Starting phenix.real_space_refine on Mon Jul 6 01:09:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kox_22983/07_2026/7kox_22983_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kox_22983/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kox_22983/07_2026/7kox_22983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kox_22983/07_2026/7kox_22983.map" model { file = "/net/cci-nas-00/data/ceres_data/7kox_22983/07_2026/7kox_22983_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kox_22983/07_2026/7kox_22983_trim.cif" } 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-dev-6108/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, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 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: 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: 8.07, 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: 3.20 Conformation dependent library (CDL) restraints added in 922.7 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: 0.70 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: 8.49 Time building geometry restraints manager: 4.36 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: 0.07 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: 4.340 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: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.210 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.550 ------------------------------------------------------------------------------- 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 : 0.874 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: 0.7405 time to fit residues: 172.1988 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 : 0.947 ------------------------------------------------------------------------------- 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 = 0.145391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087718 restraints weight = 63954.647| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.39 r_work: 0.2952 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16405 Z= 0.151 Angle : 0.799 11.814 22405 Z= 0.369 Chirality : 0.185 1.778 2570 Planarity : 0.004 0.047 2745 Dihedral : 7.023 56.403 2614 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.89 % Allowed : 5.96 % Favored : 92.15 % 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: -0.03 (0.19), residues: 1910 helix: 1.24 (0.18), residues: 820 sheet: -0.83 (0.24), residues: 405 loop : -0.96 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 132 TYR 0.010 0.001 TYR C 209 PHE 0.030 0.002 PHE C 252 TRP 0.007 0.001 TRP D 307 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (16375) covalent geometry : angle 0.79057 / 0.37 (22325) SS BOND : bond 0.00832 / 0.45 ( 10) SS BOND : angle 1.81715 / 1.16 ( 20) hydrogen bonds : bond 0.04143 / 2.68 ( 841) hydrogen bonds : angle 5.00002 / 3.44 ( 2778) link_BETA1-4 : bond 0.00210 / 0.13 ( 5) link_BETA1-4 : angle 1.28492 / 0.79 ( 15) link_NAG-ASN : bond 0.00126 / 0.07 ( 15) link_NAG-ASN : angle 2.38758 / 1.55 ( 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 184 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.964 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 280 ILE cc_start: 0.6568 (mm) cc_final: 0.6347 (mm) REVERT: B 174 ASP cc_start: 0.8347 (t70) cc_final: 0.7865 (t0) REVERT: C 174 ASP cc_start: 0.8337 (t70) cc_final: 0.7932 (t0) REVERT: C 213 ASN cc_start: 0.7960 (t0) cc_final: 0.7586 (t0) REVERT: C 448 CYS cc_start: 0.6448 (m) cc_final: 0.6214 (m) REVERT: D 174 ASP cc_start: 0.8339 (t70) cc_final: 0.7885 (t0) REVERT: E 97 GLU cc_start: 0.8194 (pp20) cc_final: 0.7981 (pp20) REVERT: E 213 ASN cc_start: 0.7936 (t0) cc_final: 0.7711 (t0) REVERT: E 448 CYS cc_start: 0.6888 (m) cc_final: 0.6623 (m) outliers start: 33 outliers final: 11 residues processed: 171 average time/residue: 0.6840 time to fit residues: 143.8739 Evaluate side-chains 146 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 263 THR 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 263 THR 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: 1.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.141561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.082489 restraints weight = 63902.485| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.45 r_work: 0.2837 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16405 Z= 0.273 Angle : 0.800 11.951 22405 Z= 0.370 Chirality : 0.186 1.748 2570 Planarity : 0.004 0.047 2745 Dihedral : 7.127 54.082 2614 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.60 % Allowed : 6.99 % 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: 0.19 (0.19), residues: 1910 helix: 1.55 (0.18), residues: 820 sheet: -0.89 (0.24), residues: 405 loop : -0.89 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 205 TYR 0.009 0.001 TYR C 209 PHE 0.021 0.002 PHE A 252 TRP 0.016 0.001 TRP B 437 HIS 0.011 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 (16375) covalent geometry : angle 0.79026 / 0.37 (22325) SS BOND : bond 0.00890 / 0.48 ( 10) SS BOND : angle 2.39825 / 1.51 ( 20) hydrogen bonds : bond 0.03821 / 2.47 ( 841) hydrogen bonds : angle 4.75315 / 3.27 ( 2778) link_BETA1-4 : bond 0.00264 / 0.14 ( 5) link_BETA1-4 : angle 1.42822 / 0.87 ( 15) link_NAG-ASN : bond 0.00367 / 0.20 ( 15) link_NAG-ASN : angle 2.37888 / 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: 28 poor density : 131 time to evaluate : 0.890 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 212 LEU cc_start: 0.8575 (tt) cc_final: 0.8272 (tm) REVERT: B 212 LEU cc_start: 0.8602 (tt) cc_final: 0.8302 (tm) REVERT: C 174 ASP cc_start: 0.8453 (t70) cc_final: 0.7924 (t0) REVERT: C 212 LEU cc_start: 0.8579 (tt) cc_final: 0.8304 (tm) REVERT: C 213 ASN cc_start: 0.8118 (t0) cc_final: 0.7771 (t0) REVERT: D 212 LEU cc_start: 0.8513 (tt) cc_final: 0.8221 (tm) REVERT: D 252 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.6541 (t80) outliers start: 28 outliers final: 16 residues processed: 147 average time/residue: 0.6651 time to fit residues: 119.6147 Evaluate side-chains 143 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 250 THR 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 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 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: 0.9980 chunk 50 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.142312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084429 restraints weight = 63711.551| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.39 r_work: 0.2849 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16405 Z= 0.148 Angle : 0.760 11.729 22405 Z= 0.346 Chirality : 0.184 1.744 2570 Planarity : 0.004 0.045 2745 Dihedral : 6.732 51.621 2614 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.49 % Allowed : 8.25 % Favored : 90.26 % 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: 0.48 (0.19), residues: 1910 helix: 1.78 (0.18), residues: 820 sheet: -0.72 (0.24), residues: 405 loop : -0.75 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 205 TYR 0.009 0.001 TYR D 14 PHE 0.020 0.001 PHE A 252 TRP 0.008 0.001 TRP B 437 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (16375) covalent geometry : angle 0.75175 / 0.34 (22325) SS BOND : bond 0.00855 / 0.47 ( 10) SS BOND : angle 1.88696 / 1.21 ( 20) hydrogen bonds : bond 0.03190 / 2.08 ( 841) hydrogen bonds : angle 4.48533 / 3.09 ( 2778) link_BETA1-4 : bond 0.00253 / 0.13 ( 5) link_BETA1-4 : angle 1.27279 / 0.78 ( 15) link_NAG-ASN : bond 0.00084 / 0.05 ( 15) link_NAG-ASN : angle 2.31817 / 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 164 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.869 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: A 212 LEU cc_start: 0.8549 (tt) cc_final: 0.8331 (tm) REVERT: B 212 LEU cc_start: 0.8522 (tt) cc_final: 0.8304 (tm) REVERT: C 174 ASP cc_start: 0.8406 (t70) cc_final: 0.7926 (t0) REVERT: C 278 MET cc_start: 0.7465 (ttm) cc_final: 0.7218 (ttm) REVERT: D 212 LEU cc_start: 0.8576 (tt) cc_final: 0.8323 (tm) REVERT: D 252 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6413 (t80) REVERT: E 212 LEU cc_start: 0.8671 (tt) cc_final: 0.8433 (tm) outliers start: 26 outliers final: 18 residues processed: 156 average time/residue: 0.6970 time to fit residues: 132.0945 Evaluate side-chains 147 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 250 THR 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 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 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: 0.8980 chunk 175 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.141492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.083165 restraints weight = 63787.604| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.40 r_work: 0.2834 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16405 Z= 0.194 Angle : 0.768 11.753 22405 Z= 0.352 Chirality : 0.184 1.733 2570 Planarity : 0.004 0.046 2745 Dihedral : 6.697 52.545 2614 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.66 % Allowed : 8.42 % Favored : 89.91 % 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: 0.58 (0.19), residues: 1910 helix: 1.87 (0.18), residues: 820 sheet: -0.68 (0.24), residues: 405 loop : -0.72 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 205 TYR 0.007 0.001 TYR A 14 PHE 0.015 0.001 PHE A 252 TRP 0.010 0.001 TRP B 437 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (16375) covalent geometry : angle 0.75930 / 0.35 (22325) SS BOND : bond 0.00840 / 0.46 ( 10) SS BOND : angle 1.99934 / 1.27 ( 20) hydrogen bonds : bond 0.03123 / 2.04 ( 841) hydrogen bonds : angle 4.39717 / 3.03 ( 2778) link_BETA1-4 : bond 0.00052 / 0.03 ( 5) link_BETA1-4 : angle 1.44942 / 0.90 ( 15) link_NAG-ASN : bond 0.00248 / 0.14 ( 15) link_NAG-ASN : angle 2.30490 / 1.44 ( 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 164 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.041 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: C 174 ASP cc_start: 0.8443 (t70) cc_final: 0.7962 (t0) REVERT: D 252 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6474 (t80) REVERT: E 40 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.9017 (mtm) outliers start: 29 outliers final: 23 residues processed: 152 average time/residue: 0.7377 time to fit residues: 135.2129 Evaluate side-chains 149 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 A residue 416 GLU Chi-restraints excluded: chain B residue 250 THR 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 252 PHE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 447 LEU 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 40 MET 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: 1.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.140999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.082571 restraints weight = 63427.140| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.42 r_work: 0.2821 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16405 Z= 0.204 Angle : 0.772 11.735 22405 Z= 0.353 Chirality : 0.184 1.727 2570 Planarity : 0.004 0.045 2745 Dihedral : 6.670 53.251 2614 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.60 % Allowed : 9.17 % Favored : 89.23 % 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: 0.61 (0.19), residues: 1910 helix: 1.90 (0.18), residues: 820 sheet: -0.65 (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 0.008 0.001 TYR D 14 PHE 0.015 0.001 PHE A 252 TRP 0.019 0.001 TRP C 437 HIS 0.009 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (16375) covalent geometry : angle 0.76320 / 0.35 (22325) SS BOND : bond 0.00827 / 0.45 ( 10) SS BOND : angle 2.05503 / 1.31 ( 20) hydrogen bonds : bond 0.03031 / 1.96 ( 841) hydrogen bonds : angle 4.34425 / 3.00 ( 2778) link_BETA1-4 : bond 0.00010 / 0.01 ( 5) link_BETA1-4 : angle 1.43852 / 0.88 ( 15) link_NAG-ASN : bond 0.00238 / 0.13 ( 15) link_NAG-ASN : angle 2.28155 / 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 158 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.913 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 252 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6472 (t80) REVERT: C 174 ASP cc_start: 0.8444 (t70) cc_final: 0.7947 (t0) REVERT: D 252 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6490 (t80) REVERT: E 40 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8992 (mtm) outliers start: 28 outliers final: 22 residues processed: 147 average time/residue: 0.6992 time to fit residues: 124.2054 Evaluate side-chains 149 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 A residue 416 GLU Chi-restraints excluded: chain B residue 250 THR 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 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 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 284 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain E residue 40 MET 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: 0.5980 chunk 105 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.142093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083346 restraints weight = 63716.418| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.41 r_work: 0.2835 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16405 Z= 0.138 Angle : 0.755 11.656 22405 Z= 0.343 Chirality : 0.183 1.725 2570 Planarity : 0.004 0.044 2745 Dihedral : 6.379 52.763 2614 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.49 % Allowed : 9.91 % Favored : 88.60 % 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: 2.01 (0.18), residues: 820 sheet: -0.49 (0.24), residues: 415 loop : -0.63 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.009 0.001 TYR D 14 PHE 0.014 0.001 PHE A 252 TRP 0.021 0.001 TRP E 437 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (16375) covalent geometry : angle 0.74708 / 0.34 (22325) SS BOND : bond 0.00846 / 0.46 ( 10) SS BOND : angle 1.86519 / 1.19 ( 20) hydrogen bonds : bond 0.02856 / 1.85 ( 841) hydrogen bonds : angle 4.25782 / 2.94 ( 2778) link_BETA1-4 : bond 0.00113 / 0.06 ( 5) link_BETA1-4 : angle 1.38968 / 0.85 ( 15) link_NAG-ASN : bond 0.00085 / 0.05 ( 15) link_NAG-ASN : angle 2.24496 / 1.40 ( 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 151 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.873 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: 0.8404 (t70) cc_final: 0.7907 (t0) REVERT: D 252 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6563 (t80) outliers start: 26 outliers final: 19 residues processed: 139 average time/residue: 0.7833 time to fit residues: 130.2805 Evaluate side-chains 145 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 250 THR 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 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 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 416 GLU 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: 0.9990 chunk 81 optimal weight: 0.5980 chunk 146 optimal weight: 20.0000 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: 2.9990 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.142156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083930 restraints weight = 63565.239| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.38 r_work: 0.2839 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16405 Z= 0.143 Angle : 0.751 11.660 22405 Z= 0.340 Chirality : 0.183 1.718 2570 Planarity : 0.003 0.044 2745 Dihedral : 6.078 52.564 2610 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.32 % Allowed : 10.26 % Favored : 88.42 % 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: 0.88 (0.19), residues: 1910 helix: 2.13 (0.18), residues: 820 sheet: -0.46 (0.24), residues: 415 loop : -0.60 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 418 TYR 0.007 0.001 TYR A 14 PHE 0.012 0.001 PHE A 252 TRP 0.009 0.001 TRP B 437 HIS 0.005 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (16375) covalent geometry : angle 0.74236 / 0.34 (22325) SS BOND : bond 0.00866 / 0.47 ( 10) SS BOND : angle 1.89030 / 1.21 ( 20) hydrogen bonds : bond 0.02754 / 1.78 ( 841) hydrogen bonds : angle 4.15729 / 2.87 ( 2778) link_BETA1-4 : bond 0.00100 / 0.06 ( 5) link_BETA1-4 : angle 1.42099 / 0.87 ( 15) link_NAG-ASN : bond 0.00116 / 0.06 ( 15) link_NAG-ASN : angle 2.20814 / 1.37 ( 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 149 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.846 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: A 252 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6412 (t80) REVERT: B 188 GLU cc_start: 0.8439 (tp30) cc_final: 0.8141 (tt0) REVERT: C 174 ASP cc_start: 0.8378 (t70) cc_final: 0.7812 (t0) REVERT: D 252 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6614 (t80) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.7852 time to fit residues: 131.2278 Evaluate side-chains 142 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 B residue 250 THR 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 447 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 252 PHE 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 416 GLU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.140709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083032 restraints weight = 63633.305| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.40 r_work: 0.2824 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16405 Z= 0.186 Angle : 0.763 11.668 22405 Z= 0.346 Chirality : 0.183 1.713 2570 Planarity : 0.004 0.044 2745 Dihedral : 6.131 53.558 2610 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.32 % Allowed : 10.54 % Favored : 88.14 % 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: 0.94 (0.19), residues: 1910 helix: 2.43 (0.18), residues: 790 sheet: -0.60 (0.23), residues: 430 loop : -0.66 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.007 0.001 TYR A 210 PHE 0.014 0.001 PHE A 252 TRP 0.010 0.001 TRP E 437 HIS 0.008 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (16375) covalent geometry : angle 0.75454 / 0.34 (22325) SS BOND : bond 0.00830 / 0.46 ( 10) SS BOND : angle 1.94057 / 1.23 ( 20) hydrogen bonds : bond 0.02810 / 1.83 ( 841) hydrogen bonds : angle 4.14682 / 2.86 ( 2778) link_BETA1-4 : bond 0.00037 / 0.02 ( 5) link_BETA1-4 : angle 1.43765 / 0.87 ( 15) link_NAG-ASN : bond 0.00236 / 0.13 ( 15) link_NAG-ASN : angle 2.19664 / 1.35 ( 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 149 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6489 (t80) REVERT: B 188 GLU cc_start: 0.8406 (tp30) cc_final: 0.8103 (tt0) REVERT: C 174 ASP cc_start: 0.8439 (t70) cc_final: 0.7949 (t0) REVERT: C 252 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.6483 (t80) REVERT: D 252 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6675 (t80) outliers start: 23 outliers final: 15 residues processed: 138 average time/residue: 0.7689 time to fit residues: 127.9552 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 : 0.902 ------------------------------------------------------------------------------- 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 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 447 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 252 PHE 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 416 GLU 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: 3.9990 chunk 4 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.140406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082612 restraints weight = 63600.329| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.38 r_work: 0.2819 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16405 Z= 0.200 Angle : 0.766 11.669 22405 Z= 0.348 Chirality : 0.183 1.719 2570 Planarity : 0.004 0.043 2745 Dihedral : 6.182 54.169 2610 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.15 % Allowed : 10.83 % Favored : 88.02 % 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: 0.93 (0.19), residues: 1910 helix: 2.38 (0.18), residues: 795 sheet: -0.61 (0.23), residues: 430 loop : -0.62 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.007 0.001 TYR B 210 PHE 0.014 0.001 PHE A 252 TRP 0.008 0.001 TRP E 437 HIS 0.007 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (16375) covalent geometry : angle 0.75799 / 0.35 (22325) SS BOND : bond 0.00819 / 0.45 ( 10) SS BOND : angle 2.00039 / 1.27 ( 20) hydrogen bonds : bond 0.02807 / 1.82 ( 841) hydrogen bonds : angle 4.14820 / 2.86 ( 2778) link_BETA1-4 : bond 0.00037 / 0.02 ( 5) link_BETA1-4 : angle 1.45575 / 0.88 ( 15) link_NAG-ASN : bond 0.00248 / 0.14 ( 15) link_NAG-ASN : angle 2.19617 / 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 144 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.033 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: A 252 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6616 (t80) REVERT: B 188 GLU cc_start: 0.8423 (tp30) cc_final: 0.8122 (tt0) REVERT: B 278 MET cc_start: 0.7509 (ttm) cc_final: 0.7186 (ttm) REVERT: C 174 ASP cc_start: 0.8448 (t70) cc_final: 0.7970 (t0) REVERT: C 252 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6559 (t80) REVERT: D 252 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6734 (t80) outliers start: 20 outliers final: 15 residues processed: 134 average time/residue: 0.7701 time to fit residues: 124.9803 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 : 0.900 ------------------------------------------------------------------------------- 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 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 B residue 465 MET Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 252 PHE 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 416 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 169 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 171 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.141697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084191 restraints weight = 63658.971| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.46 r_work: 0.2844 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16405 Z= 0.120 Angle : 0.746 11.604 22405 Z= 0.336 Chirality : 0.183 1.717 2570 Planarity : 0.003 0.043 2745 Dihedral : 5.915 53.419 2610 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.03 % Allowed : 10.83 % Favored : 88.14 % 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: 1.02 (0.19), residues: 1910 helix: 2.21 (0.18), residues: 825 sheet: -0.36 (0.24), residues: 415 loop : -0.54 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 418 TYR 0.008 0.001 TYR D 14 PHE 0.013 0.001 PHE A 252 TRP 0.008 0.001 TRP E 437 HIS 0.006 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (16375) covalent geometry : angle 0.73905 / 0.33 (22325) SS BOND : bond 0.00852 / 0.47 ( 10) SS BOND : angle 1.71305 / 1.09 ( 20) hydrogen bonds : bond 0.02621 / 1.70 ( 841) hydrogen bonds : angle 4.06879 / 2.80 ( 2778) link_BETA1-4 : bond 0.00186 / 0.10 ( 5) link_BETA1-4 : angle 1.35878 / 0.83 ( 15) link_NAG-ASN : bond 0.00050 / 0.03 ( 15) link_NAG-ASN : angle 2.11527 / 1.31 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10700.01 seconds wall clock time: 181 minutes 42.29 seconds (10902.29 seconds total)