Starting phenix.real_space_refine on Fri Jul 3 06:26:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xmf_33295/07_2026/7xmf_33295.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmf_33295/07_2026/7xmf_33295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2026/7xmf_33295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2026/7xmf_33295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2026/7xmf_33295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2026/7xmf_33295.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2026/7xmf_33295.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2026/7xmf_33295.cif" } resolution = 3.07 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= 0.026 sd= 0.105 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 924 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 S 96 5.16 5 C 7690 2.51 5 N 1851 2.21 5 O 2071 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 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: 11709 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9185 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1108} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 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: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" 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: "E" 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: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'G2W': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 Time building chain proxies: 2.24, per 1000 atoms: 0.19 Number of scatterers: 11709 At special positions: 0 Unit cell: (130, 139.36, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 F 1 9.00 O 2071 8.00 N 1851 7.00 C 7690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.02 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 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=2.57 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2301 " - " ASN A1375 " " NAG A2302 " - " ASN A 283 " " NAG B 501 " - " ASN B 93 " " NAG B 502 " - " ASN B 110 " " NAG B 503 " - " ASN B 114 " " NAG B 504 " - " ASN B 135 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 646.6 milliseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 7 sheets defined 66.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.848A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.070A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 188 through 204 removed outlier: 4.026A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.706A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 268 removed outlier: 3.666A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.707A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 417 removed outlier: 5.174A pdb=" N PHE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 745 through 762 Processing helix chain 'A' and resid 769 through 799 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 806 through 821 Processing helix chain 'A' and resid 834 through 847 removed outlier: 3.579A pdb=" N PHE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.892A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.101A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.958A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 3.751A pdb=" N ASN A1180 " --> pdb=" O LYS A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 4.397A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1249 removed outlier: 4.040A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1290 Processing helix chain 'A' and resid 1291 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.613A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 3.953A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A1414 " --> pdb=" O ILE A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1467 removed outlier: 3.751A pdb=" N PHE A1446 " --> pdb=" O ILE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1487 Processing helix chain 'A' and resid 1488 through 1490 No H-bonds generated for 'chain 'A' and resid 1488 through 1490' Processing helix chain 'A' and resid 1502 through 1514 Processing helix chain 'A' and resid 1514 through 1534 Processing helix chain 'A' and resid 1540 through 1569 Processing helix chain 'A' and resid 1572 through 1575 removed outlier: 3.712A pdb=" N THR A1575 " --> pdb=" O TYR A1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1572 through 1575' Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1616 through 1622 removed outlier: 3.929A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1626 removed outlier: 3.525A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1623 through 1626' Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 3.550A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.109A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1705 Processing helix chain 'A' and resid 1732 through 1768 Processing helix chain 'B' and resid 153 through 191 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA2, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 80 removed outlier: 6.946A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 54 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.115A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.302A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 48 757 hydrogen bonds defined for protein. 2172 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: 1.96 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3549 1.35 - 1.51: 4364 1.51 - 1.68: 3915 1.68 - 1.84: 153 1.84 - 2.01: 1 Bond restraints: 11982 Sorted by residual: bond pdb=" C17 G2W A2303 " pdb=" N05 G2W A2303 " ideal model delta sigma weight residual 1.322 1.472 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C17 G2W A2303 " pdb=" N06 G2W A2303 " ideal model delta sigma weight residual 1.334 1.480 -0.146 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C24 G2W A2303 " pdb=" C26 G2W A2303 " ideal model delta sigma weight residual 1.391 1.534 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C21 G2W A2303 " pdb=" C22 G2W A2303 " ideal model delta sigma weight residual 1.379 1.520 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C25 G2W A2303 " pdb=" C27 G2W A2303 " ideal model delta sigma weight residual 1.383 1.523 -0.140 2.00e-02 2.50e+03 4.88e+01 ... (remaining 11977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.74: 16204 5.74 - 11.47: 26 11.47 - 17.21: 4 17.21 - 22.94: 0 22.94 - 28.68: 2 Bond angle restraints: 16236 Sorted by residual: angle pdb=" C ASP A 799 " pdb=" CA ASP A 799 " pdb=" CB ASP A 799 " ideal model delta sigma weight residual 110.17 136.07 -25.90 1.97e+00 2.58e-01 1.73e+02 angle pdb=" N ASP A 799 " pdb=" CA ASP A 799 " pdb=" C ASP A 799 " ideal model delta sigma weight residual 109.81 81.13 28.68 2.21e+00 2.05e-01 1.68e+02 angle pdb=" C MET C 85 " pdb=" CA MET C 85 " pdb=" CB MET C 85 " ideal model delta sigma weight residual 111.23 94.71 16.52 1.63e+00 3.76e-01 1.03e+02 angle pdb=" C ASN C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 119.66 114.07 5.59 7.20e-01 1.93e+00 6.03e+01 angle pdb=" CA CYS C 127 " pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 114.40 128.18 -13.78 2.30e+00 1.89e-01 3.59e+01 ... (remaining 16231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6125 17.78 - 35.56: 642 35.56 - 53.34: 162 53.34 - 71.12: 43 71.12 - 88.90: 17 Dihedral angle restraints: 6989 sinusoidal: 2789 harmonic: 4200 Sorted by residual: dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual -86.00 -162.02 76.02 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" C MET C 85 " pdb=" N MET C 85 " pdb=" CA MET C 85 " pdb=" CB MET C 85 " ideal model delta harmonic sigma weight residual -122.60 -106.78 -15.82 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" CB CYS A 275 " pdb=" SG CYS A 275 " pdb=" SG CYS A 315 " pdb=" CB CYS A 315 " ideal model delta sinusoidal sigma weight residual -86.00 -136.23 50.23 1 1.00e+01 1.00e-02 3.46e+01 ... (remaining 6986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1735 0.084 - 0.168: 143 0.168 - 0.253: 8 0.253 - 0.337: 5 0.337 - 0.421: 1 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA ASP A 799 " pdb=" N ASP A 799 " pdb=" C ASP A 799 " pdb=" CB ASP A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.51e+00 ... (remaining 1889 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 799 " 0.030 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C ASP A 799 " -0.105 2.00e-02 2.50e+03 pdb=" O ASP A 799 " 0.040 2.00e-02 2.50e+03 pdb=" N PRO A 800 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 104 " 0.061 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO C 105 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 105 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 105 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 132 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO C 133 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " 0.042 5.00e-02 4.00e+02 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 87 2.54 - 3.13: 9584 3.13 - 3.72: 18467 3.72 - 4.31: 25841 4.31 - 4.90: 42467 Nonbonded interactions: 96446 Sorted by model distance: nonbonded pdb=" N ASP A 799 " pdb=" O ASP A 799 " model vdw 1.953 2.496 nonbonded pdb=" O GLY A1444 " pdb=" OG1 THR A1448 " model vdw 2.045 3.040 nonbonded pdb=" O PHE A1738 " pdb=" OG SER A1742 " model vdw 2.069 3.040 nonbonded pdb=" CD2 TYR C 128 " pdb=" NH2 ARG C 137 " model vdw 2.087 3.420 nonbonded pdb=" O GLN C 62 " pdb=" CD PRO C 132 " model vdw 2.107 3.440 ... (remaining 96441 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.41 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.650 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.539 12001 Z= 0.452 Angle : 0.989 55.413 16284 Z= 0.532 Chirality : 0.051 0.421 1892 Planarity : 0.005 0.093 1981 Dihedral : 16.297 88.900 4248 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.56 % Favored : 94.09 % Rotamer: Outliers : 3.37 % Allowed : 19.03 % Favored : 77.60 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -2.41 (0.20), residues: 1421 helix: -1.18 (0.15), residues: 873 sheet: -1.36 (0.45), residues: 137 loop : -2.23 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1622 TYR 0.018 0.002 TYR C 125 PHE 0.018 0.002 PHE C 80 TRP 0.011 0.001 TRP C 67 HIS 0.004 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.38 (11982) covalent geometry : angle 0.86787 / 0.49 (16236) SS BOND : bond 0.17992 / 5.30 ( 9) SS BOND : angle 13.58783 / 4.74 ( 18) hydrogen bonds : bond 0.11013 / 6.57 ( 757) hydrogen bonds : angle 5.33737 / 3.78 ( 2172) link_BETA1-4 : bond 0.00440 / 0.31 ( 2) link_BETA1-4 : angle 3.64863 / 1.94 ( 6) link_NAG-ASN : bond 0.00500 / 0.33 ( 8) link_NAG-ASN : angle 3.54348 / 2.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6706 (tt) cc_final: 0.6244 (mt) REVERT: A 254 PHE cc_start: 0.8027 (t80) cc_final: 0.7803 (t80) REVERT: A 279 SER cc_start: 0.8583 (t) cc_final: 0.8302 (p) REVERT: A 405 TYR cc_start: 0.7166 (t80) cc_final: 0.6960 (t80) REVERT: A 794 LYS cc_start: 0.6091 (mmmt) cc_final: 0.4868 (tttm) REVERT: A 796 ILE cc_start: 0.7027 (pp) cc_final: 0.6760 (pt) REVERT: A 1251 LYS cc_start: 0.7693 (tttt) cc_final: 0.7412 (mptt) REVERT: A 1252 THR cc_start: 0.8608 (p) cc_final: 0.8245 (t) REVERT: A 1424 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7495 (tp-100) REVERT: A 1519 ILE cc_start: 0.8581 (pt) cc_final: 0.8337 (tp) REVERT: A 1541 GLN cc_start: 0.7787 (tp40) cc_final: 0.7493 (mm-40) REVERT: A 1579 ASN cc_start: 0.7970 (m-40) cc_final: 0.7735 (m-40) REVERT: A 1720 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7714 (t) REVERT: B 118 ASP cc_start: 0.7124 (m-30) cc_final: 0.6720 (m-30) outliers start: 43 outliers final: 23 residues processed: 264 average time/residue: 0.0897 time to fit residues: 34.7225 Evaluate side-chains 202 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 146 ASN A 265 GLN A 282 ASN A 365 ASN A 395 ASN A 409 ASN A 765 HIS A 941 GLN A1459 ASN A1463 GLN A1528 ASN A1709 ASN B 61 GLN B 102 GLN B 115 HIS C 118 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.179810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.137773 restraints weight = 14690.893| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.10 r_work: 0.3330 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12001 Z= 0.148 Angle : 0.725 29.231 16284 Z= 0.350 Chirality : 0.043 0.306 1892 Planarity : 0.005 0.064 1981 Dihedral : 8.133 69.626 1600 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.23 % Allowed : 19.66 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.84 (0.22), residues: 1421 helix: 0.17 (0.17), residues: 867 sheet: -1.27 (0.45), residues: 131 loop : -1.66 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 94 TYR 0.016 0.001 TYR A1739 PHE 0.014 0.001 PHE A1440 TRP 0.011 0.001 TRP A1382 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11982) covalent geometry : angle 0.64805 / 0.33 (16236) SS BOND : bond 0.00833 / 0.32 ( 9) SS BOND : angle 1.98837 / 1.05 ( 18) hydrogen bonds : bond 0.04293 / 2.70 ( 757) hydrogen bonds : angle 4.82843 / 3.44 ( 2172) link_BETA1-4 : bond 0.00854 / 0.61 ( 2) link_BETA1-4 : angle 2.41604 / 1.28 ( 6) link_NAG-ASN : bond 0.00620 / 0.40 ( 8) link_NAG-ASN : angle 8.27735 / 5.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6830 (tt) cc_final: 0.6381 (mt) REVERT: A 130 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6179 (tpp) REVERT: A 207 LEU cc_start: 0.4003 (OUTLIER) cc_final: 0.3755 (tp) REVERT: A 243 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7398 (tppt) REVERT: A 279 SER cc_start: 0.8792 (t) cc_final: 0.8561 (p) REVERT: A 742 MET cc_start: 0.6279 (ttm) cc_final: 0.5836 (ttm) REVERT: A 794 LYS cc_start: 0.6047 (mmmt) cc_final: 0.5175 (tttm) REVERT: A 837 PHE cc_start: 0.7585 (m-10) cc_final: 0.7228 (m-10) REVERT: A 1251 LYS cc_start: 0.7792 (tttt) cc_final: 0.7426 (mptt) REVERT: A 1252 THR cc_start: 0.8695 (p) cc_final: 0.8363 (t) REVERT: A 1374 MET cc_start: 0.7402 (ttm) cc_final: 0.7045 (mtm) REVERT: A 1424 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7559 (tp-100) REVERT: A 1760 LEU cc_start: 0.8066 (mm) cc_final: 0.7850 (tp) REVERT: A 1768 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5348 (mp0) REVERT: B 154 MET cc_start: 0.6847 (tmm) cc_final: 0.6638 (tmm) REVERT: C 79 MET cc_start: 0.1016 (ppp) cc_final: -0.0915 (mmm) outliers start: 54 outliers final: 29 residues processed: 231 average time/residue: 0.0823 time to fit residues: 28.7951 Evaluate side-chains 194 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 27 optimal weight: 2.9990 chunk 139 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 765 HIS A 956 ASN A1463 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123793 restraints weight = 14846.741| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.19 r_work: 0.3394 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12001 Z= 0.169 Angle : 0.648 11.047 16284 Z= 0.328 Chirality : 0.044 0.303 1892 Planarity : 0.004 0.046 1981 Dihedral : 7.395 62.186 1579 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.62 % Allowed : 20.05 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.31 (0.22), residues: 1421 helix: 0.62 (0.17), residues: 868 sheet: -1.04 (0.45), residues: 130 loop : -1.51 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.021 0.001 TYR A1548 PHE 0.019 0.001 PHE A 963 TRP 0.010 0.001 TRP A1382 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (11982) covalent geometry : angle 0.63457 / 0.32 (16236) SS BOND : bond 0.00580 / 0.29 ( 9) SS BOND : angle 1.84438 / 0.96 ( 18) hydrogen bonds : bond 0.04163 / 2.63 ( 757) hydrogen bonds : angle 4.78536 / 3.41 ( 2172) link_BETA1-4 : bond 0.00858 / 0.61 ( 2) link_BETA1-4 : angle 2.23629 / 1.17 ( 6) link_NAG-ASN : bond 0.00435 / 0.29 ( 8) link_NAG-ASN : angle 2.88747 / 1.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7300 (tppt) REVERT: A 742 MET cc_start: 0.6260 (ttm) cc_final: 0.5903 (ttm) REVERT: A 837 PHE cc_start: 0.7696 (m-10) cc_final: 0.7236 (m-10) REVERT: A 895 CYS cc_start: 0.5536 (p) cc_final: 0.4990 (t) REVERT: A 1251 LYS cc_start: 0.7794 (tttt) cc_final: 0.7375 (mptt) REVERT: A 1374 MET cc_start: 0.7526 (ttm) cc_final: 0.7301 (mtp) REVERT: A 1424 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7404 (tp-100) REVERT: A 1477 GLU cc_start: 0.7634 (tp30) cc_final: 0.7363 (tp30) REVERT: A 1556 ILE cc_start: 0.8088 (tp) cc_final: 0.7821 (tp) REVERT: A 1760 LEU cc_start: 0.8102 (mm) cc_final: 0.7832 (tp) REVERT: A 1768 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.4562 (tm-30) REVERT: B 68 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7826 (p) REVERT: C 79 MET cc_start: 0.0689 (ppp) cc_final: -0.0993 (mmm) outliers start: 59 outliers final: 35 residues processed: 218 average time/residue: 0.0895 time to fit residues: 29.8646 Evaluate side-chains 199 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 765 HIS A 911 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.181005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125427 restraints weight = 14792.244| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.22 r_work: 0.3414 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12001 Z= 0.139 Angle : 0.614 12.163 16284 Z= 0.310 Chirality : 0.042 0.279 1892 Planarity : 0.004 0.042 1981 Dihedral : 7.176 62.497 1578 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.07 % Allowed : 20.36 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.07 (0.22), residues: 1421 helix: 0.94 (0.17), residues: 864 sheet: -0.98 (0.45), residues: 131 loop : -1.36 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.021 0.001 TYR A1548 PHE 0.014 0.001 PHE A1440 TRP 0.010 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (11982) covalent geometry : angle 0.60660 / 0.31 (16236) SS BOND : bond 0.00462 / 0.23 ( 9) SS BOND : angle 1.57254 / 0.82 ( 18) hydrogen bonds : bond 0.03929 / 2.48 ( 757) hydrogen bonds : angle 4.70438 / 3.34 ( 2172) link_BETA1-4 : bond 0.00782 / 0.56 ( 2) link_BETA1-4 : angle 2.10341 / 1.10 ( 6) link_NAG-ASN : bond 0.00261 / 0.16 ( 8) link_NAG-ASN : angle 2.05737 / 1.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7264 (tppt) REVERT: A 364 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: A 742 MET cc_start: 0.6321 (ttm) cc_final: 0.5908 (ttm) REVERT: A 794 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.5875 (mmmt) REVERT: A 796 ILE cc_start: 0.7280 (pp) cc_final: 0.7050 (pt) REVERT: A 837 PHE cc_start: 0.7652 (m-10) cc_final: 0.7320 (m-10) REVERT: A 861 ASN cc_start: 0.6498 (m-40) cc_final: 0.6015 (m-40) REVERT: A 1251 LYS cc_start: 0.7729 (tttt) cc_final: 0.7317 (mptt) REVERT: A 1276 ASN cc_start: 0.7972 (t0) cc_final: 0.7602 (m-40) REVERT: A 1556 ILE cc_start: 0.8033 (tp) cc_final: 0.7777 (tp) REVERT: A 1668 TYR cc_start: 0.8028 (m-80) cc_final: 0.7823 (m-80) REVERT: A 1760 LEU cc_start: 0.8250 (mm) cc_final: 0.8018 (tt) REVERT: A 1768 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.4427 (tm-30) REVERT: C 79 MET cc_start: 0.0649 (ppp) cc_final: -0.1192 (mmm) outliers start: 52 outliers final: 36 residues processed: 212 average time/residue: 0.0915 time to fit residues: 29.4761 Evaluate side-chains 197 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 132 optimal weight: 50.0000 chunk 35 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 765 HIS A 956 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.180837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139193 restraints weight = 14804.326| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.13 r_work: 0.3327 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12001 Z= 0.143 Angle : 0.615 10.004 16284 Z= 0.308 Chirality : 0.042 0.275 1892 Planarity : 0.004 0.042 1981 Dihedral : 6.721 59.826 1573 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.39 % Allowed : 20.75 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 1421 helix: 1.07 (0.17), residues: 861 sheet: -0.94 (0.46), residues: 131 loop : -1.28 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.024 0.001 TYR A1739 PHE 0.021 0.001 PHE A 183 TRP 0.009 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (11982) covalent geometry : angle 0.60839 / 0.31 (16236) SS BOND : bond 0.00521 / 0.28 ( 9) SS BOND : angle 1.51384 / 0.75 ( 18) hydrogen bonds : bond 0.03915 / 2.48 ( 757) hydrogen bonds : angle 4.64996 / 3.30 ( 2172) link_BETA1-4 : bond 0.00932 / 0.66 ( 2) link_BETA1-4 : angle 2.01142 / 1.05 ( 6) link_NAG-ASN : bond 0.00246 / 0.15 ( 8) link_NAG-ASN : angle 1.80215 / 1.27 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7302 (tppt) REVERT: A 364 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: A 742 MET cc_start: 0.6103 (ttm) cc_final: 0.5856 (tpp) REVERT: A 794 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.5995 (mmmt) REVERT: A 796 ILE cc_start: 0.7209 (pp) cc_final: 0.6963 (pt) REVERT: A 837 PHE cc_start: 0.7661 (m-10) cc_final: 0.7228 (m-10) REVERT: A 861 ASN cc_start: 0.6629 (m-40) cc_final: 0.6163 (m-40) REVERT: A 1251 LYS cc_start: 0.7700 (tttt) cc_final: 0.7331 (mptt) REVERT: A 1276 ASN cc_start: 0.7979 (t0) cc_final: 0.7616 (m-40) REVERT: A 1470 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: A 1556 ILE cc_start: 0.8049 (tp) cc_final: 0.7803 (tp) REVERT: A 1668 TYR cc_start: 0.7937 (m-80) cc_final: 0.7713 (m-80) REVERT: A 1768 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.4098 (tm-30) REVERT: C 79 MET cc_start: 0.0748 (ppp) cc_final: -0.1114 (mmm) outliers start: 56 outliers final: 41 residues processed: 213 average time/residue: 0.0907 time to fit residues: 29.2529 Evaluate side-chains 206 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 765 HIS B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.181558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125769 restraints weight = 14852.396| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.96 r_work: 0.3440 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12001 Z= 0.133 Angle : 0.606 9.697 16284 Z= 0.303 Chirality : 0.041 0.268 1892 Planarity : 0.004 0.041 1981 Dihedral : 6.592 59.226 1572 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.39 % Allowed : 20.44 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.33 (0.23), residues: 1421 helix: 1.14 (0.17), residues: 868 sheet: -0.93 (0.44), residues: 137 loop : -1.26 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 152 TYR 0.023 0.001 TYR A1739 PHE 0.015 0.001 PHE A 963 TRP 0.010 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11982) covalent geometry : angle 0.60050 / 0.30 (16236) SS BOND : bond 0.00438 / 0.22 ( 9) SS BOND : angle 1.41718 / 0.68 ( 18) hydrogen bonds : bond 0.03821 / 2.43 ( 757) hydrogen bonds : angle 4.61360 / 3.27 ( 2172) link_BETA1-4 : bond 0.00873 / 0.62 ( 2) link_BETA1-4 : angle 1.99856 / 1.04 ( 6) link_NAG-ASN : bond 0.00255 / 0.16 ( 8) link_NAG-ASN : angle 1.60280 / 1.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7278 (tppt) REVERT: A 364 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: A 379 MET cc_start: 0.7459 (tmm) cc_final: 0.7207 (tmm) REVERT: A 383 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8590 (t) REVERT: A 742 MET cc_start: 0.6240 (ttm) cc_final: 0.5986 (tpp) REVERT: A 794 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6177 (mmtp) REVERT: A 796 ILE cc_start: 0.7314 (pp) cc_final: 0.7011 (pt) REVERT: A 861 ASN cc_start: 0.6679 (m-40) cc_final: 0.6221 (m-40) REVERT: A 1230 ASP cc_start: 0.8071 (t0) cc_final: 0.7587 (m-30) REVERT: A 1251 LYS cc_start: 0.7606 (tttt) cc_final: 0.7276 (mptt) REVERT: A 1276 ASN cc_start: 0.7953 (t0) cc_final: 0.7581 (m-40) REVERT: A 1431 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8283 (tp) REVERT: A 1470 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: A 1556 ILE cc_start: 0.8010 (tp) cc_final: 0.7749 (tp) REVERT: A 1668 TYR cc_start: 0.7853 (m-80) cc_final: 0.7631 (m-80) REVERT: A 1768 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.3981 (tm-30) REVERT: B 159 SER cc_start: 0.8738 (t) cc_final: 0.8461 (p) REVERT: C 79 MET cc_start: 0.0663 (ppp) cc_final: -0.1199 (mmm) outliers start: 56 outliers final: 39 residues processed: 219 average time/residue: 0.0918 time to fit residues: 30.4571 Evaluate side-chains 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 66 optimal weight: 0.5980 chunk 138 optimal weight: 40.0000 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.181031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140116 restraints weight = 14752.229| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.18 r_work: 0.3336 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12001 Z= 0.125 Angle : 0.595 12.385 16284 Z= 0.296 Chirality : 0.041 0.266 1892 Planarity : 0.003 0.039 1981 Dihedral : 6.437 58.683 1570 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.23 % Allowed : 20.60 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.46 (0.23), residues: 1421 helix: 1.24 (0.17), residues: 868 sheet: -0.86 (0.44), residues: 137 loop : -1.20 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.023 0.001 TYR A1548 PHE 0.024 0.001 PHE A 183 TRP 0.009 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11982) covalent geometry : angle 0.58986 / 0.29 (16236) SS BOND : bond 0.00402 / 0.20 ( 9) SS BOND : angle 1.31809 / 0.61 ( 18) hydrogen bonds : bond 0.03765 / 2.39 ( 757) hydrogen bonds : angle 4.53691 / 3.22 ( 2172) link_BETA1-4 : bond 0.00908 / 0.65 ( 2) link_BETA1-4 : angle 1.94006 / 1.01 ( 6) link_NAG-ASN : bond 0.00250 / 0.15 ( 8) link_NAG-ASN : angle 1.48582 / 1.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8532 (p0) REVERT: A 243 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7226 (tppt) REVERT: A 364 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 379 MET cc_start: 0.7563 (tmm) cc_final: 0.7332 (tmm) REVERT: A 742 MET cc_start: 0.6052 (ttm) cc_final: 0.5841 (tpp) REVERT: A 794 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6114 (tptm) REVERT: A 796 ILE cc_start: 0.7120 (pp) cc_final: 0.6806 (pt) REVERT: A 841 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.7242 (mmm-85) REVERT: A 861 ASN cc_start: 0.6629 (m-40) cc_final: 0.6163 (m-40) REVERT: A 1230 ASP cc_start: 0.8010 (t0) cc_final: 0.7525 (m-30) REVERT: A 1251 LYS cc_start: 0.7446 (tttt) cc_final: 0.7171 (mptt) REVERT: A 1276 ASN cc_start: 0.7842 (t0) cc_final: 0.7575 (m-40) REVERT: A 1470 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: A 1556 ILE cc_start: 0.7977 (tp) cc_final: 0.7704 (tp) REVERT: A 1768 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.3415 (tm-30) REVERT: B 159 SER cc_start: 0.8728 (t) cc_final: 0.8474 (p) REVERT: C 79 MET cc_start: 0.0617 (ppp) cc_final: -0.1245 (mmm) outliers start: 54 outliers final: 38 residues processed: 222 average time/residue: 0.0785 time to fit residues: 26.0041 Evaluate side-chains 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 21 optimal weight: 0.9980 chunk 120 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 765 HIS A 766 HIS ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.181444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126068 restraints weight = 14797.775| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.92 r_work: 0.3461 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12001 Z= 0.123 Angle : 0.598 10.990 16284 Z= 0.299 Chirality : 0.041 0.265 1892 Planarity : 0.003 0.039 1981 Dihedral : 6.297 58.112 1567 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 3.37 % Allowed : 21.22 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.54 (0.23), residues: 1421 helix: 1.35 (0.17), residues: 858 sheet: -0.78 (0.44), residues: 137 loop : -1.22 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.024 0.001 TYR A1548 PHE 0.014 0.001 PHE A 963 TRP 0.010 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11982) covalent geometry : angle 0.59419 / 0.30 (16236) SS BOND : bond 0.00382 / 0.19 ( 9) SS BOND : angle 1.25733 / 0.58 ( 18) hydrogen bonds : bond 0.03725 / 2.37 ( 757) hydrogen bonds : angle 4.52330 / 3.20 ( 2172) link_BETA1-4 : bond 0.00795 / 0.57 ( 2) link_BETA1-4 : angle 1.97016 / 1.03 ( 6) link_NAG-ASN : bond 0.00245 / 0.14 ( 8) link_NAG-ASN : angle 1.40428 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8501 (p0) REVERT: A 243 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7254 (tppt) REVERT: A 364 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: A 742 MET cc_start: 0.6146 (ttm) cc_final: 0.5933 (tpp) REVERT: A 794 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6223 (mmtp) REVERT: A 796 ILE cc_start: 0.7479 (pp) cc_final: 0.7212 (pt) REVERT: A 841 ARG cc_start: 0.7501 (mmm-85) cc_final: 0.7208 (mmm-85) REVERT: A 861 ASN cc_start: 0.6682 (m-40) cc_final: 0.6233 (m-40) REVERT: A 1230 ASP cc_start: 0.7978 (t0) cc_final: 0.7464 (m-30) REVERT: A 1251 LYS cc_start: 0.7508 (tttt) cc_final: 0.7218 (mptt) REVERT: A 1276 ASN cc_start: 0.7818 (t0) cc_final: 0.7521 (m-40) REVERT: A 1436 TYR cc_start: 0.8351 (t80) cc_final: 0.7933 (t80) REVERT: A 1470 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: A 1556 ILE cc_start: 0.8113 (tp) cc_final: 0.7822 (tp) REVERT: A 1768 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.3707 (tm-30) REVERT: B 159 SER cc_start: 0.8750 (t) cc_final: 0.8526 (p) REVERT: C 79 MET cc_start: 0.0612 (ppp) cc_final: -0.1326 (mmm) outliers start: 43 outliers final: 32 residues processed: 211 average time/residue: 0.0976 time to fit residues: 30.4727 Evaluate side-chains 205 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN A 780 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.181403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138475 restraints weight = 14696.912| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.37 r_work: 0.3356 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12001 Z= 0.130 Angle : 0.603 10.651 16284 Z= 0.300 Chirality : 0.041 0.265 1892 Planarity : 0.004 0.039 1981 Dihedral : 6.268 58.019 1567 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.43 % Rotamer: Outliers : 3.68 % Allowed : 20.91 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.56 (0.23), residues: 1421 helix: 1.36 (0.17), residues: 857 sheet: -0.83 (0.44), residues: 138 loop : -1.18 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.024 0.001 TYR A1548 PHE 0.029 0.001 PHE A 183 TRP 0.009 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11982) covalent geometry : angle 0.59886 / 0.30 (16236) SS BOND : bond 0.00400 / 0.20 ( 9) SS BOND : angle 1.30105 / 0.60 ( 18) hydrogen bonds : bond 0.03735 / 2.38 ( 757) hydrogen bonds : angle 4.50759 / 3.19 ( 2172) link_BETA1-4 : bond 0.00922 / 0.66 ( 2) link_BETA1-4 : angle 1.93900 / 1.01 ( 6) link_NAG-ASN : bond 0.00235 / 0.14 ( 8) link_NAG-ASN : angle 1.40203 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8479 (p0) REVERT: A 243 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7229 (tppt) REVERT: A 364 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: A 794 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6225 (tptm) REVERT: A 796 ILE cc_start: 0.7206 (pp) cc_final: 0.6924 (pt) REVERT: A 837 PHE cc_start: 0.7473 (m-10) cc_final: 0.7172 (m-10) REVERT: A 841 ARG cc_start: 0.7472 (mmm-85) cc_final: 0.7207 (mmm-85) REVERT: A 861 ASN cc_start: 0.6623 (m-40) cc_final: 0.6170 (m-40) REVERT: A 1230 ASP cc_start: 0.7951 (t0) cc_final: 0.7418 (m-30) REVERT: A 1251 LYS cc_start: 0.7418 (tttt) cc_final: 0.7148 (mptt) REVERT: A 1276 ASN cc_start: 0.7817 (t0) cc_final: 0.7547 (m-40) REVERT: A 1431 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8150 (tp) REVERT: A 1470 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: A 1556 ILE cc_start: 0.8022 (tp) cc_final: 0.7752 (tp) REVERT: A 1768 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.3647 (tm-30) REVERT: B 159 SER cc_start: 0.8741 (t) cc_final: 0.8497 (p) REVERT: C 79 MET cc_start: 0.0608 (ppp) cc_final: -0.1156 (mmm) outliers start: 47 outliers final: 38 residues processed: 214 average time/residue: 0.0937 time to fit residues: 29.7049 Evaluate side-chains 209 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 130 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN A1762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.181541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139575 restraints weight = 14792.237| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.25 r_work: 0.3347 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12001 Z= 0.130 Angle : 0.618 10.485 16284 Z= 0.307 Chirality : 0.041 0.264 1892 Planarity : 0.004 0.039 1981 Dihedral : 6.269 57.825 1567 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 3.13 % Allowed : 21.61 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.54 (0.23), residues: 1421 helix: 1.34 (0.17), residues: 858 sheet: -0.80 (0.44), residues: 138 loop : -1.22 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.025 0.001 TYR A1573 PHE 0.014 0.001 PHE A 963 TRP 0.011 0.001 TRP A1578 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11982) covalent geometry : angle 0.61396 / 0.31 (16236) SS BOND : bond 0.00392 / 0.20 ( 9) SS BOND : angle 1.27230 / 0.59 ( 18) hydrogen bonds : bond 0.03707 / 2.36 ( 757) hydrogen bonds : angle 4.51549 / 3.19 ( 2172) link_BETA1-4 : bond 0.00934 / 0.66 ( 2) link_BETA1-4 : angle 1.93819 / 1.02 ( 6) link_NAG-ASN : bond 0.00246 / 0.15 ( 8) link_NAG-ASN : angle 1.38602 / 0.98 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6183 (mp) REVERT: A 243 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7238 (tppt) REVERT: A 307 GLU cc_start: 0.7186 (tp30) cc_final: 0.6958 (mp0) REVERT: A 364 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: A 794 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6328 (mmtp) REVERT: A 796 ILE cc_start: 0.7473 (pp) cc_final: 0.7262 (pt) REVERT: A 837 PHE cc_start: 0.7497 (m-10) cc_final: 0.7244 (m-10) REVERT: A 841 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.7237 (mmm-85) REVERT: A 861 ASN cc_start: 0.6628 (m-40) cc_final: 0.6173 (m-40) REVERT: A 1230 ASP cc_start: 0.7980 (t0) cc_final: 0.7443 (m-30) REVERT: A 1251 LYS cc_start: 0.7379 (tttt) cc_final: 0.7159 (mptt) REVERT: A 1276 ASN cc_start: 0.7820 (t0) cc_final: 0.7516 (m-40) REVERT: A 1436 TYR cc_start: 0.8352 (t80) cc_final: 0.7925 (t80) REVERT: A 1470 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: A 1556 ILE cc_start: 0.7970 (tp) cc_final: 0.7703 (tp) REVERT: A 1768 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.3843 (tm-30) REVERT: B 159 SER cc_start: 0.8739 (t) cc_final: 0.8489 (p) REVERT: C 79 MET cc_start: 0.0606 (ppp) cc_final: -0.1492 (mmm) outliers start: 40 outliers final: 31 residues processed: 202 average time/residue: 0.0983 time to fit residues: 29.6274 Evaluate side-chains 200 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 111 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 131 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN A1579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.182362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139796 restraints weight = 14701.701| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.59 r_work: 0.3373 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12001 Z= 0.121 Angle : 0.620 10.780 16284 Z= 0.305 Chirality : 0.041 0.263 1892 Planarity : 0.003 0.039 1981 Dihedral : 6.241 57.352 1567 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 2.58 % Allowed : 22.63 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.60 (0.23), residues: 1421 helix: 1.42 (0.17), residues: 852 sheet: -0.76 (0.44), residues: 138 loop : -1.23 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.024 0.001 TYR A1548 PHE 0.013 0.001 PHE A 963 TRP 0.010 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11982) covalent geometry : angle 0.61595 / 0.30 (16236) SS BOND : bond 0.00359 / 0.18 ( 9) SS BOND : angle 1.20726 / 0.55 ( 18) hydrogen bonds : bond 0.03634 / 2.32 ( 757) hydrogen bonds : angle 4.50288 / 3.19 ( 2172) link_BETA1-4 : bond 0.00806 / 0.58 ( 2) link_BETA1-4 : angle 1.91542 / 1.00 ( 6) link_NAG-ASN : bond 0.00241 / 0.14 ( 8) link_NAG-ASN : angle 1.31701 / 0.92 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.14 seconds wall clock time: 55 minutes 24.95 seconds (3324.95 seconds total)