Starting phenix.real_space_refine on Mon Sep 14 16:16:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kox_22983/09_2026/7kox_22983_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kox_22983/09_2026/7kox_22983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kox_22983/09_2026/7kox_22983_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kox_22983/09_2026/7kox_22983_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kox_22983/09_2026/7kox_22983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kox_22983/09_2026/7kox_22983.map" } resolution = 2.7 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= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 S 110 5.16 5 Cl 5 4.86 5 C 10390 2.51 5 N 2535 2.21 5 O 2895 1.98 5 H 15410 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 31350 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 6198 Classifications: {'peptide': 386} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 365} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 8.24, per 1000 atoms: 0.26 Number of scatterers: 31350 At special positions: 0 Unit cell: (95.45, 97.11, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 Cl 5 17.00 S 110 16.00 O 2895 8.00 N 2535 7.00 C 10390 6.00 H 15410 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.05 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.05 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.05 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.05 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 23 " " NAG B 501 " - " ASN B 67 " " NAG B 502 " - " ASN B 23 " " NAG C 501 " - " ASN C 67 " " NAG C 502 " - " ASN C 23 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 23 " " NAG E 501 " - " ASN E 67 " " NAG E 502 " - " ASN E 23 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN B 110 " " NAG H 1 " - " ASN C 110 " " NAG I 1 " - " ASN D 110 " " NAG J 1 " - " ASN E 110 " Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 882.6 milliseconds 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 43.6% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.618A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 4.102A pdb=" N ILE A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 231 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.694A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 294 Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.704A pdb=" N ALA A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 465 removed outlier: 3.808A pdb=" N PHE A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.593A pdb=" N ALA A 473 " --> pdb=" O ASN A 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.618A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.102A pdb=" N ILE B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 231 Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.694A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 294 Processing helix chain 'B' and resid 305 through 320 Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.703A pdb=" N ALA B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 465 removed outlier: 3.808A pdb=" N PHE B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.593A pdb=" N ALA B 473 " --> pdb=" O ASN B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.617A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.101A pdb=" N ILE C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 231 Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.694A pdb=" N ILE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 294 Processing helix chain 'C' and resid 305 through 320 Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.704A pdb=" N ALA C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 465 removed outlier: 3.808A pdb=" N PHE C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.593A pdb=" N ALA C 473 " --> pdb=" O ASN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.617A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 4.102A pdb=" N ILE D 84 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 231 Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.694A pdb=" N ILE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 294 Processing helix chain 'D' and resid 305 through 320 Processing helix chain 'D' and resid 414 through 432 removed outlier: 3.704A pdb=" N ALA D 432 " --> pdb=" O ASP D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 465 removed outlier: 3.808A pdb=" N PHE D 439 " --> pdb=" O SER D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.593A pdb=" N ALA D 473 " --> pdb=" O ASN D 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.618A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.102A pdb=" N ILE E 84 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 231 Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.693A pdb=" N ILE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 294 Processing helix chain 'E' and resid 305 through 320 Processing helix chain 'E' and resid 414 through 432 removed outlier: 3.703A pdb=" N ALA E 432 " --> pdb=" O ASP E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 465 removed outlier: 3.808A pdb=" N PHE E 439 " --> pdb=" O SER E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.593A pdb=" N ALA E 473 " --> pdb=" O ASN E 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.977A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.977A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.817A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.976A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.976A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.816A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.976A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.976A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.817A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.977A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.977A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR D 29 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.817A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.977A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.977A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR E 29 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 6.817A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 946 hydrogen bonds defined for protein. 2778 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: 9.38 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15370 1.03 - 1.24: 1921 1.24 - 1.44: 5304 1.44 - 1.65: 9025 1.65 - 1.85: 165 Bond restraints: 31785 Sorted by residual: bond pdb=" CB MET B 304 " pdb=" CG MET B 304 " ideal model delta sigma weight residual 1.520 1.411 0.109 3.00e-02 1.11e+03 1.32e+01 bond pdb=" CB MET D 304 " pdb=" CG MET D 304 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.31e+01 bond pdb=" CB MET C 304 " pdb=" CG MET C 304 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.30e+01 bond pdb=" CB MET A 304 " pdb=" CG MET A 304 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.30e+01 bond pdb=" CB MET E 304 " pdb=" CG MET E 304 " ideal model delta sigma weight residual 1.520 1.413 0.107 3.00e-02 1.11e+03 1.28e+01 ... (remaining 31780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.60: 56990 6.60 - 13.20: 140 13.20 - 19.80: 20 19.80 - 26.39: 130 26.39 - 32.99: 30 Bond angle restraints: 57310 Sorted by residual: angle pdb=" CG LEU A 254 " pdb=" CD1 LEU A 254 " pdb="HD12 LEU A 254 " ideal model delta sigma weight residual 109.00 76.01 32.99 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CG LEU D 254 " pdb=" CD1 LEU D 254 " pdb="HD12 LEU D 254 " ideal model delta sigma weight residual 109.00 76.03 32.97 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CG LEU C 254 " pdb=" CD1 LEU C 254 " pdb="HD12 LEU C 254 " ideal model delta sigma weight residual 109.00 76.03 32.97 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CG LEU E 254 " pdb=" CD1 LEU E 254 " pdb="HD12 LEU E 254 " ideal model delta sigma weight residual 109.00 76.03 32.97 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CG LEU B 254 " pdb=" CD1 LEU B 254 " pdb="HD12 LEU B 254 " ideal model delta sigma weight residual 109.00 76.05 32.95 3.00e+00 1.11e-01 1.21e+02 ... (remaining 57305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 13665 15.66 - 31.31: 1260 31.31 - 46.97: 310 46.97 - 62.63: 170 62.63 - 78.29: 20 Dihedral angle restraints: 15425 sinusoidal: 8410 harmonic: 7015 Sorted by residual: dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 33.07 59.93 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS E 127 " pdb=" SG CYS E 127 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual 93.00 33.07 59.93 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 33.08 59.92 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 15422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.568: 2535 0.568 - 1.135: 0 1.135 - 1.703: 15 1.703 - 2.270: 15 2.270 - 2.838: 5 Chirality restraints: 2570 Sorted by residual: chirality pdb=" CG LEU E 249 " pdb=" CB LEU E 249 " pdb=" CD1 LEU E 249 " pdb=" CD2 LEU E 249 " both_signs ideal model delta sigma weight residual False -2.59 0.25 -2.84 2.00e-01 2.50e+01 2.01e+02 chirality pdb=" CG LEU B 249 " pdb=" CB LEU B 249 " pdb=" CD1 LEU B 249 " pdb=" CD2 LEU B 249 " both_signs ideal model delta sigma weight residual False -2.59 0.25 -2.84 2.00e-01 2.50e+01 2.01e+02 chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 0.24 -2.83 2.00e-01 2.50e+01 2.01e+02 ... (remaining 2567 not shown) Planarity restraints: 4575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 213 " -0.013 2.00e-02 2.50e+03 4.14e-02 2.57e+01 pdb=" CG ASN B 213 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN B 213 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN B 213 " 0.048 2.00e-02 2.50e+03 pdb="HD21 ASN B 213 " 0.027 2.00e-02 2.50e+03 pdb="HD22 ASN B 213 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 213 " -0.014 2.00e-02 2.50e+03 4.12e-02 2.55e+01 pdb=" CG ASN C 213 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 213 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN C 213 " 0.047 2.00e-02 2.50e+03 pdb="HD21 ASN C 213 " 0.027 2.00e-02 2.50e+03 pdb="HD22 ASN C 213 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 213 " 0.013 2.00e-02 2.50e+03 4.12e-02 2.55e+01 pdb=" CG ASN E 213 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN E 213 " -0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN E 213 " -0.047 2.00e-02 2.50e+03 pdb="HD21 ASN E 213 " -0.027 2.00e-02 2.50e+03 pdb="HD22 ASN E 213 " 0.051 2.00e-02 2.50e+03 ... (remaining 4572 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 573 2.09 - 2.72: 51854 2.72 - 3.35: 87715 3.35 - 3.97: 113260 3.97 - 4.60: 177252 Nonbonded interactions: 430654 Sorted by model distance: nonbonded pdb=" HG SER C 183 " pdb=" OD1 ASP C 196 " model vdw 1.468 2.450 nonbonded pdb=" HG SER B 183 " pdb=" OD1 ASP B 196 " model vdw 1.469 2.450 nonbonded pdb=" HG SER E 183 " pdb=" OD1 ASP E 196 " model vdw 1.469 2.450 nonbonded pdb=" HG SER D 183 " pdb=" OD1 ASP D 196 " model vdw 1.469 2.450 nonbonded pdb=" HG SER A 183 " pdb=" OD1 ASP A 196 " model vdw 1.469 2.450 ... (remaining 430649 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 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: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 34.830 Find NCS groups from input model: 0.300 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:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 0.117 16405 Z= 0.428 Angle : 1.138 13.431 22405 Z= 0.662 Chirality : 0.228 2.838 2570 Planarity : 0.005 0.047 2745 Dihedral : 13.587 75.109 6250 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.57 % Allowed : 1.15 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.69 (0.18), residues: 1910 helix: 0.55 (0.17), residues: 815 sheet: -1.10 (0.25), residues: 390 loop : -1.13 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 132 TYR 0.037 0.002 TYR C 210 PHE 0.041 0.002 PHE C 252 TRP 0.008 0.001 TRP D 315 HIS 0.003 0.001 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.43 (16375) covalent geometry : angle 1.12090 / 0.66 (22325) SS BOND : bond 0.01227 / 0.68 ( 10) SS BOND : angle 4.45262 / 2.79 ( 20) hydrogen bonds : bond 0.12569 / 8.02 ( 841) hydrogen bonds : angle 6.34621 / 4.37 ( 2778) link_BETA1-4 : bond 0.00030 / 0.01 ( 5) link_BETA1-4 : angle 0.92037 / 0.59 ( 15) link_NAG-ASN : bond 0.00306 / 0.16 ( 15) link_NAG-ASN : angle 3.52672 / 2.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 CYS cc_start: 0.6906 (m) cc_final: 0.6502 (m) REVERT: D 448 CYS cc_start: 0.6832 (m) cc_final: 0.6450 (m) REVERT: E 97 GLU cc_start: 0.7822 (pp20) cc_final: 0.7603 (pp20) outliers start: 10 outliers final: 9 residues processed: 194 average time/residue: 0.7165 time to fit residues: 167.3186 Evaluate side-chains 148 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.145403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087821 restraints weight = 63915.607| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.39 r_work: 0.2950 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16405 Z= 0.157 Angle : 0.800 11.814 22405 Z= 0.370 Chirality : 0.186 1.770 2570 Planarity : 0.004 0.047 2745 Dihedral : 7.110 56.316 2614 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.72 % Allowed : 6.19 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.06 (0.19), residues: 1910 helix: 1.20 (0.18), residues: 820 sheet: -0.85 (0.24), residues: 405 loop : -0.95 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 132 TYR 0.009 0.001 TYR A 209 PHE 0.029 0.002 PHE C 252 TRP 0.006 0.001 TRP B 59 HIS 0.003 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (16375) covalent geometry : angle 0.79139 / 0.37 (22325) SS BOND : bond 0.00877 / 0.48 ( 10) SS BOND : angle 1.94229 / 1.24 ( 20) hydrogen bonds : bond 0.04452 / 2.87 ( 841) hydrogen bonds : angle 5.05656 / 3.48 ( 2778) link_BETA1-4 : bond 0.00083 / 0.04 ( 5) link_BETA1-4 : angle 1.25229 / 0.78 ( 15) link_NAG-ASN : bond 0.00126 / 0.07 ( 15) link_NAG-ASN : angle 2.45732 / 1.59 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ILE cc_start: 0.6556 (mm) cc_final: 0.6339 (mm) REVERT: B 174 ASP cc_start: 0.8354 (t70) cc_final: 0.7886 (t0) REVERT: C 174 ASP cc_start: 0.8330 (t70) cc_final: 0.7908 (t0) REVERT: C 213 ASN cc_start: 0.7939 (t0) cc_final: 0.7538 (t0) REVERT: C 448 CYS cc_start: 0.6382 (m) cc_final: 0.6160 (m) REVERT: D 174 ASP cc_start: 0.8348 (t70) cc_final: 0.7889 (t0) REVERT: E 213 ASN cc_start: 0.7907 (t0) cc_final: 0.7674 (t0) REVERT: E 448 CYS cc_start: 0.6887 (m) cc_final: 0.6609 (m) outliers start: 30 outliers final: 9 residues processed: 172 average time/residue: 0.6320 time to fit residues: 133.8776 Evaluate side-chains 145 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.141610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.082432 restraints weight = 63879.096| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.40 r_work: 0.2845 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16405 Z= 0.257 Angle : 0.802 12.185 22405 Z= 0.371 Chirality : 0.186 1.752 2570 Planarity : 0.004 0.048 2745 Dihedral : 7.065 53.576 2614 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.49 % Allowed : 7.11 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.20 (0.19), residues: 1910 helix: 1.57 (0.18), residues: 820 sheet: -0.90 (0.24), residues: 405 loop : -0.90 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.009 0.001 TYR C 209 PHE 0.023 0.002 PHE A 252 TRP 0.020 0.001 TRP B 437 HIS 0.014 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (16375) covalent geometry : angle 0.79240 / 0.37 (22325) SS BOND : bond 0.00911 / 0.50 ( 10) SS BOND : angle 2.30664 / 1.46 ( 20) hydrogen bonds : bond 0.03722 / 2.40 ( 841) hydrogen bonds : angle 4.70240 / 3.24 ( 2778) link_BETA1-4 : bond 0.00287 / 0.14 ( 5) link_BETA1-4 : angle 1.47039 / 0.92 ( 15) link_NAG-ASN : bond 0.00360 / 0.20 ( 15) link_NAG-ASN : angle 2.38005 / 1.50 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8526 (tt) cc_final: 0.8250 (tm) REVERT: B 212 LEU cc_start: 0.8591 (tt) cc_final: 0.8313 (tm) REVERT: C 174 ASP cc_start: 0.8452 (t70) cc_final: 0.7912 (t0) REVERT: C 212 LEU cc_start: 0.8605 (tt) cc_final: 0.8360 (tm) REVERT: D 188 GLU cc_start: 0.8295 (tp30) cc_final: 0.7756 (tt0) REVERT: D 212 LEU cc_start: 0.8551 (tt) cc_final: 0.8223 (tm) REVERT: D 252 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6476 (t80) REVERT: E 212 LEU cc_start: 0.8602 (tt) cc_final: 0.8339 (tm) outliers start: 26 outliers final: 14 residues processed: 148 average time/residue: 0.6574 time to fit residues: 119.6995 Evaluate side-chains 141 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 53 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 171 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.142217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.084050 restraints weight = 63655.608| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.39 r_work: 0.2840 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16405 Z= 0.155 Angle : 0.761 11.758 22405 Z= 0.347 Chirality : 0.184 1.741 2570 Planarity : 0.004 0.045 2745 Dihedral : 6.787 51.848 2614 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.49 % Allowed : 8.31 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.47 (0.19), residues: 1910 helix: 1.78 (0.18), residues: 820 sheet: -0.73 (0.24), residues: 405 loop : -0.77 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 205 TYR 0.009 0.001 TYR D 14 PHE 0.013 0.001 PHE C 252 TRP 0.008 0.001 TRP B 437 HIS 0.006 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (16375) covalent geometry : angle 0.75259 / 0.34 (22325) SS BOND : bond 0.00844 / 0.46 ( 10) SS BOND : angle 1.91719 / 1.23 ( 20) hydrogen bonds : bond 0.03193 / 2.08 ( 841) hydrogen bonds : angle 4.48932 / 3.09 ( 2778) link_BETA1-4 : bond 0.00067 / 0.04 ( 5) link_BETA1-4 : angle 1.28220 / 0.78 ( 15) link_NAG-ASN : bond 0.00092 / 0.05 ( 15) link_NAG-ASN : angle 2.32336 / 1.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8572 (tt) cc_final: 0.8355 (tm) REVERT: A 229 PHE cc_start: 0.7001 (m-10) cc_final: 0.6784 (m-80) REVERT: B 212 LEU cc_start: 0.8605 (tt) cc_final: 0.8397 (tm) REVERT: C 174 ASP cc_start: 0.8429 (t70) cc_final: 0.7946 (t0) REVERT: C 278 MET cc_start: 0.7531 (ttm) cc_final: 0.7297 (ttm) REVERT: C 448 CYS cc_start: 0.7266 (m) cc_final: 0.6996 (t) REVERT: D 212 LEU cc_start: 0.8561 (tt) cc_final: 0.8338 (tm) REVERT: D 252 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6434 (t80) REVERT: E 212 LEU cc_start: 0.8652 (tt) cc_final: 0.8426 (tm) outliers start: 26 outliers final: 16 residues processed: 148 average time/residue: 0.6822 time to fit residues: 122.4621 Evaluate side-chains 147 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.081289 restraints weight = 64146.061| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.38 r_work: 0.2806 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16405 Z= 0.300 Angle : 0.803 11.781 22405 Z= 0.373 Chirality : 0.185 1.731 2570 Planarity : 0.004 0.046 2745 Dihedral : 7.058 54.956 2614 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.55 % Allowed : 9.00 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.55 (0.19), residues: 1910 helix: 2.04 (0.18), residues: 790 sheet: -0.75 (0.23), residues: 430 loop : -0.82 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 205 TYR 0.010 0.001 TYR A 210 PHE 0.018 0.001 PHE D 99 TRP 0.020 0.001 TRP E 437 HIS 0.008 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.30 (16375) covalent geometry : angle 0.79308 / 0.37 (22325) SS BOND : bond 0.00835 / 0.46 ( 10) SS BOND : angle 2.32673 / 1.47 ( 20) hydrogen bonds : bond 0.03343 / 2.18 ( 841) hydrogen bonds : angle 4.47186 / 3.09 ( 2778) link_BETA1-4 : bond 0.00270 / 0.14 ( 5) link_BETA1-4 : angle 1.57158 / 0.97 ( 15) link_NAG-ASN : bond 0.00483 / 0.28 ( 15) link_NAG-ASN : angle 2.37510 / 1.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.7173 (m-10) cc_final: 0.6936 (m-80) REVERT: C 229 PHE cc_start: 0.7255 (m-10) cc_final: 0.6746 (m-10) REVERT: C 448 CYS cc_start: 0.7253 (m) cc_final: 0.7041 (t) REVERT: D 252 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6620 (t80) outliers start: 27 outliers final: 23 residues processed: 160 average time/residue: 0.6996 time to fit residues: 135.9202 Evaluate side-chains 144 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 88 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 97 optimal weight: 0.0570 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.141291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082761 restraints weight = 63384.120| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.38 r_work: 0.2819 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16405 Z= 0.168 Angle : 0.775 11.699 22405 Z= 0.355 Chirality : 0.183 1.735 2570 Planarity : 0.004 0.045 2745 Dihedral : 6.801 53.814 2613 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.66 % Allowed : 10.03 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.59 (0.19), residues: 1910 helix: 1.87 (0.18), residues: 820 sheet: -0.64 (0.24), residues: 405 loop : -0.71 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.010 0.001 TYR D 14 PHE 0.011 0.001 PHE A 99 TRP 0.015 0.001 TRP C 437 HIS 0.008 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (16375) covalent geometry : angle 0.76671 / 0.35 (22325) SS BOND : bond 0.00850 / 0.46 ( 10) SS BOND : angle 1.94608 / 1.24 ( 20) hydrogen bonds : bond 0.03100 / 2.02 ( 841) hydrogen bonds : angle 4.39591 / 3.04 ( 2778) link_BETA1-4 : bond 0.00060 / 0.03 ( 5) link_BETA1-4 : angle 1.42912 / 0.87 ( 15) link_NAG-ASN : bond 0.00158 / 0.09 ( 15) link_NAG-ASN : angle 2.29046 / 1.42 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.7054 (m-80) cc_final: 0.6836 (m-80) REVERT: C 174 ASP cc_start: 0.8439 (t70) cc_final: 0.7945 (t0) REVERT: C 229 PHE cc_start: 0.7178 (m-10) cc_final: 0.6561 (m-10) REVERT: D 252 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6548 (t80) outliers start: 29 outliers final: 21 residues processed: 143 average time/residue: 0.7284 time to fit residues: 125.9314 Evaluate side-chains 145 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.082013 restraints weight = 63823.215| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.38 r_work: 0.2807 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16405 Z= 0.198 Angle : 0.774 11.679 22405 Z= 0.354 Chirality : 0.184 1.723 2570 Planarity : 0.004 0.044 2745 Dihedral : 6.698 54.753 2613 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.38 % Allowed : 10.72 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.74 (0.19), residues: 1910 helix: 2.19 (0.18), residues: 790 sheet: -0.66 (0.23), residues: 430 loop : -0.69 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.009 0.001 TYR A 14 PHE 0.013 0.001 PHE A 99 TRP 0.010 0.001 TRP B 437 HIS 0.006 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (16375) covalent geometry : angle 0.76541 / 0.35 (22325) SS BOND : bond 0.00869 / 0.48 ( 10) SS BOND : angle 2.06907 / 1.31 ( 20) hydrogen bonds : bond 0.03044 / 1.97 ( 841) hydrogen bonds : angle 4.28936 / 2.96 ( 2778) link_BETA1-4 : bond 0.00043 / 0.02 ( 5) link_BETA1-4 : angle 1.55061 / 0.94 ( 15) link_NAG-ASN : bond 0.00276 / 0.16 ( 15) link_NAG-ASN : angle 2.29313 / 1.42 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 GLU cc_start: 0.8435 (tp30) cc_final: 0.8178 (tt0) REVERT: C 174 ASP cc_start: 0.8436 (t70) cc_final: 0.7877 (t0) REVERT: D 252 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.6655 (t80) outliers start: 24 outliers final: 17 residues processed: 145 average time/residue: 0.7059 time to fit residues: 123.1219 Evaluate side-chains 143 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 13 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.141696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.083543 restraints weight = 63448.805| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.42 r_work: 0.2836 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16405 Z= 0.133 Angle : 0.761 11.649 22405 Z= 0.346 Chirality : 0.183 1.724 2570 Planarity : 0.004 0.044 2745 Dihedral : 6.422 54.834 2611 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.38 % Allowed : 10.66 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.78 (0.19), residues: 1910 helix: 1.99 (0.18), residues: 820 sheet: -0.45 (0.24), residues: 415 loop : -0.63 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 418 TYR 0.009 0.001 TYR D 14 PHE 0.009 0.001 PHE D 252 TRP 0.010 0.001 TRP E 437 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (16375) covalent geometry : angle 0.75279 / 0.34 (22325) SS BOND : bond 0.00860 / 0.47 ( 10) SS BOND : angle 1.78632 / 1.13 ( 20) hydrogen bonds : bond 0.02843 / 1.85 ( 841) hydrogen bonds : angle 4.22222 / 2.92 ( 2778) link_BETA1-4 : bond 0.00116 / 0.07 ( 5) link_BETA1-4 : angle 1.41010 / 0.86 ( 15) link_NAG-ASN : bond 0.00073 / 0.04 ( 15) link_NAG-ASN : angle 2.23608 / 1.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 174 ASP cc_start: 0.8407 (t70) cc_final: 0.7904 (t0) REVERT: C 252 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.6461 (t80) REVERT: D 252 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6698 (t80) outliers start: 24 outliers final: 16 residues processed: 138 average time/residue: 0.7188 time to fit residues: 119.5081 Evaluate side-chains 139 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 110 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.082132 restraints weight = 63676.321| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.41 r_work: 0.2816 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16405 Z= 0.199 Angle : 0.769 11.687 22405 Z= 0.350 Chirality : 0.183 1.717 2570 Planarity : 0.004 0.044 2745 Dihedral : 6.448 54.821 2611 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.38 % Allowed : 10.77 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.83 (0.19), residues: 1910 helix: 2.25 (0.18), residues: 795 sheet: -0.61 (0.23), residues: 430 loop : -0.65 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.007 0.001 TYR A 14 PHE 0.012 0.001 PHE A 99 TRP 0.010 0.001 TRP E 437 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (16375) covalent geometry : angle 0.76003 / 0.35 (22325) SS BOND : bond 0.00891 / 0.49 ( 10) SS BOND : angle 2.05540 / 1.29 ( 20) hydrogen bonds : bond 0.02882 / 1.87 ( 841) hydrogen bonds : angle 4.18856 / 2.89 ( 2778) link_BETA1-4 : bond 0.00056 / 0.04 ( 5) link_BETA1-4 : angle 1.50684 / 0.92 ( 15) link_NAG-ASN : bond 0.00277 / 0.16 ( 15) link_NAG-ASN : angle 2.24323 / 1.38 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 GLU cc_start: 0.8463 (tp30) cc_final: 0.8157 (tt0) REVERT: C 174 ASP cc_start: 0.8459 (t70) cc_final: 0.7973 (t0) REVERT: C 252 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6442 (t80) REVERT: D 252 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6753 (t80) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.6878 time to fit residues: 112.6921 Evaluate side-chains 140 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 21 optimal weight: 0.0000 chunk 30 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.141192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.083753 restraints weight = 63311.260| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.40 r_work: 0.2831 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16405 Z= 0.144 Angle : 0.757 11.637 22405 Z= 0.343 Chirality : 0.183 1.718 2570 Planarity : 0.003 0.043 2745 Dihedral : 6.245 54.235 2611 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.09 % Allowed : 11.17 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.96 (0.19), residues: 1910 helix: 2.33 (0.18), residues: 795 sheet: -0.47 (0.23), residues: 440 loop : -0.60 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.009 0.001 TYR D 14 PHE 0.009 0.001 PHE D 252 TRP 0.010 0.001 TRP E 437 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (16375) covalent geometry : angle 0.74962 / 0.34 (22325) SS BOND : bond 0.00850 / 0.47 ( 10) SS BOND : angle 1.77248 / 1.12 ( 20) hydrogen bonds : bond 0.02728 / 1.78 ( 841) hydrogen bonds : angle 4.13449 / 2.85 ( 2778) link_BETA1-4 : bond 0.00198 / 0.11 ( 5) link_BETA1-4 : angle 1.42365 / 0.88 ( 15) link_NAG-ASN : bond 0.00092 / 0.05 ( 15) link_NAG-ASN : angle 2.18100 / 1.35 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 GLU cc_start: 0.8415 (tp30) cc_final: 0.8120 (tt0) REVERT: C 174 ASP cc_start: 0.8434 (t70) cc_final: 0.7941 (t0) REVERT: C 252 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6455 (t80) REVERT: D 252 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6722 (t80) outliers start: 19 outliers final: 14 residues processed: 133 average time/residue: 0.6836 time to fit residues: 109.9769 Evaluate side-chains 135 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 146 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 165 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.141635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084098 restraints weight = 63504.888| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.39 r_work: 0.2844 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16405 Z= 0.135 Angle : 0.750 11.610 22405 Z= 0.339 Chirality : 0.183 1.716 2570 Planarity : 0.003 0.043 2745 Dihedral : 6.005 53.991 2611 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.80 % Allowed : 11.69 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.96 (0.19), residues: 1910 helix: 2.13 (0.18), residues: 825 sheet: -0.39 (0.23), residues: 420 loop : -0.50 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.008 0.001 TYR D 14 PHE 0.009 0.001 PHE D 252 TRP 0.010 0.001 TRP E 437 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (16375) covalent geometry : angle 0.74205 / 0.34 (22325) SS BOND : bond 0.00995 / 0.54 ( 10) SS BOND : angle 1.83192 / 1.16 ( 20) hydrogen bonds : bond 0.02648 / 1.73 ( 841) hydrogen bonds : angle 4.05610 / 2.80 ( 2778) link_BETA1-4 : bond 0.00115 / 0.06 ( 5) link_BETA1-4 : angle 1.42298 / 0.87 ( 15) link_NAG-ASN : bond 0.00092 / 0.05 ( 15) link_NAG-ASN : angle 2.13220 / 1.32 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10450.52 seconds wall clock time: 177 minutes 17.91 seconds (10637.91 seconds total)