Starting phenix.real_space_refine on Wed Mar 4 09:38:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmf_33295/03_2026/7xmf_33295.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmf_33295/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xmf_33295/03_2026/7xmf_33295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmf_33295/03_2026/7xmf_33295.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmf_33295/03_2026/7xmf_33295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmf_33295/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.37, per 1000 atoms: 0.20 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: 1.05 Conformation dependent library (CDL) restraints added in 558.4 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: 0.39 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: 2.02 Time building geometry restraints manager: 1.40 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 - 23.88: 6600 23.88 - 47.76: 500 47.76 - 71.64: 79 71.64 - 95.52: 17 95.52 - 119.40: 3 Dihedral angle restraints: 7199 sinusoidal: 2999 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 7196 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.810 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 16.545 119.403 4458 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 covalent geometry : bond 0.00787 (11982) covalent geometry : angle 0.86787 (16236) SS BOND : bond 0.17992 ( 9) SS BOND : angle 13.58783 ( 18) hydrogen bonds : bond 0.11013 ( 757) hydrogen bonds : angle 5.33737 ( 2172) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 3.64863 ( 6) link_NAG-ASN : bond 0.00500 ( 8) link_NAG-ASN : angle 3.54348 ( 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 : 0.447 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: 0.0985 time to fit residues: 38.0082 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 : 0.424 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.179802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137072 restraints weight = 14682.520| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.19 r_work: 0.3329 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 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 = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12001 Z= 0.148 Angle : 0.734 29.441 16284 Z= 0.354 Chirality : 0.043 0.309 1892 Planarity : 0.005 0.064 1981 Dihedral : 10.027 110.549 1810 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.92 % Allowed : 20.05 % Favored : 76.04 % 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: -0.89 (0.22), residues: 1421 helix: 0.13 (0.17), residues: 866 sheet: -1.26 (0.45), residues: 131 loop : -1.68 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 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 766 Details of bonding type rmsd covalent geometry : bond 0.00322 (11982) covalent geometry : angle 0.65304 (16236) SS BOND : bond 0.00837 ( 9) SS BOND : angle 2.08450 ( 18) hydrogen bonds : bond 0.04359 ( 757) hydrogen bonds : angle 4.84040 ( 2172) link_BETA1-4 : bond 0.00572 ( 2) link_BETA1-4 : angle 3.32133 ( 6) link_NAG-ASN : bond 0.00641 ( 8) link_NAG-ASN : angle 8.44715 ( 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 233 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6789 (tt) cc_final: 0.6341 (mt) REVERT: A 130 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6081 (tpp) REVERT: A 207 LEU cc_start: 0.3929 (OUTLIER) cc_final: 0.3673 (tp) REVERT: A 243 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7396 (tppt) REVERT: A 279 SER cc_start: 0.8820 (t) cc_final: 0.8599 (p) REVERT: A 742 MET cc_start: 0.6235 (ttm) cc_final: 0.5819 (ttm) REVERT: A 794 LYS cc_start: 0.6210 (mmmt) cc_final: 0.5222 (tttm) REVERT: A 837 PHE cc_start: 0.7656 (m-10) cc_final: 0.7181 (m-10) REVERT: A 1251 LYS cc_start: 0.7804 (tttt) cc_final: 0.7423 (mptt) REVERT: A 1252 THR cc_start: 0.8693 (p) cc_final: 0.8344 (t) REVERT: A 1374 MET cc_start: 0.7413 (ttm) cc_final: 0.7049 (mtm) REVERT: A 1424 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7561 (tp-100) REVERT: A 1760 LEU cc_start: 0.8069 (mm) cc_final: 0.7832 (tp) REVERT: A 1768 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5409 (mp0) REVERT: C 79 MET cc_start: 0.0988 (ppp) cc_final: -0.0982 (mmm) outliers start: 50 outliers final: 26 residues processed: 226 average time/residue: 0.0906 time to fit residues: 30.7228 Evaluate side-chains 192 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 1270 LEU 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: 0.7980 chunk 139 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.0000 chunk 14 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4239 r_free = 0.4239 target = 0.181351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128215 restraints weight = 14861.516| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.27 r_work: 0.3397 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1936 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= 0.142 Angle : 0.634 10.221 16284 Z= 0.320 Chirality : 0.043 0.273 1892 Planarity : 0.004 0.041 1981 Dihedral : 10.324 119.620 1789 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.54 % Allowed : 19.89 % 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: -0.26 (0.22), residues: 1421 helix: 0.67 (0.17), residues: 869 sheet: -1.08 (0.45), residues: 131 loop : -1.51 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 94 TYR 0.021 0.001 TYR A1548 PHE 0.018 0.001 PHE A 963 TRP 0.011 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00307 (11982) covalent geometry : angle 0.61717 (16236) SS BOND : bond 0.00497 ( 9) SS BOND : angle 1.66581 ( 18) hydrogen bonds : bond 0.04010 ( 757) hydrogen bonds : angle 4.71227 ( 2172) link_BETA1-4 : bond 0.00550 ( 2) link_BETA1-4 : angle 3.35875 ( 6) link_NAG-ASN : bond 0.00383 ( 8) link_NAG-ASN : angle 3.15789 ( 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 236 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7182 (tppt) REVERT: A 364 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: A 742 MET cc_start: 0.6230 (ttm) cc_final: 0.5880 (ttm) REVERT: A 794 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5381 (mmmt) REVERT: A 796 ILE cc_start: 0.7202 (pp) cc_final: 0.6948 (pt) REVERT: A 861 ASN cc_start: 0.6511 (m-40) cc_final: 0.5800 (m-40) REVERT: A 895 CYS cc_start: 0.5905 (p) cc_final: 0.5325 (t) REVERT: A 1251 LYS cc_start: 0.7719 (tttt) cc_final: 0.7326 (mptt) REVERT: A 1374 MET cc_start: 0.7528 (ttm) cc_final: 0.7266 (mtp) REVERT: A 1477 GLU cc_start: 0.7605 (tp30) cc_final: 0.7314 (tp30) REVERT: A 1556 ILE cc_start: 0.8042 (tp) cc_final: 0.7775 (tp) REVERT: A 1573 TYR cc_start: 0.7785 (t80) cc_final: 0.7552 (t80) REVERT: A 1760 LEU cc_start: 0.8081 (mm) cc_final: 0.7797 (tp) REVERT: B 68 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7777 (p) REVERT: C 79 MET cc_start: 0.0877 (ppp) cc_final: -0.0769 (mmm) outliers start: 58 outliers final: 30 residues processed: 226 average time/residue: 0.0920 time to fit residues: 31.3750 Evaluate side-chains 197 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 226 SER 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 844 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 959 VAL Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1270 LEU 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 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 B residue 43 CYS Chi-restraints excluded: chain B residue 68 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 9.9990 chunk 119 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 115 optimal weight: 0.0170 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.0170 chunk 62 optimal weight: 7.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS A 766 HIS A 911 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.182738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140531 restraints weight = 14779.023| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.37 r_work: 0.3397 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12001 Z= 0.116 Angle : 0.604 11.779 16284 Z= 0.301 Chirality : 0.041 0.247 1892 Planarity : 0.004 0.040 1981 Dihedral : 9.932 118.993 1785 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.60 % Allowed : 20.75 % Favored : 75.65 % 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: 0.10 (0.22), residues: 1421 helix: 0.95 (0.17), residues: 872 sheet: -0.94 (0.45), residues: 131 loop : -1.37 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1358 TYR 0.024 0.001 TYR A1739 PHE 0.014 0.001 PHE A1440 TRP 0.011 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00237 (11982) covalent geometry : angle 0.59495 (16236) SS BOND : bond 0.00384 ( 9) SS BOND : angle 1.34781 ( 18) hydrogen bonds : bond 0.03767 ( 757) hydrogen bonds : angle 4.57618 ( 2172) link_BETA1-4 : bond 0.00678 ( 2) link_BETA1-4 : angle 3.09127 ( 6) link_NAG-ASN : bond 0.00269 ( 8) link_NAG-ASN : angle 2.15763 ( 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: 46 poor density : 172 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7209 (tppt) REVERT: A 364 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: A 410 GLN cc_start: 0.7296 (mm110) cc_final: 0.7047 (mm110) REVERT: A 742 MET cc_start: 0.6219 (ttm) cc_final: 0.5808 (ttm) REVERT: A 861 ASN cc_start: 0.6580 (m-40) cc_final: 0.5971 (m-40) REVERT: A 1230 ASP cc_start: 0.8044 (t0) cc_final: 0.7486 (m-30) REVERT: A 1251 LYS cc_start: 0.7628 (tttt) cc_final: 0.7284 (mptt) REVERT: A 1276 ASN cc_start: 0.7844 (t0) cc_final: 0.7643 (m-40) REVERT: A 1556 ILE cc_start: 0.8031 (tp) cc_final: 0.7792 (tp) REVERT: A 1760 LEU cc_start: 0.8170 (mm) cc_final: 0.7915 (tp) REVERT: C 79 MET cc_start: 0.0632 (ppp) cc_final: -0.1154 (mmm) outliers start: 46 outliers final: 29 residues processed: 213 average time/residue: 0.0899 time to fit residues: 29.4600 Evaluate side-chains 196 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 SER 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 896 VAL 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 1240 GLU 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 1683 THR Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 43 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 132 optimal weight: 40.0000 chunk 35 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.181500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138711 restraints weight = 14798.120| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.56 r_work: 0.3369 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12001 Z= 0.129 Angle : 0.596 9.775 16284 Z= 0.298 Chirality : 0.041 0.250 1892 Planarity : 0.004 0.044 1981 Dihedral : 9.638 118.483 1779 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.84 % Allowed : 20.28 % Favored : 75.88 % 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: 0.27 (0.23), residues: 1421 helix: 1.06 (0.17), residues: 871 sheet: -0.88 (0.45), residues: 131 loop : -1.25 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 841 TYR 0.022 0.001 TYR A1548 PHE 0.014 0.001 PHE A 963 TRP 0.009 0.001 TRP A 928 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00283 (11982) covalent geometry : angle 0.58756 (16236) SS BOND : bond 0.00432 ( 9) SS BOND : angle 1.36932 ( 18) hydrogen bonds : bond 0.03787 ( 757) hydrogen bonds : angle 4.55453 ( 2172) link_BETA1-4 : bond 0.00613 ( 2) link_BETA1-4 : angle 3.03036 ( 6) link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 1.99686 ( 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 219 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7202 (tppt) REVERT: A 364 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: A 383 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8543 (t) REVERT: A 742 MET cc_start: 0.6091 (ttm) cc_final: 0.5852 (tpp) REVERT: A 794 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5975 (mmmt) REVERT: A 861 ASN cc_start: 0.6567 (m-40) cc_final: 0.5983 (m-40) REVERT: A 1230 ASP cc_start: 0.8006 (t0) cc_final: 0.7495 (m-30) REVERT: A 1251 LYS cc_start: 0.7543 (tttt) cc_final: 0.7237 (mptt) REVERT: A 1276 ASN cc_start: 0.7918 (t0) cc_final: 0.7692 (m-40) REVERT: A 1556 ILE cc_start: 0.7992 (tp) cc_final: 0.7751 (tp) REVERT: A 1573 TYR cc_start: 0.7905 (t80) cc_final: 0.7680 (t80) REVERT: C 79 MET cc_start: 0.0727 (ppp) cc_final: -0.1154 (mmm) outliers start: 49 outliers final: 35 residues processed: 212 average time/residue: 0.0942 time to fit residues: 30.1561 Evaluate side-chains 203 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 146 ASN 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 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 844 LYS 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 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1240 GLU 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 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 1683 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 34 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.181953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126864 restraints weight = 14857.169| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.18 r_work: 0.3428 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12001 Z= 0.138 Angle : 0.606 9.807 16284 Z= 0.303 Chirality : 0.041 0.252 1892 Planarity : 0.004 0.039 1981 Dihedral : 9.531 116.769 1779 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.99 % Allowed : 20.28 % Favored : 75.72 % 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: 0.37 (0.23), residues: 1421 helix: 1.13 (0.17), residues: 870 sheet: -0.85 (0.44), residues: 137 loop : -1.19 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 300 TYR 0.023 0.001 TYR A1548 PHE 0.023 0.001 PHE A 183 TRP 0.008 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00306 (11982) covalent geometry : angle 0.59798 (16236) SS BOND : bond 0.00457 ( 9) SS BOND : angle 1.40801 ( 18) hydrogen bonds : bond 0.03798 ( 757) hydrogen bonds : angle 4.55549 ( 2172) link_BETA1-4 : bond 0.00650 ( 2) link_BETA1-4 : angle 3.00327 ( 6) link_NAG-ASN : bond 0.00265 ( 8) link_NAG-ASN : angle 1.79315 ( 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: 51 poor density : 175 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8528 (p0) REVERT: A 243 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7187 (tppt) REVERT: A 364 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: A 383 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8523 (t) REVERT: A 410 GLN cc_start: 0.7304 (mm110) cc_final: 0.7099 (mm110) REVERT: A 742 MET cc_start: 0.6177 (ttm) cc_final: 0.5915 (tpp) REVERT: A 794 LYS cc_start: 0.6829 (mmmt) cc_final: 0.6000 (mmmt) REVERT: A 841 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7330 (mmm-85) REVERT: A 861 ASN cc_start: 0.6563 (m-40) cc_final: 0.5984 (m-40) REVERT: A 1230 ASP cc_start: 0.8099 (t0) cc_final: 0.7578 (m-30) REVERT: A 1251 LYS cc_start: 0.7504 (tttt) cc_final: 0.7193 (mptt) REVERT: A 1276 ASN cc_start: 0.7880 (t0) cc_final: 0.7645 (m-40) REVERT: A 1470 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: A 1556 ILE cc_start: 0.8105 (tp) cc_final: 0.7836 (tp) REVERT: A 1768 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.4162 (tm-30) REVERT: B 152 ARG cc_start: 0.8504 (ptm160) cc_final: 0.8301 (ptm160) REVERT: C 79 MET cc_start: 0.0627 (ppp) cc_final: -0.1178 (mmm) outliers start: 51 outliers final: 40 residues processed: 220 average time/residue: 0.0958 time to fit residues: 31.4759 Evaluate side-chains 212 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 844 LYS 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 1240 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 66 optimal weight: 0.9990 chunk 138 optimal weight: 40.0000 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1424 GLN A1762 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.180730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125082 restraints weight = 14785.726| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.22 r_work: 0.3406 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12001 Z= 0.156 Angle : 0.624 10.088 16284 Z= 0.310 Chirality : 0.042 0.274 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.460 115.132 1777 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.23 % Allowed : 20.36 % 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: 0.41 (0.23), residues: 1421 helix: 1.19 (0.17), residues: 862 sheet: -0.90 (0.44), residues: 137 loop : -1.15 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1616 TYR 0.023 0.001 TYR A1548 PHE 0.015 0.001 PHE A 963 TRP 0.007 0.001 TRP A1382 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00359 (11982) covalent geometry : angle 0.61577 (16236) SS BOND : bond 0.00517 ( 9) SS BOND : angle 1.53621 ( 18) hydrogen bonds : bond 0.03886 ( 757) hydrogen bonds : angle 4.61578 ( 2172) link_BETA1-4 : bond 0.00608 ( 2) link_BETA1-4 : angle 2.99990 ( 6) link_NAG-ASN : bond 0.00289 ( 8) link_NAG-ASN : angle 1.82394 ( 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 225 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8564 (p0) REVERT: A 243 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7265 (tppt) REVERT: A 364 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 383 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8523 (t) REVERT: A 742 MET cc_start: 0.6080 (ttm) cc_final: 0.5868 (tpp) REVERT: A 794 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6275 (tptm) REVERT: A 841 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7344 (mmm-85) REVERT: A 861 ASN cc_start: 0.6587 (m-40) cc_final: 0.6029 (m-40) REVERT: A 1230 ASP cc_start: 0.8070 (t0) cc_final: 0.7567 (m-30) REVERT: A 1251 LYS cc_start: 0.7485 (tttt) cc_final: 0.7176 (mptt) REVERT: A 1276 ASN cc_start: 0.7849 (t0) cc_final: 0.7643 (m-40) REVERT: A 1470 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: A 1556 ILE cc_start: 0.8076 (tp) cc_final: 0.7810 (tp) REVERT: A 1768 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.3576 (tm-30) REVERT: C 79 MET cc_start: 0.0632 (ppp) cc_final: -0.1091 (mmm) outliers start: 54 outliers final: 40 residues processed: 215 average time/residue: 0.0968 time to fit residues: 31.3238 Evaluate side-chains 215 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 752 ILE 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 844 LYS 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 1240 GLU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 21 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1762 ASN B 61 GLN 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 = 0.181475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126493 restraints weight = 14822.428| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.30 r_work: 0.3412 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12001 Z= 0.141 Angle : 0.618 9.821 16284 Z= 0.308 Chirality : 0.042 0.264 1892 Planarity : 0.004 0.040 1981 Dihedral : 9.366 113.671 1777 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 3.76 % Allowed : 20.99 % 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: 0.45 (0.23), residues: 1421 helix: 1.21 (0.17), residues: 864 sheet: -0.85 (0.44), residues: 137 loop : -1.15 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.024 0.001 TYR A1548 PHE 0.025 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 covalent geometry : bond 0.00317 (11982) covalent geometry : angle 0.61058 (16236) SS BOND : bond 0.00457 ( 9) SS BOND : angle 1.42056 ( 18) hydrogen bonds : bond 0.03817 ( 757) hydrogen bonds : angle 4.60774 ( 2172) link_BETA1-4 : bond 0.00620 ( 2) link_BETA1-4 : angle 2.98095 ( 6) link_NAG-ASN : bond 0.00280 ( 8) link_NAG-ASN : angle 1.72456 ( 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 217 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8531 (p0) REVERT: A 243 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7265 (tppt) REVERT: A 364 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 383 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8527 (t) REVERT: A 742 MET cc_start: 0.6198 (ttm) cc_final: 0.5957 (tpp) REVERT: A 794 LYS cc_start: 0.6775 (mmmt) cc_final: 0.6128 (mmtp) REVERT: A 841 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7344 (mmm-85) REVERT: A 861 ASN cc_start: 0.6668 (m-40) cc_final: 0.6098 (m-40) REVERT: A 1230 ASP cc_start: 0.8080 (t0) cc_final: 0.7584 (m-30) REVERT: A 1251 LYS cc_start: 0.7483 (tttt) cc_final: 0.7184 (mptt) REVERT: A 1276 ASN cc_start: 0.7831 (t0) cc_final: 0.7544 (m-40) REVERT: A 1436 TYR cc_start: 0.8424 (t80) cc_final: 0.7423 (t80) REVERT: A 1470 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: A 1556 ILE cc_start: 0.8114 (tp) cc_final: 0.7823 (tp) REVERT: A 1768 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.3651 (tm-30) REVERT: C 79 MET cc_start: 0.0638 (ppp) cc_final: -0.1098 (mmm) outliers start: 48 outliers final: 39 residues processed: 207 average time/residue: 0.0966 time to fit residues: 29.7296 Evaluate side-chains 208 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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 383 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 844 LYS 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 1240 GLU 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 69 LYS Chi-restraints excluded: chain B residue 78 LEU 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: 0.6980 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.0570 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 765 HIS A1762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.180336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128618 restraints weight = 14714.271| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.31 r_work: 0.3402 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12001 Z= 0.145 Angle : 0.619 10.465 16284 Z= 0.307 Chirality : 0.042 0.265 1892 Planarity : 0.004 0.039 1981 Dihedral : 9.305 112.072 1777 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 3.92 % Allowed : 20.91 % 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: 0.47 (0.23), residues: 1421 helix: 1.26 (0.17), residues: 857 sheet: -0.83 (0.44), residues: 137 loop : -1.17 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.023 0.001 TYR A1548 PHE 0.014 0.001 PHE A 963 TRP 0.010 0.001 TRP A1578 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00328 (11982) covalent geometry : angle 0.61210 (16236) SS BOND : bond 0.00458 ( 9) SS BOND : angle 1.43190 ( 18) hydrogen bonds : bond 0.03858 ( 757) hydrogen bonds : angle 4.60303 ( 2172) link_BETA1-4 : bond 0.00649 ( 2) link_BETA1-4 : angle 2.92760 ( 6) link_NAG-ASN : bond 0.00265 ( 8) link_NAG-ASN : angle 1.68860 ( 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 217 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8524 (p0) REVERT: A 243 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7126 (tppt) REVERT: A 364 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: A 383 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8493 (t) REVERT: A 794 LYS cc_start: 0.6557 (mmmt) cc_final: 0.6241 (tptm) REVERT: A 841 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.7310 (mmm-85) REVERT: A 861 ASN cc_start: 0.6591 (m-40) cc_final: 0.6011 (m-40) REVERT: A 1230 ASP cc_start: 0.8108 (t0) cc_final: 0.7550 (m-30) REVERT: A 1251 LYS cc_start: 0.7429 (tttt) cc_final: 0.7130 (mptt) REVERT: A 1276 ASN cc_start: 0.7820 (t0) cc_final: 0.7517 (m-40) REVERT: A 1470 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6754 (mp10) REVERT: A 1556 ILE cc_start: 0.8022 (tp) cc_final: 0.7734 (tp) REVERT: A 1768 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.3742 (tm-30) REVERT: C 79 MET cc_start: 0.0620 (ppp) cc_final: -0.1224 (mmm) outliers start: 50 outliers final: 40 residues processed: 209 average time/residue: 0.0962 time to fit residues: 30.0851 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 : 0.407 ------------------------------------------------------------------------------- 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 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 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 383 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 781 LEU 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 1240 GLU 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 78 LEU 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: 1.9990 chunk 39 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 765 HIS A1762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.180551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128868 restraints weight = 14798.911| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.27 r_work: 0.3412 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12001 Z= 0.143 Angle : 0.635 10.561 16284 Z= 0.314 Chirality : 0.042 0.264 1892 Planarity : 0.004 0.040 1981 Dihedral : 9.260 110.599 1777 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 3.60 % Allowed : 21.22 % 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: 0.48 (0.22), residues: 1421 helix: 1.30 (0.17), residues: 852 sheet: -0.82 (0.44), residues: 137 loop : -1.22 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.031 0.001 TYR A1573 PHE 0.025 0.001 PHE A 183 TRP 0.010 0.001 TRP A1578 HIS 0.002 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00321 (11982) covalent geometry : angle 0.62865 (16236) SS BOND : bond 0.00441 ( 9) SS BOND : angle 1.40088 ( 18) hydrogen bonds : bond 0.03831 ( 757) hydrogen bonds : angle 4.61060 ( 2172) link_BETA1-4 : bond 0.00711 ( 2) link_BETA1-4 : angle 2.92687 ( 6) link_NAG-ASN : bond 0.00256 ( 8) link_NAG-ASN : angle 1.66911 ( 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 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 TRP cc_start: 0.7749 (m-10) cc_final: 0.7534 (m-10) REVERT: A 243 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7170 (tppt) REVERT: A 364 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: A 383 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 794 LYS cc_start: 0.6939 (mmmt) cc_final: 0.6355 (mmtp) REVERT: A 837 PHE cc_start: 0.7597 (m-10) cc_final: 0.7333 (m-10) REVERT: A 841 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.7241 (mmm-85) REVERT: A 861 ASN cc_start: 0.6588 (m-40) cc_final: 0.6006 (m-40) REVERT: A 1230 ASP cc_start: 0.8094 (t0) cc_final: 0.7497 (m-30) REVERT: A 1251 LYS cc_start: 0.7415 (tttt) cc_final: 0.7127 (mptt) REVERT: A 1276 ASN cc_start: 0.7819 (t0) cc_final: 0.7521 (m-40) REVERT: A 1470 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: A 1556 ILE cc_start: 0.8009 (tp) cc_final: 0.7721 (tp) REVERT: A 1754 MET cc_start: 0.8604 (mtt) cc_final: 0.8310 (mtt) REVERT: A 1768 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.3812 (tm-30) REVERT: C 79 MET cc_start: 0.0615 (ppp) cc_final: -0.1354 (mmm) outliers start: 46 outliers final: 40 residues processed: 203 average time/residue: 0.0956 time to fit residues: 29.0378 Evaluate side-chains 206 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 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 383 VAL 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 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 1240 GLU 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 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 78 LEU 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: 10.0000 chunk 65 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 111 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 99 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 780 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.182462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.141324 restraints weight = 14729.574| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.12 r_work: 0.3374 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12001 Z= 0.118 Angle : 0.607 10.504 16284 Z= 0.301 Chirality : 0.041 0.245 1892 Planarity : 0.003 0.039 1981 Dihedral : 9.109 109.867 1777 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 2.82 % Allowed : 22.08 % Favored : 75.10 % 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: 1.41 (0.17), residues: 852 sheet: -0.82 (0.44), residues: 138 loop : -1.19 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.024 0.001 TYR A1548 PHE 0.013 0.001 PHE A 963 TRP 0.011 0.001 TRP A1382 HIS 0.002 0.000 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00245 (11982) covalent geometry : angle 0.60156 (16236) SS BOND : bond 0.00336 ( 9) SS BOND : angle 1.21741 ( 18) hydrogen bonds : bond 0.03682 ( 757) hydrogen bonds : angle 4.50934 ( 2172) link_BETA1-4 : bond 0.00744 ( 2) link_BETA1-4 : angle 2.89979 ( 6) link_NAG-ASN : bond 0.00231 ( 8) link_NAG-ASN : angle 1.51877 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3612.87 seconds wall clock time: 62 minutes 23.45 seconds (3743.45 seconds total)