Starting phenix.real_space_refine on Fri Sep 11 04:04:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oeu_7795/09_2026/6oeu_7795.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oeu_7795/09_2026/6oeu_7795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oeu_7795/09_2026/6oeu_7795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oeu_7795/09_2026/6oeu_7795.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6oeu_7795/09_2026/6oeu_7795.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oeu_7795/09_2026/6oeu_7795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oeu_7795/09_2026/6oeu_7795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oeu_7795/09_2026/6oeu_7795.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4734 2.51 5 N 1215 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7310 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7198 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 39, 'TRANS': 924} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'TYR:plan': 11, 'ASN:plan1': 8, 'ARG:plan': 5, 'GLN:plan1': 5, 'TRP:plan': 5, 'GLU:plan': 8, 'ASP:plan': 9, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 267 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.65, per 1000 atoms: 0.23 Number of scatterers: 7310 At special positions: 0 Unit cell: (133, 83, 87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1327 8.00 N 1215 7.00 C 4734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG E 1 " - " ASN A1000 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 325.0 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 59.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 77 through 94 removed outlier: 4.616A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.692A pdb=" N GLY A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 146 removed outlier: 4.015A pdb=" N ARG A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.991A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.676A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.834A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 342' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 409 removed outlier: 3.606A pdb=" N GLN A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 438 through 456 removed outlier: 3.603A pdb=" N VAL A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 502 through 525 removed outlier: 4.478A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 517 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 561 removed outlier: 5.271A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 602 Proline residue: A 593 - end of helix removed outlier: 3.559A pdb=" N ARG A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 746 through 770 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.660A pdb=" N ASP A 779 " --> pdb=" O ASP A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 removed outlier: 3.843A pdb=" N ASP A 789 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.980A pdb=" N ASN A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 838 " --> pdb=" O GLU A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 838' Processing helix chain 'A' and resid 843 through 866 removed outlier: 3.627A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.674A pdb=" N SER A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 938 removed outlier: 3.595A pdb=" N TYR A 934 " --> pdb=" O ASP A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1004 removed outlier: 3.689A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 removed outlier: 3.549A pdb=" N TRP A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1048 removed outlier: 3.537A pdb=" N TRP A1027 " --> pdb=" O GLY A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1075 Processing helix chain 'A' and resid 1079 through 1102 removed outlier: 4.105A pdb=" N VAL A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY A1091 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1106 removed outlier: 3.685A pdb=" N THR A1106 " --> pdb=" O ALA A1103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1103 through 1106' Processing helix chain 'A' and resid 1112 through 1138 removed outlier: 3.574A pdb=" N VAL A1116 " --> pdb=" O ASN A1112 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Proline residue: A1125 - end of helix Processing helix chain 'A' and resid 1139 through 1142 Processing helix chain 'A' and resid 1147 through 1175 removed outlier: 5.149A pdb=" N LEU A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Proline residue: A1172 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.674A pdb=" N ASN A 154 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 366 " --> pdb=" O ASN A 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 800 through 801 Processing sheet with id=AA4, first strand: chain 'A' and resid 972 through 975 407 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1341 1.33 - 1.45: 1835 1.45 - 1.58: 4234 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 7466 Sorted by residual: bond pdb=" N ILE A 342 " pdb=" CA ILE A 342 " ideal model delta sigma weight residual 1.456 1.504 -0.048 9.50e-03 1.11e+04 2.51e+01 bond pdb=" N VAL A 275 " pdb=" CA VAL A 275 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.04e-02 9.25e+03 2.05e+01 bond pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta sigma weight residual 1.455 1.484 -0.029 7.00e-03 2.04e+04 1.69e+01 bond pdb=" N ILE A 963 " pdb=" CA ILE A 963 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.00e-03 1.23e+04 1.43e+01 bond pdb=" N GLY A 214 " pdb=" CA GLY A 214 " ideal model delta sigma weight residual 1.446 1.486 -0.040 1.06e-02 8.90e+03 1.39e+01 ... (remaining 7461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 9789 3.82 - 7.64: 372 7.64 - 11.45: 8 11.45 - 15.27: 1 15.27 - 19.09: 2 Bond angle restraints: 10172 Sorted by residual: angle pdb=" N SER A 415 " pdb=" CA SER A 415 " pdb=" C SER A 415 " ideal model delta sigma weight residual 110.23 91.14 19.09 1.45e+00 4.76e-01 1.73e+02 angle pdb=" N LEU A 121 " pdb=" CA LEU A 121 " pdb=" C LEU A 121 " ideal model delta sigma weight residual 108.69 93.01 15.68 1.77e+00 3.19e-01 7.85e+01 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 112.45 101.16 11.29 1.39e+00 5.18e-01 6.60e+01 angle pdb=" C SER A 415 " pdb=" CA SER A 415 " pdb=" CB SER A 415 " ideal model delta sigma weight residual 109.72 122.46 -12.74 1.66e+00 3.63e-01 5.89e+01 angle pdb=" N PRO A 252 " pdb=" CA PRO A 252 " pdb=" CB PRO A 252 " ideal model delta sigma weight residual 103.08 110.31 -7.23 9.70e-01 1.06e+00 5.56e+01 ... (remaining 10167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 3801 17.04 - 34.07: 424 34.07 - 51.11: 88 51.11 - 68.14: 8 68.14 - 85.18: 4 Dihedral angle restraints: 4325 sinusoidal: 1525 harmonic: 2800 Sorted by residual: dihedral pdb=" CA SER A 313 " pdb=" C SER A 313 " pdb=" N THR A 314 " pdb=" CA THR A 314 " ideal model delta harmonic sigma weight residual -180.00 -144.14 -35.86 0 5.00e+00 4.00e-02 5.14e+01 dihedral pdb=" C ALA A 246 " pdb=" N ALA A 246 " pdb=" CA ALA A 246 " pdb=" CB ALA A 246 " ideal model delta harmonic sigma weight residual -122.60 -106.73 -15.87 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" CA HIS A 201 " pdb=" C HIS A 201 " pdb=" N LEU A 202 " pdb=" CA LEU A 202 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 4322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 1214 0.333 - 0.666: 2 0.666 - 0.999: 1 0.999 - 1.332: 0 1.332 - 1.665: 3 Chirality restraints: 1220 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.73 -1.67 2.00e-02 2.50e+03 6.93e+03 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 -0.96 -1.44 2.00e-02 2.50e+03 5.18e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-02 2.50e+03 4.53e+03 ... (remaining 1217 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1000 " -0.263 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" CG ASN A1000 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A1000 " 0.080 2.00e-02 2.50e+03 pdb=" ND2 ASN A1000 " 0.389 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 229 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ILE A 229 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE A 229 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A 230 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 156 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C GLN A 156 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN A 156 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 157 " 0.018 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 168 2.71 - 3.25: 7011 3.25 - 3.80: 11318 3.80 - 4.35: 14002 4.35 - 4.90: 23666 Nonbonded interactions: 56165 Sorted by model distance: nonbonded pdb=" ND2 ASN A 141 " pdb=" C1 NAG B 1 " model vdw 2.157 3.550 nonbonded pdb=" ND2 ASN A 414 " pdb=" O5 NAG D 1 " model vdw 2.322 3.120 nonbonded pdb=" ND2 ASN A 414 " pdb=" C2 NAG D 1 " model vdw 2.396 3.550 nonbonded pdb=" O GLY A1129 " pdb=" OG SER A1132 " model vdw 2.397 3.040 nonbonded pdb=" O SER A 799 " pdb=" OG SER A 799 " model vdw 2.399 3.040 ... (remaining 56160 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 'B' selection = chain 'C' selection = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 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 : 0.015 0.449 7471 Z= 1.129 Angle : 2.122 52.484 10187 Z= 1.431 Chirality : 0.112 1.665 1220 Planarity : 0.005 0.037 1278 Dihedral : 14.787 85.177 2517 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.33 % Favored : 89.56 % Rotamer: Outliers : 0.85 % Allowed : 12.36 % Favored : 86.79 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.22), residues: 958 helix: -1.66 (0.18), residues: 542 sheet: -2.05 (0.71), residues: 43 loop : -3.88 (0.26), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 995 TYR 0.029 0.003 TYR A1001 PHE 0.035 0.003 PHE A 757 TRP 0.021 0.003 TRP A 337 HIS 0.009 0.002 HIS A 950 Details of bonding type rmsd/Z covalent geometry : bond 0.01427 / 1.10 ( 7466) covalent geometry : angle 1.88166 / 1.39 (10172) hydrogen bonds : bond 0.14257 / 9.40 ( 407) hydrogen bonds : angle 7.80439 / 5.44 ( 1191) link_BETA1-4 : bond 0.07159 / 4.23 ( 4) link_BETA1-4 : angle 25.71556 / 15.36 ( 12) link_NAG-ASN : bond 0.44943 / 29.96 ( 1) link_NAG-ASN : angle 25.33300 / 17.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.7103 (t0) cc_final: 0.6897 (t0) REVERT: A 520 HIS cc_start: 0.7256 (t70) cc_final: 0.6121 (m-70) REVERT: A 979 ASN cc_start: 0.7621 (t0) cc_final: 0.6994 (t0) REVERT: A 1004 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7131 (tp) REVERT: A 1066 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6792 (mt-10) REVERT: A 1105 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6426 (pt) outliers start: 6 outliers final: 1 residues processed: 180 average time/residue: 0.0919 time to fit residues: 22.1282 Evaluate side-chains 119 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN A 124 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 312 ASN A 527 GLN A1166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.204307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178678 restraints weight = 10225.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.183211 restraints weight = 5999.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.185599 restraints weight = 3740.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.186166 restraints weight = 2760.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186720 restraints weight = 2643.132| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7471 Z= 0.148 Angle : 0.722 10.791 10187 Z= 0.358 Chirality : 0.044 0.340 1220 Planarity : 0.005 0.044 1278 Dihedral : 6.018 33.812 1030 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.70 % Allowed : 18.47 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.26), residues: 958 helix: -0.21 (0.21), residues: 559 sheet: -1.58 (0.76), residues: 43 loop : -3.19 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1114 TYR 0.011 0.002 TYR A 452 PHE 0.032 0.002 PHE A 798 TRP 0.010 0.001 TRP A 926 HIS 0.004 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 7466) covalent geometry : angle 0.71077 / 0.36 (10172) hydrogen bonds : bond 0.04507 / 2.82 ( 407) hydrogen bonds : angle 5.28137 / 3.72 ( 1191) link_BETA1-4 : bond 0.00524 / 0.36 ( 4) link_BETA1-4 : angle 2.30865 / 1.28 ( 12) link_NAG-ASN : bond 0.00746 / 0.50 ( 1) link_NAG-ASN : angle 6.14648 / 4.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3458 (tptt) cc_final: 0.2920 (mmtm) REVERT: A 154 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8617 (p0) REVERT: A 158 MET cc_start: 0.7954 (ttp) cc_final: 0.7569 (ttm) REVERT: A 602 ARG cc_start: 0.5006 (mmt180) cc_final: 0.3034 (ptp-170) REVERT: A 789 ASP cc_start: 0.6600 (m-30) cc_final: 0.6148 (m-30) outliers start: 19 outliers final: 8 residues processed: 147 average time/residue: 0.0642 time to fit residues: 13.6038 Evaluate side-chains 123 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 1117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 361 GLN A 375 HIS A 520 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.203706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177566 restraints weight = 10417.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.181931 restraints weight = 6448.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.184047 restraints weight = 4116.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.185442 restraints weight = 3105.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185917 restraints weight = 3020.070| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7471 Z= 0.135 Angle : 0.650 9.696 10187 Z= 0.323 Chirality : 0.043 0.346 1220 Planarity : 0.005 0.051 1278 Dihedral : 5.315 18.355 1025 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.41 % Allowed : 22.02 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.27), residues: 958 helix: 0.19 (0.21), residues: 566 sheet: -1.45 (0.79), residues: 43 loop : -3.04 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.016 0.001 TYR A 452 PHE 0.035 0.002 PHE A 798 TRP 0.010 0.001 TRP A 863 HIS 0.015 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7466) covalent geometry : angle 0.63712 / 0.32 (10172) hydrogen bonds : bond 0.04005 / 2.51 ( 407) hydrogen bonds : angle 5.00659 / 3.56 ( 1191) link_BETA1-4 : bond 0.00555 / 0.36 ( 4) link_BETA1-4 : angle 1.92136 / 0.99 ( 12) link_NAG-ASN : bond 0.01562 / 1.04 ( 1) link_NAG-ASN : angle 6.47687 / 5.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3317 (tptt) cc_final: 0.3006 (mmtm) REVERT: A 158 MET cc_start: 0.7956 (ttp) cc_final: 0.7519 (ttm) REVERT: A 602 ARG cc_start: 0.4603 (mmt180) cc_final: 0.2918 (ptp-170) REVERT: A 789 ASP cc_start: 0.6816 (m-30) cc_final: 0.6484 (m-30) outliers start: 24 outliers final: 12 residues processed: 134 average time/residue: 0.0698 time to fit residues: 13.5740 Evaluate side-chains 125 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 0.0470 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 520 HIS A 929 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.201927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.177098 restraints weight = 10984.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.179705 restraints weight = 7103.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.181553 restraints weight = 4973.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.182600 restraints weight = 3999.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.182954 restraints weight = 3427.905| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7471 Z= 0.123 Angle : 0.620 8.885 10187 Z= 0.305 Chirality : 0.041 0.324 1220 Planarity : 0.004 0.051 1278 Dihedral : 5.035 17.850 1025 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.69 % Allowed : 23.58 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.27), residues: 958 helix: 0.47 (0.22), residues: 568 sheet: -1.14 (0.81), residues: 43 loop : -2.85 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.019 0.001 TYR A 452 PHE 0.032 0.002 PHE A 798 TRP 0.009 0.001 TRP A 863 HIS 0.011 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7466) covalent geometry : angle 0.60765 / 0.30 (10172) hydrogen bonds : bond 0.03685 / 2.30 ( 407) hydrogen bonds : angle 4.80813 / 3.43 ( 1191) link_BETA1-4 : bond 0.00485 / 0.31 ( 4) link_BETA1-4 : angle 1.78260 / 0.95 ( 12) link_NAG-ASN : bond 0.01448 / 0.97 ( 1) link_NAG-ASN : angle 6.26469 / 4.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.3482 (tptt) cc_final: 0.3207 (mmtm) REVERT: A 158 MET cc_start: 0.7892 (ttp) cc_final: 0.7565 (ttm) REVERT: A 372 MET cc_start: 0.8577 (tpp) cc_final: 0.8116 (ttm) REVERT: A 602 ARG cc_start: 0.4560 (mmt180) cc_final: 0.2872 (ptp-170) REVERT: A 789 ASP cc_start: 0.6727 (m-30) cc_final: 0.6459 (m-30) outliers start: 26 outliers final: 19 residues processed: 137 average time/residue: 0.0669 time to fit residues: 13.2127 Evaluate side-chains 132 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 70 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.201914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178093 restraints weight = 10890.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.180786 restraints weight = 6835.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.183305 restraints weight = 4688.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183870 restraints weight = 3637.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.184477 restraints weight = 3187.407| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7471 Z= 0.120 Angle : 0.614 8.544 10187 Z= 0.302 Chirality : 0.041 0.314 1220 Planarity : 0.005 0.068 1278 Dihedral : 4.849 20.783 1025 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.98 % Allowed : 23.58 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.27), residues: 958 helix: 0.53 (0.22), residues: 577 sheet: -0.88 (0.83), residues: 45 loop : -2.81 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.020 0.001 TYR A 452 PHE 0.021 0.001 PHE A 798 TRP 0.009 0.001 TRP A 863 HIS 0.011 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7466) covalent geometry : angle 0.60315 / 0.30 (10172) hydrogen bonds : bond 0.03521 / 2.18 ( 407) hydrogen bonds : angle 4.69078 / 3.35 ( 1191) link_BETA1-4 : bond 0.00459 / 0.30 ( 4) link_BETA1-4 : angle 1.60394 / 0.86 ( 12) link_NAG-ASN : bond 0.01429 / 0.95 ( 1) link_NAG-ASN : angle 6.06038 / 4.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.7900 (ttp) cc_final: 0.7556 (ttm) REVERT: A 602 ARG cc_start: 0.4534 (mmt180) cc_final: 0.2832 (ptp-170) REVERT: A 789 ASP cc_start: 0.6576 (m-30) cc_final: 0.6332 (m-30) outliers start: 28 outliers final: 19 residues processed: 139 average time/residue: 0.0699 time to fit residues: 13.8842 Evaluate side-chains 131 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 90 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.200949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178228 restraints weight = 10581.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.180943 restraints weight = 6213.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.183231 restraints weight = 4253.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.183753 restraints weight = 3264.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.185263 restraints weight = 2942.508| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7471 Z= 0.115 Angle : 0.603 8.264 10187 Z= 0.297 Chirality : 0.041 0.305 1220 Planarity : 0.004 0.052 1278 Dihedral : 4.718 20.087 1025 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.98 % Allowed : 25.00 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.27), residues: 958 helix: 0.70 (0.22), residues: 575 sheet: -0.65 (0.84), residues: 45 loop : -2.77 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.021 0.001 TYR A 452 PHE 0.020 0.001 PHE A 798 TRP 0.009 0.001 TRP A 863 HIS 0.010 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7466) covalent geometry : angle 0.59228 / 0.29 (10172) hydrogen bonds : bond 0.03429 / 2.13 ( 407) hydrogen bonds : angle 4.59001 / 3.27 ( 1191) link_BETA1-4 : bond 0.00433 / 0.28 ( 4) link_BETA1-4 : angle 1.58864 / 0.87 ( 12) link_NAG-ASN : bond 0.01321 / 0.88 ( 1) link_NAG-ASN : angle 5.90039 / 4.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 372 MET cc_start: 0.8510 (tpp) cc_final: 0.8029 (ttm) REVERT: A 373 TYR cc_start: 0.6949 (t80) cc_final: 0.6007 (t80) REVERT: A 602 ARG cc_start: 0.4544 (mmt180) cc_final: 0.2828 (ptp-170) REVERT: A 789 ASP cc_start: 0.6526 (m-30) cc_final: 0.6299 (m-30) REVERT: A 1166 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7423 (t0) outliers start: 28 outliers final: 23 residues processed: 131 average time/residue: 0.0694 time to fit residues: 13.2795 Evaluate side-chains 131 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1166 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.0010 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.0670 overall best weight: 0.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.202399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178481 restraints weight = 10859.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.182419 restraints weight = 6448.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.183457 restraints weight = 4509.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184489 restraints weight = 3529.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.186035 restraints weight = 3182.324| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7471 Z= 0.119 Angle : 0.630 8.655 10187 Z= 0.307 Chirality : 0.042 0.367 1220 Planarity : 0.004 0.051 1278 Dihedral : 4.624 18.272 1025 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.55 % Allowed : 24.57 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.27), residues: 958 helix: 0.77 (0.22), residues: 579 sheet: -0.53 (0.84), residues: 45 loop : -2.74 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.019 0.001 TYR A 452 PHE 0.019 0.001 PHE A 798 TRP 0.025 0.001 TRP A 948 HIS 0.010 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7466) covalent geometry : angle 0.62048 / 0.30 (10172) hydrogen bonds : bond 0.03380 / 2.09 ( 407) hydrogen bonds : angle 4.52843 / 3.22 ( 1191) link_BETA1-4 : bond 0.00397 / 0.26 ( 4) link_BETA1-4 : angle 1.55020 / 0.85 ( 12) link_NAG-ASN : bond 0.01296 / 0.86 ( 1) link_NAG-ASN : angle 5.84828 / 4.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8586 (mp10) cc_final: 0.8371 (mp10) REVERT: A 158 MET cc_start: 0.7813 (ttp) cc_final: 0.7434 (ttm) REVERT: A 372 MET cc_start: 0.8479 (tpp) cc_final: 0.8104 (ttm) REVERT: A 373 TYR cc_start: 0.6984 (t80) cc_final: 0.5966 (t80) REVERT: A 602 ARG cc_start: 0.4505 (mmt180) cc_final: 0.2700 (ptp-170) REVERT: A 1166 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7449 (t0) outliers start: 32 outliers final: 28 residues processed: 132 average time/residue: 0.0547 time to fit residues: 10.6929 Evaluate side-chains 134 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1166 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A 802 ASN A1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.197485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174291 restraints weight = 10756.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177674 restraints weight = 6417.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.180365 restraints weight = 4224.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.180552 restraints weight = 3107.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.181023 restraints weight = 2877.573| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7471 Z= 0.154 Angle : 0.680 10.327 10187 Z= 0.326 Chirality : 0.043 0.325 1220 Planarity : 0.005 0.053 1278 Dihedral : 4.759 17.059 1025 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.69 % Allowed : 25.28 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.27), residues: 958 helix: 0.67 (0.22), residues: 580 sheet: -0.33 (0.84), residues: 45 loop : -2.76 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.019 0.001 TYR A 452 PHE 0.017 0.002 PHE A 798 TRP 0.014 0.001 TRP A 948 HIS 0.010 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7466) covalent geometry : angle 0.67054 / 0.32 (10172) hydrogen bonds : bond 0.03555 / 2.21 ( 407) hydrogen bonds : angle 4.57502 / 3.25 ( 1191) link_BETA1-4 : bond 0.00488 / 0.32 ( 4) link_BETA1-4 : angle 1.62948 / 0.91 ( 12) link_NAG-ASN : bond 0.01234 / 0.82 ( 1) link_NAG-ASN : angle 5.86083 / 4.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8697 (mp10) cc_final: 0.8465 (mp10) REVERT: A 158 MET cc_start: 0.7959 (ttp) cc_final: 0.7571 (ttm) REVERT: A 365 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: A 373 TYR cc_start: 0.6911 (t80) cc_final: 0.5991 (t80) REVERT: A 602 ARG cc_start: 0.4694 (mmt180) cc_final: 0.2895 (ptp-170) outliers start: 33 outliers final: 27 residues processed: 125 average time/residue: 0.0640 time to fit residues: 11.7059 Evaluate side-chains 127 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A 802 ASN A1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.199165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.176147 restraints weight = 10573.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.179348 restraints weight = 6356.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.182341 restraints weight = 4199.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.182545 restraints weight = 3000.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182908 restraints weight = 2788.413| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7471 Z= 0.125 Angle : 0.657 11.234 10187 Z= 0.315 Chirality : 0.042 0.305 1220 Planarity : 0.004 0.051 1278 Dihedral : 4.688 17.008 1025 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.55 % Allowed : 25.14 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.28), residues: 958 helix: 0.80 (0.22), residues: 580 sheet: -0.27 (0.83), residues: 45 loop : -2.72 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.021 0.001 TYR A 452 PHE 0.017 0.001 PHE A 798 TRP 0.019 0.001 TRP A1027 HIS 0.010 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7466) covalent geometry : angle 0.64784 / 0.31 (10172) hydrogen bonds : bond 0.03391 / 2.11 ( 407) hydrogen bonds : angle 4.52290 / 3.21 ( 1191) link_BETA1-4 : bond 0.00396 / 0.26 ( 4) link_BETA1-4 : angle 1.53958 / 0.86 ( 12) link_NAG-ASN : bond 0.01267 / 0.84 ( 1) link_NAG-ASN : angle 5.79708 / 4.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.7916 (ttp) cc_final: 0.7518 (ttm) REVERT: A 365 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8432 (mp10) REVERT: A 373 TYR cc_start: 0.6880 (t80) cc_final: 0.5972 (t80) REVERT: A 602 ARG cc_start: 0.4542 (mmt180) cc_final: 0.2817 (ptp-170) outliers start: 32 outliers final: 28 residues processed: 126 average time/residue: 0.0573 time to fit residues: 10.6035 Evaluate side-chains 127 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1122 MET Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A 802 ASN A1166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.197437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.173684 restraints weight = 10930.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176884 restraints weight = 7099.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.178283 restraints weight = 4957.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178977 restraints weight = 3637.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.179970 restraints weight = 3392.982| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7471 Z= 0.169 Angle : 0.703 11.908 10187 Z= 0.341 Chirality : 0.044 0.327 1220 Planarity : 0.005 0.052 1278 Dihedral : 4.797 17.256 1025 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.26 % Allowed : 25.99 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.27), residues: 958 helix: 0.75 (0.21), residues: 580 sheet: -0.12 (0.86), residues: 42 loop : -2.77 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.020 0.001 TYR A 452 PHE 0.018 0.002 PHE A 798 TRP 0.074 0.003 TRP A 948 HIS 0.011 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 7466) covalent geometry : angle 0.69415 / 0.34 (10172) hydrogen bonds : bond 0.03530 / 2.21 ( 407) hydrogen bonds : angle 4.56305 / 3.23 ( 1191) link_BETA1-4 : bond 0.00387 / 0.25 ( 4) link_BETA1-4 : angle 1.57757 / 0.90 ( 12) link_NAG-ASN : bond 0.01238 / 0.83 ( 1) link_NAG-ASN : angle 5.84135 / 4.65 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.7955 (ttp) cc_final: 0.7570 (ttm) REVERT: A 365 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: A 373 TYR cc_start: 0.6704 (t80) cc_final: 0.5894 (t80) REVERT: A 602 ARG cc_start: 0.4454 (mmt180) cc_final: 0.2741 (ptp-170) outliers start: 30 outliers final: 27 residues processed: 123 average time/residue: 0.0647 time to fit residues: 11.6895 Evaluate side-chains 129 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1121 HIS Chi-restraints excluded: chain A residue 1122 MET Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.0060 chunk 23 optimal weight: 0.0270 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.197750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174433 restraints weight = 10926.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177819 restraints weight = 6691.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178553 restraints weight = 4737.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179635 restraints weight = 3845.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.179931 restraints weight = 3248.070| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7471 Z= 0.142 Angle : 0.681 11.093 10187 Z= 0.330 Chirality : 0.043 0.313 1220 Planarity : 0.005 0.052 1278 Dihedral : 4.755 17.431 1025 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.55 % Allowed : 25.28 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.27), residues: 958 helix: 0.75 (0.22), residues: 576 sheet: -0.15 (0.84), residues: 43 loop : -2.73 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.020 0.001 TYR A 452 PHE 0.016 0.001 PHE A 798 TRP 0.052 0.002 TRP A 948 HIS 0.011 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7466) covalent geometry : angle 0.67240 / 0.33 (10172) hydrogen bonds : bond 0.03505 / 2.16 ( 407) hydrogen bonds : angle 4.55869 / 3.23 ( 1191) link_BETA1-4 : bond 0.00391 / 0.26 ( 4) link_BETA1-4 : angle 1.56040 / 0.88 ( 12) link_NAG-ASN : bond 0.01240 / 0.83 ( 1) link_NAG-ASN : angle 5.80874 / 4.60 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.94 seconds wall clock time: 21 minutes 41.70 seconds (1301.70 seconds total)