Starting phenix.real_space_refine on Wed Jul 30 17:38:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmf_33295/07_2025/7xmf_33295.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmf_33295/07_2025/7xmf_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_33295/07_2025/7xmf_33295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2025/7xmf_33295.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2025/7xmf_33295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmf_33295/07_2025/7xmf_33295.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 1, 'ASP: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: 7.41, per 1000 atoms: 0.63 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: 2.90 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.14 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: 3.74 Time building geometry restraints manager: 3.43 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- 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 : 16.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP C 67 HIS 0.004 0.001 HIS A 766 PHE 0.018 0.002 PHE C 80 TYR 0.018 0.002 TYR C 125 ARG 0.003 0.001 ARG A1622 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 8) link_NAG-ASN : angle 3.54348 ( 24) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 3.64863 ( 6) hydrogen bonds : bond 0.11013 ( 757) hydrogen bonds : angle 5.33737 ( 2172) SS BOND : bond 0.17992 ( 9) SS BOND : angle 13.58783 ( 18) covalent geometry : bond 0.00787 (11982) covalent geometry : angle 0.86787 (16236) *********************** 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 : 1.159 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: 0.8304 (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: 0.7494 (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: 0.7716 (t) REVERT: B 118 ASP cc_start: 0.7125 (m-30) cc_final: 0.6720 (m-30) outliers start: 43 outliers final: 23 residues processed: 264 average time/residue: 0.2442 time to fit residues: 93.6391 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 : 1.373 ------------------------------------------------------------------------------- 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 120 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 B 61 GLN B 102 GLN B 115 HIS C 118 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135757 restraints weight = 14575.518| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.08 r_work: 0.3336 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 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 = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12001 Z= 0.158 Angle : 0.731 28.179 16284 Z= 0.353 Chirality : 0.044 0.315 1892 Planarity : 0.005 0.064 1981 Dihedral : 9.972 110.299 1810 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.15 % Allowed : 19.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1421 helix: 0.17 (0.17), residues: 867 sheet: -1.24 (0.45), residues: 131 loop : -1.67 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.002 0.001 HIS A 766 PHE 0.014 0.001 PHE A1440 TYR 0.016 0.001 TYR A1739 ARG 0.008 0.001 ARG C 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 8) link_NAG-ASN : angle 8.24824 ( 24) link_BETA1-4 : bond 0.00415 ( 2) link_BETA1-4 : angle 3.34978 ( 6) hydrogen bonds : bond 0.04314 ( 757) hydrogen bonds : angle 4.84772 ( 2172) SS BOND : bond 0.00548 ( 9) SS BOND : angle 2.04471 ( 18) covalent geometry : bond 0.00352 (11982) covalent geometry : angle 0.65290 (16236) *********************** 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: 53 poor density : 180 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6828 (tt) cc_final: 0.6374 (mt) REVERT: A 130 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6162 (tpp) REVERT: A 207 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3743 (tp) REVERT: A 279 SER cc_start: 0.8813 (t) cc_final: 0.8568 (p) REVERT: A 742 MET cc_start: 0.6293 (ttm) cc_final: 0.5855 (ttm) REVERT: A 794 LYS cc_start: 0.6120 (mmmt) cc_final: 0.5036 (tttm) REVERT: A 837 PHE cc_start: 0.7597 (m-10) cc_final: 0.7173 (m-10) REVERT: A 1251 LYS cc_start: 0.7785 (tttt) cc_final: 0.7406 (mptt) REVERT: A 1252 THR cc_start: 0.8681 (p) cc_final: 0.8341 (t) REVERT: A 1374 MET cc_start: 0.7366 (ttm) cc_final: 0.6998 (mtm) REVERT: A 1424 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7782 (tp-100) REVERT: A 1760 LEU cc_start: 0.8053 (mm) cc_final: 0.7826 (tp) REVERT: A 1768 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5334 (mp0) REVERT: B 68 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7819 (p) REVERT: C 79 MET cc_start: 0.1015 (ppp) cc_final: -0.0950 (mmm) outliers start: 53 outliers final: 28 residues processed: 227 average time/residue: 0.2060 time to fit residues: 70.5680 Evaluate side-chains 193 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 92 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.180422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124706 restraints weight = 14777.623| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.22 r_work: 0.3388 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12001 Z= 0.152 Angle : 0.639 10.650 16284 Z= 0.322 Chirality : 0.043 0.290 1892 Planarity : 0.004 0.044 1981 Dihedral : 10.155 110.710 1789 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.78 % Allowed : 20.28 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1421 helix: 0.67 (0.17), residues: 867 sheet: -1.03 (0.46), residues: 130 loop : -1.53 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.002 0.001 HIS A 909 PHE 0.017 0.001 PHE A 963 TYR 0.021 0.001 TYR A1548 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 8) link_NAG-ASN : angle 2.66558 ( 24) link_BETA1-4 : bond 0.00594 ( 2) link_BETA1-4 : angle 3.20534 ( 6) hydrogen bonds : bond 0.04085 ( 757) hydrogen bonds : angle 4.74819 ( 2172) SS BOND : bond 0.00537 ( 9) SS BOND : angle 1.74318 ( 18) covalent geometry : bond 0.00339 (11982) covalent geometry : angle 0.62578 (16236) *********************** 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: 61 poor density : 175 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.3928 (OUTLIER) cc_final: 0.3697 (tp) REVERT: A 243 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7261 (tppt) REVERT: A 742 MET cc_start: 0.6241 (ttm) cc_final: 0.5875 (ttm) REVERT: A 794 LYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5387 (mmmt) REVERT: A 796 ILE cc_start: 0.7229 (pp) cc_final: 0.6983 (pt) REVERT: A 837 PHE cc_start: 0.7695 (m-10) cc_final: 0.7333 (m-10) REVERT: A 895 CYS cc_start: 0.5839 (p) cc_final: 0.5470 (t) REVERT: A 1251 LYS cc_start: 0.7773 (tttt) cc_final: 0.7380 (mptt) REVERT: A 1374 MET cc_start: 0.7523 (ttm) cc_final: 0.7260 (mtp) REVERT: A 1424 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7391 (tp-100) REVERT: A 1556 ILE cc_start: 0.8091 (tp) cc_final: 0.7818 (tp) REVERT: A 1760 LEU cc_start: 0.8133 (mm) cc_final: 0.7885 (tp) REVERT: A 1768 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.4384 (tm-30) REVERT: B 68 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7809 (p) REVERT: C 79 MET cc_start: 0.0674 (ppp) cc_final: -0.0977 (mmm) outliers start: 61 outliers final: 33 residues processed: 226 average time/residue: 0.2065 time to fit residues: 70.3763 Evaluate side-chains 200 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 68 VAL 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 B residue 190 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 107 optimal weight: 0.0030 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 956 ASN A1709 ASN B 134 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.182439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127515 restraints weight = 14707.807| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.17 r_work: 0.3442 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12001 Z= 0.121 Angle : 0.613 11.932 16284 Z= 0.307 Chirality : 0.041 0.256 1892 Planarity : 0.004 0.040 1981 Dihedral : 10.044 114.551 1788 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.52 % Allowed : 21.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1421 helix: 0.97 (0.17), residues: 864 sheet: -0.97 (0.45), residues: 131 loop : -1.33 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 PHE 0.014 0.001 PHE A1440 TYR 0.027 0.001 TYR A1739 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 8) link_NAG-ASN : angle 2.17604 ( 24) link_BETA1-4 : bond 0.00549 ( 2) link_BETA1-4 : angle 3.15363 ( 6) hydrogen bonds : bond 0.03869 ( 757) hydrogen bonds : angle 4.65703 ( 2172) SS BOND : bond 0.00411 ( 9) SS BOND : angle 1.51079 ( 18) covalent geometry : bond 0.00254 (11982) covalent geometry : angle 0.60335 (16236) *********************** 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 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7263 (tppt) REVERT: A 364 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: A 742 MET cc_start: 0.6279 (ttm) cc_final: 0.5858 (ttm) REVERT: A 796 ILE cc_start: 0.7272 (pp) cc_final: 0.7042 (pt) REVERT: A 837 PHE cc_start: 0.7562 (m-10) cc_final: 0.7234 (m-10) REVERT: A 861 ASN cc_start: 0.6615 (m-40) cc_final: 0.6081 (m-40) REVERT: A 1251 LYS cc_start: 0.7704 (tttt) cc_final: 0.7316 (mptt) REVERT: A 1276 ASN cc_start: 0.7934 (t0) cc_final: 0.7607 (m-40) REVERT: A 1556 ILE cc_start: 0.8037 (tp) cc_final: 0.7782 (tp) REVERT: A 1668 TYR cc_start: 0.7853 (m-80) cc_final: 0.7617 (m-80) REVERT: A 1760 LEU cc_start: 0.8233 (mm) cc_final: 0.7966 (tp) REVERT: C 79 MET cc_start: 0.0712 (ppp) cc_final: -0.1029 (mmm) outliers start: 45 outliers final: 31 residues processed: 206 average time/residue: 0.2018 time to fit residues: 63.2925 Evaluate side-chains 190 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 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 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 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 137 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS A 911 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.182269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141218 restraints weight = 14689.731| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.34 r_work: 0.3347 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12001 Z= 0.126 Angle : 0.605 9.779 16284 Z= 0.302 Chirality : 0.041 0.251 1892 Planarity : 0.004 0.044 1981 Dihedral : 9.646 113.533 1783 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.54 % Allowed : 19.97 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1421 helix: 1.07 (0.17), residues: 871 sheet: -0.89 (0.45), residues: 131 loop : -1.29 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 PHE 0.021 0.001 PHE A 183 TYR 0.023 0.001 TYR A1548 ARG 0.002 0.000 ARG B 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 8) link_NAG-ASN : angle 2.06224 ( 24) link_BETA1-4 : bond 0.00549 ( 2) link_BETA1-4 : angle 3.04967 ( 6) hydrogen bonds : bond 0.03797 ( 757) hydrogen bonds : angle 4.58749 ( 2172) SS BOND : bond 0.00435 ( 9) SS BOND : angle 1.39121 ( 18) covalent geometry : bond 0.00273 (11982) covalent geometry : angle 0.59577 (16236) *********************** 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 226 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7268 (tppt) REVERT: A 298 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6764 (p0) REVERT: A 364 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: A 742 MET cc_start: 0.6076 (ttm) cc_final: 0.5826 (tpp) REVERT: A 794 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.5985 (mmmt) REVERT: A 796 ILE cc_start: 0.7190 (pp) cc_final: 0.6924 (pt) REVERT: A 861 ASN cc_start: 0.6639 (m-40) cc_final: 0.6160 (m-40) REVERT: A 1230 ASP cc_start: 0.8076 (t0) cc_final: 0.7564 (m-30) REVERT: A 1251 LYS cc_start: 0.7597 (tttt) cc_final: 0.7276 (mptt) REVERT: A 1276 ASN cc_start: 0.7943 (t0) cc_final: 0.7600 (m-40) REVERT: A 1470 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: A 1556 ILE cc_start: 0.8006 (tp) cc_final: 0.7758 (tp) REVERT: A 1668 TYR cc_start: 0.7807 (m-80) cc_final: 0.7582 (m-80) REVERT: A 1691 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 1760 LEU cc_start: 0.8220 (mm) cc_final: 0.7982 (tt) REVERT: A 1768 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.4405 (tm-30) REVERT: B 152 ARG cc_start: 0.8346 (ptm160) cc_final: 0.8117 (ptm160) REVERT: C 79 MET cc_start: 0.0566 (ppp) cc_final: -0.1299 (mmm) outliers start: 58 outliers final: 38 residues processed: 219 average time/residue: 0.2185 time to fit residues: 72.3763 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 : 1.362 ------------------------------------------------------------------------------- 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 298 ASP Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 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 1691 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 105 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 138 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.180931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124809 restraints weight = 14776.179| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.96 r_work: 0.3436 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2493 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= 0.149 Angle : 0.617 9.862 16284 Z= 0.309 Chirality : 0.042 0.266 1892 Planarity : 0.004 0.039 1981 Dihedral : 9.557 112.743 1781 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.70 % Allowed : 19.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1421 helix: 1.12 (0.17), residues: 867 sheet: -0.90 (0.44), residues: 137 loop : -1.27 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 PHE 0.014 0.001 PHE A 963 TYR 0.023 0.001 TYR A1548 ARG 0.002 0.000 ARG B 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 8) link_NAG-ASN : angle 2.00537 ( 24) link_BETA1-4 : bond 0.00593 ( 2) link_BETA1-4 : angle 3.00198 ( 6) hydrogen bonds : bond 0.03857 ( 757) hydrogen bonds : angle 4.62684 ( 2172) SS BOND : bond 0.00490 ( 9) SS BOND : angle 1.48893 ( 18) covalent geometry : bond 0.00337 (11982) covalent geometry : angle 0.60848 (16236) *********************** 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 231 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7247 (tppt) REVERT: A 298 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6759 (p0) REVERT: A 364 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: A 742 MET cc_start: 0.6081 (ttm) cc_final: 0.5867 (tpp) REVERT: A 794 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6070 (mmtp) REVERT: A 796 ILE cc_start: 0.7298 (pp) cc_final: 0.6995 (pt) REVERT: A 861 ASN cc_start: 0.6630 (m-40) cc_final: 0.6169 (m-40) REVERT: A 1230 ASP cc_start: 0.8051 (t0) cc_final: 0.7553 (m-30) REVERT: A 1251 LYS cc_start: 0.7531 (tttt) cc_final: 0.7216 (mptt) REVERT: A 1276 ASN cc_start: 0.7923 (t0) cc_final: 0.7554 (m-40) REVERT: A 1470 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: A 1556 ILE cc_start: 0.8003 (tp) cc_final: 0.7757 (tp) REVERT: A 1668 TYR cc_start: 0.7916 (m-80) cc_final: 0.7694 (m-80) REVERT: A 1760 LEU cc_start: 0.8261 (mm) cc_final: 0.7985 (tt) REVERT: A 1768 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.4246 (tm-30) REVERT: C 79 MET cc_start: 0.0661 (ppp) cc_final: -0.1190 (mmm) outliers start: 60 outliers final: 43 residues processed: 220 average time/residue: 0.2140 time to fit residues: 70.8422 Evaluate side-chains 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 298 ASP 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 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 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 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 91 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 55 CYS 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 108 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.180383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128100 restraints weight = 14867.726| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.39 r_work: 0.3384 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2596 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= 0.140 Angle : 0.605 9.803 16284 Z= 0.302 Chirality : 0.041 0.263 1892 Planarity : 0.004 0.040 1981 Dihedral : 9.425 111.929 1780 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.15 % Allowed : 20.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1421 helix: 1.19 (0.17), residues: 868 sheet: -0.88 (0.44), residues: 137 loop : -1.24 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 PHE 0.022 0.001 PHE A 183 TYR 0.023 0.001 TYR A1548 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 8) link_NAG-ASN : angle 1.91879 ( 24) link_BETA1-4 : bond 0.00701 ( 2) link_BETA1-4 : angle 3.00670 ( 6) hydrogen bonds : bond 0.03815 ( 757) hydrogen bonds : angle 4.56675 ( 2172) SS BOND : bond 0.00456 ( 9) SS BOND : angle 1.42947 ( 18) covalent geometry : bond 0.00314 (11982) covalent geometry : angle 0.59622 (16236) *********************** 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 226 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8537 (p0) REVERT: A 243 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7167 (tppt) REVERT: A 364 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: A 742 MET cc_start: 0.6058 (ttm) cc_final: 0.5820 (tpp) REVERT: A 794 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5963 (mmmt) REVERT: A 796 ILE cc_start: 0.7157 (pp) cc_final: 0.6846 (pt) REVERT: A 841 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7329 (mmm-85) REVERT: A 861 ASN cc_start: 0.6530 (m-40) cc_final: 0.6052 (m-40) REVERT: A 1230 ASP cc_start: 0.8140 (t0) cc_final: 0.7599 (m-30) REVERT: A 1251 LYS cc_start: 0.7483 (tttt) cc_final: 0.7155 (mptt) REVERT: A 1276 ASN cc_start: 0.7885 (t0) cc_final: 0.7496 (m-40) REVERT: A 1436 TYR cc_start: 0.8455 (t80) cc_final: 0.7965 (t80) REVERT: A 1470 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.6934 (mp10) REVERT: A 1556 ILE cc_start: 0.7929 (tp) cc_final: 0.7674 (tp) REVERT: A 1668 TYR cc_start: 0.7968 (m-80) cc_final: 0.7732 (m-80) REVERT: A 1760 LEU cc_start: 0.8310 (mm) cc_final: 0.7951 (tt) REVERT: A 1768 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.4124 (tm-30) REVERT: B 159 SER cc_start: 0.8769 (t) cc_final: 0.8453 (p) REVERT: C 79 MET cc_start: 0.0633 (ppp) cc_final: -0.1115 (mmm) outliers start: 53 outliers final: 40 residues processed: 217 average time/residue: 0.2143 time to fit residues: 69.3640 Evaluate side-chains 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 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 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 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 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 780 ASN A1762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.180316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127183 restraints weight = 14767.372| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.29 r_work: 0.3399 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2679 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= 0.140 Angle : 0.617 9.913 16284 Z= 0.308 Chirality : 0.041 0.262 1892 Planarity : 0.004 0.040 1981 Dihedral : 9.366 111.012 1779 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 3.52 % Allowed : 21.14 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1421 helix: 1.20 (0.17), residues: 868 sheet: -0.85 (0.44), residues: 137 loop : -1.21 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 PHE 0.017 0.001 PHE A 963 TYR 0.023 0.001 TYR A1548 ARG 0.002 0.000 ARG A1619 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 8) link_NAG-ASN : angle 1.87729 ( 24) link_BETA1-4 : bond 0.00701 ( 2) link_BETA1-4 : angle 2.95831 ( 6) hydrogen bonds : bond 0.03807 ( 757) hydrogen bonds : angle 4.56342 ( 2172) SS BOND : bond 0.00434 ( 9) SS BOND : angle 1.38148 ( 18) covalent geometry : bond 0.00313 (11982) covalent geometry : angle 0.60964 (16236) *********************** 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 212 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8560 (p0) REVERT: A 243 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7197 (tppt) REVERT: A 364 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: A 742 MET cc_start: 0.6154 (ttm) cc_final: 0.5905 (tpp) REVERT: A 794 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6097 (mmtp) REVERT: A 796 ILE cc_start: 0.7364 (pp) cc_final: 0.7114 (pt) REVERT: A 841 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.7296 (mmm-85) REVERT: A 861 ASN cc_start: 0.6580 (m-40) cc_final: 0.6107 (m-40) REVERT: A 1230 ASP cc_start: 0.8089 (t0) cc_final: 0.7585 (m-30) REVERT: A 1251 LYS cc_start: 0.7485 (tttt) cc_final: 0.7177 (mptt) REVERT: A 1276 ASN cc_start: 0.7884 (t0) cc_final: 0.7507 (m-40) REVERT: A 1470 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: A 1556 ILE cc_start: 0.8060 (tp) cc_final: 0.7784 (tp) REVERT: A 1668 TYR cc_start: 0.7925 (m-80) cc_final: 0.7699 (m-80) REVERT: A 1760 LEU cc_start: 0.8310 (mm) cc_final: 0.8006 (tt) REVERT: A 1768 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.3790 (tm-30) REVERT: B 159 SER cc_start: 0.8761 (t) cc_final: 0.8383 (m) REVERT: C 79 MET cc_start: 0.0641 (ppp) cc_final: -0.1139 (mmm) outliers start: 45 outliers final: 35 residues processed: 205 average time/residue: 0.2057 time to fit residues: 63.0415 Evaluate side-chains 203 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 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 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS 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 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 157 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 123 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 135 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 121 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1762 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.181892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140550 restraints weight = 14717.924| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.14 r_work: 0.3361 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12001 Z= 0.121 Angle : 0.595 10.352 16284 Z= 0.296 Chirality : 0.041 0.247 1892 Planarity : 0.003 0.039 1981 Dihedral : 9.220 109.843 1779 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.78 % Rotamer: Outliers : 3.05 % Allowed : 21.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1421 helix: 1.38 (0.17), residues: 857 sheet: -0.82 (0.44), residues: 138 loop : -1.20 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.002 0.000 HIS C 139 PHE 0.028 0.001 PHE A 183 TYR 0.024 0.001 TYR A1548 ARG 0.002 0.000 ARG B 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 8) link_NAG-ASN : angle 1.73492 ( 24) link_BETA1-4 : bond 0.00670 ( 2) link_BETA1-4 : angle 2.90673 ( 6) hydrogen bonds : bond 0.03699 ( 757) hydrogen bonds : angle 4.49744 ( 2172) SS BOND : bond 0.00365 ( 9) SS BOND : angle 1.24254 ( 18) covalent geometry : bond 0.00261 (11982) covalent geometry : angle 0.58798 (16236) *********************** 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: 39 poor density : 178 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8454 (p0) REVERT: A 190 TRP cc_start: 0.7781 (m-10) cc_final: 0.7568 (m-10) REVERT: A 243 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7229 (tppt) REVERT: A 311 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: A 364 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: A 794 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6067 (mmmt) REVERT: A 796 ILE cc_start: 0.7213 (pp) cc_final: 0.6877 (pt) REVERT: A 841 ARG cc_start: 0.7477 (mmm-85) cc_final: 0.7207 (mmm-85) REVERT: A 861 ASN cc_start: 0.6616 (m-40) cc_final: 0.6155 (m-40) REVERT: A 1230 ASP cc_start: 0.7935 (t0) cc_final: 0.7415 (m-30) REVERT: A 1251 LYS cc_start: 0.7430 (tttt) cc_final: 0.7162 (mptt) REVERT: A 1276 ASN cc_start: 0.7817 (t0) cc_final: 0.7551 (m-40) REVERT: A 1470 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: A 1556 ILE cc_start: 0.8084 (tp) cc_final: 0.7798 (tp) REVERT: A 1668 TYR cc_start: 0.7770 (m-80) cc_final: 0.7550 (m-80) REVERT: A 1760 LEU cc_start: 0.8268 (mm) cc_final: 0.7966 (tt) REVERT: A 1768 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.3638 (tm-30) REVERT: B 159 SER cc_start: 0.8745 (t) cc_final: 0.8428 (m) REVERT: C 79 MET cc_start: 0.0611 (ppp) cc_final: -0.1261 (mmm) outliers start: 39 outliers final: 29 residues processed: 210 average time/residue: 0.2155 time to fit residues: 66.6923 Evaluate side-chains 205 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 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 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 794 LYS 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 1216 ILE Chi-restraints excluded: chain A residue 1324 VAL 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 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 93 ASN Chi-restraints excluded: chain B residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 134 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1762 ASN 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 = 0.181807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140073 restraints weight = 14684.278| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.20 r_work: 0.3364 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12001 Z= 0.126 Angle : 0.624 10.590 16284 Z= 0.307 Chirality : 0.041 0.247 1892 Planarity : 0.004 0.039 1981 Dihedral : 9.124 108.810 1777 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 2.98 % Allowed : 21.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1421 helix: 1.37 (0.17), residues: 858 sheet: -0.80 (0.44), residues: 138 loop : -1.21 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.002 0.000 HIS C 139 PHE 0.022 0.001 PHE A1666 TYR 0.035 0.001 TYR A1739 ARG 0.002 0.000 ARG A1619 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 1.70785 ( 24) link_BETA1-4 : bond 0.00687 ( 2) link_BETA1-4 : angle 2.89837 ( 6) hydrogen bonds : bond 0.03693 ( 757) hydrogen bonds : angle 4.53414 ( 2172) SS BOND : bond 0.00371 ( 9) SS BOND : angle 1.24699 ( 18) covalent geometry : bond 0.00271 (11982) covalent geometry : angle 0.61779 (16236) ********************** 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 210 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8463 (p0) REVERT: A 190 TRP cc_start: 0.7737 (m-10) cc_final: 0.7536 (m-10) REVERT: A 243 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7250 (tppt) REVERT: A 311 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: A 364 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: A 794 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6199 (mmtp) REVERT: A 796 ILE cc_start: 0.7551 (pp) cc_final: 0.7312 (pt) REVERT: A 837 PHE cc_start: 0.7453 (m-10) cc_final: 0.7202 (m-10) REVERT: A 841 ARG cc_start: 0.7502 (mmm-85) cc_final: 0.7215 (mmm-85) REVERT: A 861 ASN cc_start: 0.6628 (m-40) cc_final: 0.6169 (m-40) REVERT: A 1230 ASP cc_start: 0.7947 (t0) cc_final: 0.7428 (m-30) REVERT: A 1276 ASN cc_start: 0.7834 (t0) cc_final: 0.7560 (m-40) REVERT: A 1470 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: A 1556 ILE cc_start: 0.8091 (tp) cc_final: 0.7800 (tp) REVERT: A 1668 TYR cc_start: 0.7775 (m-80) cc_final: 0.7543 (m-80) REVERT: A 1760 LEU cc_start: 0.8278 (mm) cc_final: 0.7977 (tt) REVERT: A 1768 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.3734 (tm-30) REVERT: B 159 SER cc_start: 0.8725 (t) cc_final: 0.8425 (m) REVERT: C 79 MET cc_start: 0.0575 (ppp) cc_final: -0.1569 (mmm) outliers start: 38 outliers final: 29 residues processed: 203 average time/residue: 0.2873 time to fit residues: 87.2046 Evaluate side-chains 204 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 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 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 LYS 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 1216 ILE Chi-restraints excluded: chain A residue 1324 VAL 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 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 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 114 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN 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 = 0.181262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126537 restraints weight = 14636.648| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.16 r_work: 0.3438 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12001 Z= 0.134 Angle : 0.620 11.032 16284 Z= 0.306 Chirality : 0.042 0.249 1892 Planarity : 0.004 0.039 1981 Dihedral : 9.090 107.661 1777 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.43 % Rotamer: Outliers : 3.21 % Allowed : 20.99 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1421 helix: 1.38 (0.17), residues: 852 sheet: -0.80 (0.44), residues: 138 loop : -1.22 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 PHE 0.017 0.001 PHE A1666 TYR 0.031 0.001 TYR A1739 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 8) link_NAG-ASN : angle 1.73296 ( 24) link_BETA1-4 : bond 0.00720 ( 2) link_BETA1-4 : angle 2.88402 ( 6) hydrogen bonds : bond 0.03716 ( 757) hydrogen bonds : angle 4.53177 ( 2172) SS BOND : bond 0.00409 ( 9) SS BOND : angle 1.30903 ( 18) covalent geometry : bond 0.00297 (11982) covalent geometry : angle 0.61294 (16236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7523.06 seconds wall clock time: 130 minutes 13.33 seconds (7813.33 seconds total)