 35.15 - 70.29: 186 70.29 - 105.44: 15 105.44 - 140.58: 6 140.58 - 175.73: 2 Dihedral angle restraints: 7259 sinusoidal: 3082 harmonic: 4177 Sorted by residual: dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 43 " pdb=" CB CYS B 43 " ideal model delta sinusoidal sigma weight residual -86.00 -174.77 88.77 1 1.00e+01 1.00e-02 9.39e+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 -157.44 71.44 1 1.00e+01 1.00e-02 6.54e+01 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 -18.39 -67.61 1 1.00e+01 1.00e-02 5.94e+01 ... (remaining 7256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.295: 1903 0.295 - 0.590: 14 0.590 - 0.885: 7 0.885 - 1.180: 1 1.180 - 1.475: 6 Chirality restraints: 1931 Sorted by residual: chirality pdb=" C07 9Z9 D2002 " pdb=" C06 9Z9 D2002 " pdb=" C08 9Z9 D2002 " pdb=" C15 9Z9 D2002 " both_signs ideal model delta sigma weight residual False -2.70 -1.22 -1.48 2.00e-01 2.50e+01 5.44e+01 chirality pdb=" C07 9Z9 D2003 " pdb=" C06 9Z9 D2003 " pdb=" C08 9Z9 D2003 " pdb=" C15 9Z9 D2003 " both_signs ideal model delta sigma weight residual False -2.70 -1.23 -1.47 2.00e-01 2.50e+01 5.37e+01 chirality pdb=" C07 9Z9 D2013 " pdb=" C06 9Z9 D2013 " pdb=" C08 9Z9 D2013 " pdb=" C15 9Z9 D2013 " both_signs ideal model delta sigma weight residual False -2.70 -1.27 -1.43 2.00e-01 2.50e+01 5.12e+01 ... (remaining 1928 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D1382 " -0.032 2.00e-02 2.50e+03 6.24e-02 3.89e+01 pdb=" C SER D1382 " 0.108 2.00e-02 2.50e+03 pdb=" O SER D1382 " -0.040 2.00e-02 2.50e+03 pdb=" N ASP D1383 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 131 " 0.093 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO C 132 " -0.236 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D1454 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C PHE D1454 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE D1454 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY D1455 " -0.016 2.00e-02 2.50e+03 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 501 2.72 - 3.27: 12633 3.27 - 3.81: 19577 3.81 - 4.36: 23827 4.36 - 4.90: 40804 Nonbonded interactions: 97342 Sorted by model distance: nonbonded pdb=" OE1 GLN D 267 " pdb=" NH1 ARG D1624 " model vdw 2.176 3.120 nonbonded pdb=" NE2 GLN B 61 " pdb=" O ASN B 114 " model vdw 2.249 3.120 nonbonded pdb=" O PHE D1268 " pdb=" NE1 TRP D1274 " model vdw 2.270 3.120 nonbonded pdb=" O TRP B 92 " pdb=" NH2 ARG B 96 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR B 53 " pdb=" NH1 ARG B 125 " model vdw 2.289 3.120 ... (remaining 97337 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.130 Find NCS groups from input model: 0.050 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.022 0.425 12353 Z= 1.089 Angle : 1.089 23.380 16718 Z= 0.485 Chirality : 0.110 1.475 1931 Planarity : 0.005 0.136 1992 Dihedral : 16.576 175.728 4536 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.24 % Allowed : 0.47 % Favored : 99.29 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.15 (0.23), residues: 1414 helix: 1.18 (0.19), residues: 806 sheet: -1.82 (0.46), residues: 114 loop : -1.84 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 152 TYR 0.017 0.001 TYR D 384 PHE 0.028 0.001 PHE D1594 TRP 0.037 0.001 TRP D1419 HIS 0.002 0.001 HIS D 781 Details of bonding type rmsd/Z covalent geometry : bond 0.02179 / 1.09 (12329) covalent geometry : angle 1.07123 / 0.48 (16670) SS BOND : bond 0.01087 / 0.71 ( 9) SS BOND : angle 3.32232 / 1.94 ( 18) hydrogen bonds : bond 0.09632 / 6.07 ( 706) hydrogen bonds : angle 4.25527 / 2.92 ( 2016) Misc. bond : bond 0.00092 / 0.05 ( 5) link_BETA1-4 : bond 0.01825 / 0.97 ( 3) link_BETA1-4 : angle 4.27473 / 2.30 ( 9) link_NAG-ASN : bond 0.00425 / 0.26 ( 7) link_NAG-ASN : angle 4.01992 / 2.32 ( 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 240 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 237 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: B 113 TYR cc_start: 0.7825 (m-80) cc_final: 0.7611 (m-80) REVERT: C 79 MET cc_start: 0.3796 (tmm) cc_final: 0.3057 (tpp) REVERT: C 113 MET cc_start: 0.5602 (tpt) cc_final: 0.4177 (tmm) REVERT: D 270 MET cc_start: 0.7891 (tpp) cc_final: 0.7306 (ttt) REVERT: D 928 ASP cc_start: 0.8238 (p0) cc_final: 0.7624 (p0) REVERT: D 1193 TRP cc_start: 0.7646 (t-100) cc_final: 0.6715 (t-100) REVERT: D 1604 MET cc_start: 0.5298 (ttp) cc_final: 0.4883 (ttt) outliers start: 3 outliers final: 3 residues processed: 239 average time/residue: 0.0842 time to fit residues: 30.9967 Evaluate side-chains 215 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 212 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1384 CYS Chi-restraints excluded: chain D residue 1389 LYS Chi-restraints excluded: chain D residue 1390 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 GLN D 141 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN D1390 GLN D1470 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.215732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.188318 restraints weight = 30195.419| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.84 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12353 Z= 0.131 Angle : 0.644 10.342 16718 Z= 0.314 Chirality : 0.042 0.297 1931 Planarity : 0.004 0.088 1992 Dihedral : 13.229 173.018 1877 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.86 % Allowed : 9.19 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.05 (0.23), residues: 1414 helix: 1.27 (0.18), residues: 811 sheet: -1.75 (0.47), residues: 114 loop : -1.83 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1624 TYR 0.014 0.001 TYR D 384 PHE 0.024 0.001 PHE D1594 TRP 0.012 0.001 TRP D1419 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (12329) covalent geometry : angle 0.62471 / 0.31 (16670) SS BOND : bond 0.00286 / 0.16 ( 9) SS BOND : angle 1.44071 / 0.87 ( 18) hydrogen bonds : bond 0.03914 / 2.60 ( 706) hydrogen bonds : angle 4.10195 / 2.80 ( 2016) Misc. bond : bond 0.00056 / 0.03 ( 5) link_BETA1-4 : bond 0.01743 / 0.95 ( 3) link_BETA1-4 : angle 3.86258 / 2.09 ( 9) link_NAG-ASN : bond 0.00500 / 0.29 ( 7) link_NAG-ASN : angle 3.47888 / 2.03 ( 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 248 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 TYR cc_start: 0.8150 (m-80) cc_final: 0.7764 (m-80) REVERT: C 79 MET cc_start: 0.3436 (tmm) cc_final: 0.3104 (tpp) REVERT: C 113 MET cc_start: 0.4558 (tpt) cc_final: 0.3788 (tmm) REVERT: D 270 MET cc_start: 0.8227 (tpp) cc_final: 0.8022 (ttt) REVERT: D 1193 TRP cc_start: 0.7582 (t-100) cc_final: 0.6612 (t-100) REVERT: D 1604 MET cc_start: 0.5043 (ttp) cc_final: 0.4678 (ttt) REVERT: D 1731 ILE cc_start: 0.7839 (tt) cc_final: 0.7574 (tt) outliers start: 11 outliers final: 8 residues processed: 242 average time/residue: 0.0809 time to fit residues: 29.7947 Evaluate side-chains 228 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 1195 LEU Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1649 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 0.0040 chunk 32 optimal weight: 0.0070 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 GLN ** D1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1720 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.209548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.181262 restraints weight = 32082.946| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.96 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12353 Z= 0.189 Angle : 0.665 9.976 16718 Z= 0.324 Chirality : 0.044 0.315 1931 Planarity : 0.004 0.075 1992 Dihedral : 12.107 169.663 1869 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.73 % Allowed : 12.73 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.22 (0.23), residues: 1414 helix: 1.10 (0.18), residues: 816 sheet: -1.86 (0.46), residues: 115 loop : -1.87 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1633 TYR 0.019 0.002 TYR D 165 PHE 0.024 0.002 PHE D1594 TRP 0.009 0.001 TRP D1419 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (12329) covalent geometry : angle 0.64816 / 0.32 (16670) SS BOND : bond 0.00416 / 0.28 ( 9) SS BOND : angle 1.59008 / 0.99 ( 18) hydrogen bonds : bond 0.03814 / 2.53 ( 706) hydrogen bonds : angle 4.30772 / 2.96 ( 2016) Misc. bond : bond 0.00106 / 0.06 ( 5) link_BETA1-4 : bond 0.01766 / 0.95 ( 3) link_BETA1-4 : angle 3.99637 / 2.14 ( 9) link_NAG-ASN : bond 0.00420 / 0.26 ( 7) link_NAG-ASN : angle 3.00571 / 1.84 ( 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 248 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.3566 (tmm) cc_final: 0.3200 (tpp) REVERT: C 113 MET cc_start: 0.4464 (tpt) cc_final: 0.4000 (tmm) REVERT: D 135 MET cc_start: 0.7334 (tpp) cc_final: 0.6987 (mmm) REVERT: D 1193 TRP cc_start: 0.7501 (t-100) cc_final: 0.6659 (t-100) REVERT: D 1441 ASN cc_start: 0.8215 (m-40) cc_final: 0.7982 (m-40) outliers start: 22 outliers final: 16 residues processed: 235 average time/residue: 0.0821 time to fit residues: 29.4135 Evaluate side-chains 222 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 1288 VAL Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1384 CYS Chi-restraints excluded: chain D residue 1649 MET Chi-restraints excluded: chain D residue 1721 SER Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 83 optimal weight: 0.0050 chunk 112 optimal weight: 6.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.211274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.182957 restraints weight = 34221.540| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 3.98 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12353 Z= 0.121 Angle : 0.608 8.930 16718 Z= 0.298 Chirality : 0.041 0.296 1931 Planarity : 0.004 0.067 1992 Dihedral : 11.384 171.545 1869 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.49 % Allowed : 15.32 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.05 (0.23), residues: 1414 helix: 1.28 (0.18), residues: 813 sheet: -1.87 (0.46), residues: 117 loop : -1.86 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1392 TYR 0.013 0.001 TYR B 73 PHE 0.020 0.001 PHE D 167 TRP 0.010 0.001 TRP D1711 HIS 0.002 0.000 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (12329) covalent geometry : angle 0.59207 / 0.29 (16670) SS BOND : bond 0.00237 / 0.15 ( 9) SS BOND : angle 1.07681 / 0.66 ( 18) hydrogen bonds : bond 0.03575 / 2.37 ( 706) hydrogen bonds : angle 4.15990 / 2.85 ( 2016) Misc. bond : bond 0.00063 / 0.04 ( 5) link_BETA1-4 : bond 0.01626 / 0.88 ( 3) link_BETA1-4 : angle 3.76020 / 2.05 ( 9) link_NAG-ASN : bond 0.00610 / 0.33 ( 7) link_NAG-ASN : angle 2.94222 / 1.77 ( 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 251 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 MET cc_start: 0.3593 (tmm) cc_final: 0.3058 (tpp) REVERT: C 113 MET cc_start: 0.4413 (tpt) cc_final: 0.4089 (tmm) REVERT: D 270 MET cc_start: 0.8349 (tpp) cc_final: 0.7546 (ttt) REVERT: D 1193 TRP cc_start: 0.7544 (t-100) cc_final: 0.6651 (t-100) REVERT: D 1226 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6974 (tm-30) outliers start: 19 outliers final: 11 residues processed: 242 average time/residue: 0.0882 time to fit residues: 32.5050 Evaluate side-chains 225 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 1198 THR Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1384 CYS Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 106 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 0.0270 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN D 430 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.206078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.178098 restraints weight = 30314.215| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.83 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3972 r_free = 0.3972 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3972 r_free = 0.3972 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12353 Z= 0.163 Angle : 0.646 12.470 16718 Z= 0.311 Chirality : 0.042 0.308 1931 Planarity : 0.004 0.063 1992 Dihedral : 11.092 173.386 1869 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.44 % Allowed : 16.03 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.14 (0.23), residues: 1414 helix: 1.18 (0.18), residues: 816 sheet: -1.86 (0.46), residues: 117 loop : -1.86 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 152 TYR 0.015 0.001 TYR D 165 PHE 0.012 0.001 PHE D1751 TRP 0.008 0.001 TRP D1711 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (12329) covalent geometry : angle 0.63018 / 0.31 (16670) SS BOND : bond 0.00306 / 0.22 ( 9) SS BOND : angle 1.22285 / 0.75 ( 18) hydrogen bonds : bond 0.03609 / 2.40 ( 706) hydrogen bonds : angle 4.25248 / 2.92 ( 2016) Misc. bond : bond 0.00084 / 0.05 ( 5) link_BETA1-4 : bond 0.01618 / 0.88 ( 3) link_BETA1-4 : angle 3.95981 / 2.13 ( 9) link_NAG-ASN : bond 0.00698 / 0.37 ( 7) link_NAG-ASN : angle 3.05103 / 1.81 ( 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 251 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 LYS cc_start: 0.8012 (ttpp) cc_final: 0.7738 (ttpt) REVERT: B 72 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7494 (ttm-80) REVERT: C 79 MET cc_start: 0.3713 (tmm) cc_final: 0.3127 (tpp) REVERT: D 217 THR cc_start: 0.7363 (m) cc_final: 0.7158 (p) REVERT: D 968 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.6827 (tmm) REVERT: D 1193 TRP cc_start: 0.7529 (t-100) cc_final: 0.6699 (t-100) REVERT: D 1367 MET cc_start: 0.6446 (tpt) cc_final: 0.6149 (tpt) REVERT: D 1649 MET cc_start: 0.7859 (tmm) cc_final: 0.7598 (ttp) outliers start: 31 outliers final: 21 residues processed: 234 average time/residue: 0.0811 time to fit residues: 28.8063 Evaluate side-chains 229 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1198 THR Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1288 VAL Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1384 CYS Chi-restraints excluded: chain D residue 1496 MET Chi-restraints excluded: chain D residue 1721 SER Chi-restraints excluded: chain D residue 1731 ILE Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 55 optimal weight: 0.0570 chunk 69 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 136 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.208637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.181165 restraints weight = 25955.891| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.62 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12353 Z= 0.121 Angle : 0.623 16.266 16718 Z= 0.299 Chirality : 0.041 0.289 1931 Planarity : 0.004 0.062 1992 Dihedral : 10.755 177.034 1869 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.65 % Allowed : 18.38 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.05 (0.23), residues: 1414 helix: 1.28 (0.18), residues: 813 sheet: -1.78 (0.47), residues: 117 loop : -1.88 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1633 TYR 0.017 0.001 TYR D 165 PHE 0.016 0.001 PHE D1759 TRP 0.010 0.001 TRP D1711 HIS 0.007 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (12329) covalent geometry : angle 0.60775 / 0.30 (16670) SS BOND : bond 0.00224 / 0.15 ( 9) SS BOND : angle 1.03557 / 0.64 ( 18) hydrogen bonds : bond 0.03540 / 2.35 ( 706) hydrogen bonds : angle 4.14333 / 2.84 ( 2016) Misc. bond : bond 0.00051 / 0.03 ( 5) link_BETA1-4 : bond 0.01586 / 0.86 ( 3) link_BETA1-4 : angle 3.77636 / 2.06 ( 9) link_NAG-ASN : bond 0.00764 / 0.40 ( 7) link_NAG-ASN : angle 2.92231 / 1.73 ( 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 245 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7743 (ttpt) REVERT: C 79 MET cc_start: 0.3613 (tmm) cc_final: 0.3046 (tpp) REVERT: D 242 GLN cc_start: 0.7988 (pp30) cc_final: 0.7783 (pp30) REVERT: D 968 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.6780 (tmm) REVERT: D 1193 TRP cc_start: 0.7533 (t-100) cc_final: 0.6599 (t-100) REVERT: D 1226 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7079 (tm-30) REVERT: D 1367 MET cc_start: 0.6525 (tpt) cc_final: 0.6186 (tpt) REVERT: D 1666 MET cc_start: 0.8692 (ttm) cc_final: 0.7794 (mtm) outliers start: 21 outliers final: 17 residues processed: 232 average time/residue: 0.0771 time to fit residues: 27.2451 Evaluate side-chains 229 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1198 THR Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1384 CYS Chi-restraints excluded: chain D residue 1496 MET Chi-restraints excluded: chain D residue 1731 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 136 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.204238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164116 restraints weight = 21832.545| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.93 r_work: 0.3457 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12353 Z= 0.194 Angle : 0.670 14.990 16718 Z= 0.323 Chirality : 0.043 0.307 1931 Planarity : 0.004 0.059 1992 Dihedral : 10.862 179.597 1869 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.91 % Allowed : 18.38 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.21 (0.23), residues: 1414 helix: 1.09 (0.18), residues: 822 sheet: -1.76 (0.46), residues: 117 loop : -1.90 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 135 TYR 0.014 0.001 TYR D 427 PHE 0.022 0.002 PHE D 167 TRP 0.008 0.001 TRP D1711 HIS 0.022 0.002 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (12329) covalent geometry : angle 0.65387 / 0.32 (16670) SS BOND : bond 0.00347 / 0.26 ( 9) SS BOND : angle 1.24868 / 0.77 ( 18) hydrogen bonds : bond 0.03676 / 2.44 ( 706) hydrogen bonds : angle 4.27250 / 2.94 ( 2016) Misc. bond : bond 0.00105 / 0.06 ( 5) link_BETA1-4 : bond 0.01557 / 0.84 ( 3) link_BETA1-4 : angle 4.05381 / 2.19 ( 9) link_NAG-ASN : bond 0.00679 / 0.36 ( 7) link_NAG-ASN : angle 3.04504 / 1.79 ( 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 253 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7844 (ttpt) REVERT: B 103 ASP cc_start: 0.8476 (t0) cc_final: 0.8270 (t0) REVERT: C 79 MET cc_start: 0.4252 (tmm) cc_final: 0.3397 (tpp) REVERT: D 828 ASP cc_start: 0.8507 (t0) cc_final: 0.8270 (t0) REVERT: D 968 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.6997 (tmm) REVERT: D 1193 TRP cc_start: 0.7683 (t-100) cc_final: 0.6573 (t-100) REVERT: D 1226 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7195 (tm-30) REVERT: D 1309 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8701 (mm) REVERT: D 1367 MET cc_start: 0.7133 (tpt) cc_final: 0.6791 (tpt) outliers start: 37 outliers final: 29 residues processed: 237 average time/residue: 0.0844 time to fit residues: 30.0492 Evaluate side-chains 240 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 958 THR Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1198 THR Chi-restraints excluded: chain D residue 1212 ILE Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1384 CYS Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1459 THR Chi-restraints excluded: chain D residue 1467 ILE Chi-restraints excluded: chain D residue 1597 VAL Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1721 SER Chi-restraints excluded: chain D residue 1731 ILE Chi-restraints excluded: chain D residue 1732 HIS Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 37 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN D 430 GLN D1562 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.204916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167116 restraints weight = 22504.154| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.09 r_work: 0.3483 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12353 Z= 0.170 Angle : 0.656 14.492 16718 Z= 0.316 Chirality : 0.043 0.306 1931 Planarity : 0.004 0.062 1992 Dihedral : 10.608 172.217 1869 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.14 % Allowed : 18.62 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.25 (0.23), residues: 1414 helix: 1.05 (0.18), residues: 824 sheet: -1.74 (0.46), residues: 117 loop : -1.91 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1633 TYR 0.014 0.001 TYR D1445 PHE 0.013 0.001 PHE D1751 TRP 0.009 0.001 TRP D1711 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (12329) covalent geometry : angle 0.64030 / 0.31 (16670) SS BOND : bond 0.00290 / 0.21 ( 9) SS BOND : angle 1.16656 / 0.72 ( 18) hydrogen bonds : bond 0.03665 / 2.43 ( 706) hydrogen bonds : angle 4.26404 / 2.94 ( 2016) Misc. bond : bond 0.00089 / 0.05 ( 5) link_BETA1-4 : bond 0.01589 / 0.86 ( 3) link_BETA1-4 : angle 4.02701 / 2.18 ( 9) link_NAG-ASN : bond 0.00576 / 0.31 ( 7) link_NAG-ASN : angle 3.01942 / 1.79 ( 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 255 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7844 (ttpt) REVERT: B 152 ARG cc_start: 0.8081 (ptm160) cc_final: 0.7652 (ptm160) REVERT: C 79 MET cc_start: 0.4227 (tmm) cc_final: 0.3372 (tpp) REVERT: D 132 MET cc_start: 0.6267 (tpt) cc_final: 0.6062 (ttt) REVERT: D 968 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7008 (tmm) REVERT: D 1193 TRP cc_start: 0.7682 (t-100) cc_final: 0.6936 (t-100) REVERT: D 1197 LYS cc_start: 0.7653 (mttm) cc_final: 0.6889 (mtpp) REVERT: D 1309 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8733 (mm) REVERT: D 1367 MET cc_start: 0.7150 (tpt) cc_final: 0.6784 (tpt) REVERT: D 1749 PHE cc_start: 0.7899 (t80) cc_final: 0.7691 (t80) outliers start: 40 outliers final: 31 residues processed: 239 average time/residue: 0.0759 time to fit residues: 27.5542 Evaluate side-chains 237 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 958 THR Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1198 THR Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1384 CYS Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1459 THR Chi-restraints excluded: chain D residue 1467 ILE Chi-restraints excluded: chain D residue 1598 ILE Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1721 SER Chi-restraints excluded: chain D residue 1731 ILE Chi-restraints excluded: chain D residue 1732 HIS Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 38 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 136 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.205422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167420 restraints weight = 22539.854| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.09 r_work: 0.3380 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12353 Z= 0.159 Angle : 0.662 15.673 16718 Z= 0.318 Chirality : 0.043 0.301 1931 Planarity : 0.004 0.064 1992 Dihedral : 10.430 164.136 1869 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.06 % Allowed : 18.85 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.23 (0.23), residues: 1414 helix: 1.05 (0.18), residues: 824 sheet: -1.72 (0.47), residues: 117 loop : -1.89 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1633 TYR 0.017 0.001 TYR D 165 PHE 0.027 0.001 PHE D 167 TRP 0.009 0.001 TRP D1711 HIS 0.007 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (12329) covalent geometry : angle 0.64736 / 0.31 (16670) SS BOND : bond 0.00264 / 0.19 ( 9) SS BOND : angle 1.12378 / 0.69 ( 18) hydrogen bonds : bond 0.03665 / 2.43 ( 706) hydrogen bonds : angle 4.28074 / 2.95 ( 2016) Misc. bond : bond 0.00082 / 0.05 ( 5) link_BETA1-4 : bond 0.01577 / 0.85 ( 3) link_BETA1-4 : angle 3.99250 / 2.16 ( 9) link_NAG-ASN : bond 0.00676 / 0.36 ( 7) link_NAG-ASN : angle 2.96257 / 1.76 ( 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 245 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 ARG cc_start: 0.8075 (ptm160) cc_final: 0.7750 (ptm160) REVERT: C 79 MET cc_start: 0.4275 (tmm) cc_final: 0.3393 (tpp) REVERT: D 828 ASP cc_start: 0.8527 (t0) cc_final: 0.8280 (t0) REVERT: D 968 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7009 (tmm) REVERT: D 1193 TRP cc_start: 0.7684 (t-100) cc_final: 0.6661 (t-100) REVERT: D 1197 LYS cc_start: 0.7593 (mttm) cc_final: 0.6997 (mtpp) REVERT: D 1309 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8681 (mm) REVERT: D 1367 MET cc_start: 0.7160 (tpt) cc_final: 0.6793 (tpt) outliers start: 39 outliers final: 31 residues processed: 230 average time/residue: 0.0841 time to fit residues: 29.0152 Evaluate side-chains 236 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 958 THR Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1198 THR Chi-restraints excluded: chain D residue 1212 ILE Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1384 CYS Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1459 THR Chi-restraints excluded: chain D residue 1467 ILE Chi-restraints excluded: chain D residue 1597 VAL Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1721 SER Chi-restraints excluded: chain D residue 1731 ILE Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 139 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 136 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN D1539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.206574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.169830 restraints weight = 28660.955| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 6.82 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12353 Z= 0.146 Angle : 0.667 15.950 16718 Z= 0.319 Chirality : 0.043 0.296 1931 Planarity : 0.004 0.061 1992 Dihedral : 10.200 154.348 1869 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.91 % Allowed : 19.32 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.21 (0.23), residues: 1414 helix: 1.07 (0.18), residues: 824 sheet: -1.74 (0.47), residues: 117 loop : -1.86 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1633 TYR 0.013 0.001 TYR D1445 PHE 0.015 0.001 PHE D 256 TRP 0.009 0.001 TRP D1711 HIS 0.018 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (12329) covalent geometry : angle 0.65301 / 0.32 (16670) SS BOND : bond 0.00231 / 0.16 ( 9) SS BOND : angle 1.06469 / 0.65 ( 18) hydrogen bonds : bond 0.03663 / 2.43 ( 706) hydrogen bonds : angle 4.26925 / 2.94 ( 2016) Misc. bond : bond 0.00069 / 0.04 ( 5) link_BETA1-4 : bond 0.01592 / 0.86 ( 3) link_BETA1-4 : angle 3.93702 / 2.14 ( 9) link_NAG-ASN : bond 0.00750 / 0.40 ( 7) link_NAG-ASN : angle 2.87975 / 1.71 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 ARG cc_start: 0.8194 (ptm160) cc_final: 0.7808 (ptm160) REVERT: C 79 MET cc_start: 0.4330 (tmm) cc_final: 0.3390 (tpp) REVERT: D 828 ASP cc_start: 0.8283 (t0) cc_final: 0.8037 (t0) REVERT: D 968 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.6768 (tmm) REVERT: D 1193 TRP cc_start: 0.7830 (t-100) cc_final: 0.6764 (t-100) REVERT: D 1197 LYS cc_start: 0.7753 (mttm) cc_final: 0.7184 (mtpp) REVERT: D 1309 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8654 (mm) REVERT: D 1367 MET cc_start: 0.6545 (tpt) cc_final: 0.6077 (tpt) outliers start: 37 outliers final: 30 residues processed: 233 average time/residue: 0.0919 time to fit residues: 32.2633 Evaluate side-chains 237 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 885 LEU Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 958 THR Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1198 THR Chi-restraints excluded: chain D residue 1212 ILE Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1467 ILE Chi-restraints excluded: chain D residue 1597 VAL Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1731 ILE Chi-restraints excluded: chain D residue 1732 HIS Chi-restraints excluded: chain D residue 1745 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN D1441 ASN D1539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.206258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178133 restraints weight = 33260.965| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 3.93 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 12353 Z= 0.199 Angle : 0.931 59.113 16718 Z= 0.502 Chirality : 0.047 0.750 1931 Planarity : 0.004 0.061 1992 Dihedral : 10.200 154.244 1869 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.99 % Allowed : 19.17 % Favored : 77.85 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.21 (0.23), residues: 1414 helix: 1.06 (0.18), residues: 824 sheet: -1.75 (0.46), residues: 117 loop : -1.85 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1633 TYR 0.013 0.001 TYR D1445 PHE 0.012 0.001 PHE D 256 TRP 0.009 0.001 TRP D1711 HIS 0.010 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (12329) covalent geometry : angle 0.92093 / 0.50 (16670) SS BOND : bond 0.00245 / 0.18 ( 9) SS BOND : angle 1.48475 / 0.89 ( 18) hydrogen bonds : bond 0.03678 / 2.44 ( 706) hydrogen bonds : angle 4.28336 / 2.94 ( 2016) Misc. bond : bond 0.00073 / 0.04 ( 5) link_BETA1-4 : bond 0.01594 / 0.86 ( 3) link_BETA1-4 : angle 3.94616 / 2.14 ( 9) link_NAG-ASN : bond 0.00735 / 0.39 ( 7) link_NAG-ASN : angle 2.88499 / 1.71 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.95 seconds wall clock time: 38 minutes 23.74 seconds (2303.74 seconds total)