Starting phenix.real_space_refine on Sat Jul 4 02:08:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7onj_12996/07_2026/7onj_12996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7onj_12996/07_2026/7onj_12996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7onj_12996/07_2026/7onj_12996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7onj_12996/07_2026/7onj_12996.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7onj_12996/07_2026/7onj_12996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7onj_12996/07_2026/7onj_12996.cif" model { file = "/net/cci-nas-00/data/ceres_data/7onj_12996/07_2026/7onj_12996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7onj_12996/07_2026/7onj_12996.cif" } resolution = 2.3 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= 0.009 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 10955 2.51 5 N 2450 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 16947 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "A" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "G" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "C" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 3.70, per 1000 atoms: 0.22 Number of scatterers: 16947 At special positions: 0 Unit cell: (98.9055, 98.9055, 137.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 3493 8.00 N 2450 7.00 C 10955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 470.3 milliseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 56.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 Processing helix chain 'A' and resid 92 through 128 removed outlier: 5.306A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'G' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 89 Processing helix chain 'G' and resid 92 through 128 removed outlier: 5.306A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 245 through 265 Processing helix chain 'B' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 89 Processing helix chain 'B' and resid 92 through 128 removed outlier: 5.305A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 89 Processing helix chain 'C' and resid 92 through 128 removed outlier: 5.306A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 89 Processing helix chain 'D' and resid 92 through 128 removed outlier: 5.306A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 89 Processing helix chain 'E' and resid 92 through 128 removed outlier: 5.305A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 89 Processing helix chain 'F' and resid 92 through 128 removed outlier: 5.305A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.536A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.610A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279 removed outlier: 6.680A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS G 278 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.611A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.611A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.611A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.610A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.610A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.611A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2384 1.32 - 1.44: 4260 1.44 - 1.56: 10163 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 16905 Sorted by residual: bond pdb=" O3P PEE C 303 " pdb=" P PEE C 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" O3P PEE D 303 " pdb=" P PEE D 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" O3P PEE G 403 " pdb=" P PEE G 403 " ideal model delta sigma weight residual 1.636 1.589 0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 16900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 21916 2.20 - 4.41: 742 4.41 - 6.61: 36 6.61 - 8.81: 0 8.81 - 11.02: 7 Bond angle restraints: 22701 Sorted by residual: angle pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 92.91 103.93 -11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O3P PEE G 403 " pdb=" P PEE G 403 " pdb=" O4P PEE G 403 " ideal model delta sigma weight residual 92.91 103.90 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 103.90 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE B 303 " pdb=" P PEE B 303 " pdb=" O4P PEE B 303 " ideal model delta sigma weight residual 92.91 103.89 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE F 405 " pdb=" P PEE F 405 " pdb=" O4P PEE F 405 " ideal model delta sigma weight residual 92.91 103.89 -10.98 3.00e+00 1.11e-01 1.34e+01 ... (remaining 22696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.71: 9247 27.71 - 55.42: 294 55.42 - 83.14: 35 83.14 - 110.85: 28 110.85 - 138.56: 49 Dihedral angle restraints: 9653 sinusoidal: 4396 harmonic: 5257 Sorted by residual: dihedral pdb=" CBQ AV0 E 302 " pdb=" CBS AV0 E 302 " pdb=" CCM AV0 E 302 " pdb=" O1 AV0 E 302 " ideal model delta sinusoidal sigma weight residual 70.26 -68.30 138.56 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" CBQ AV0 D 302 " pdb=" CBS AV0 D 302 " pdb=" CCM AV0 D 302 " pdb=" O1 AV0 D 302 " ideal model delta sinusoidal sigma weight residual 70.26 -68.28 138.54 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" CBQ AV0 A 307 " pdb=" CBS AV0 A 307 " pdb=" CCM AV0 A 307 " pdb=" O1 AV0 A 307 " ideal model delta sinusoidal sigma weight residual 70.26 -68.28 138.54 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 9650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2286 0.054 - 0.108: 512 0.108 - 0.163: 83 0.163 - 0.217: 38 0.217 - 0.271: 7 Chirality restraints: 2926 Sorted by residual: chirality pdb=" C2 PEE B 303 " pdb=" C1 PEE B 303 " pdb=" C3 PEE B 303 " pdb=" O2 PEE B 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.60 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2 PEE D 303 " pdb=" C1 PEE D 303 " pdb=" C3 PEE D 303 " pdb=" O2 PEE D 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.60 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2 PEE E 303 " pdb=" C1 PEE E 303 " pdb=" C3 PEE E 303 " pdb=" O2 PEE E 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.60 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2923 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 83 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C ILE B 83 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE B 83 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA B 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 83 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C ILE E 83 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE E 83 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA E 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 83 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C ILE G 83 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE G 83 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA G 84 " -0.007 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 610 2.70 - 3.25: 16477 3.25 - 3.80: 28506 3.80 - 4.35: 36414 4.35 - 4.90: 61031 Nonbonded interactions: 143038 Sorted by model distance: nonbonded pdb=" OAR AV0 A 307 " pdb=" OAN AV0 G 405 " model vdw 2.155 3.040 nonbonded pdb=" OAN AV0 B 305 " pdb=" OAR AV0 C 302 " model vdw 2.155 3.040 nonbonded pdb=" OAN AV0 A 303 " pdb=" OAR AV0 B 302 " model vdw 2.155 3.040 nonbonded pdb=" OAN AV0 E 305 " pdb=" OAR AV0 F 404 " model vdw 2.155 3.040 nonbonded pdb=" OAR AV0 G 409 " pdb=" OAN AV0 F 407 " model vdw 2.155 3.040 ... (remaining 143033 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'B' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'C' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'D' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'E' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'F' and (resid 19 through 280 or resid 407 or (resid 409 and (name CAA or \ name CAB or name CAW or name CAX or name CAY or name CAZ or name CBA or name CB \ B or name CBC or name CBD or name CBE or name CBF or name CBG or name CBH or nam \ e CBI or name CBJ or name CBK or name CBL or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCF or name CCH or name CCJ or name CCL or name CC \ M or name CCQ or name O1 or name OAL or name OAN or name OAP or name OBV or name \ OBX or name OCB)))) selection = (chain 'G' and (resid 19 through 280 or (resid 407 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or (resid 409 and (nam \ e CAA or name CAB or name CAW or name CAX or name CAY or name CAZ or name CBA or \ name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or name CB \ H or name CBI or name CBJ or name CBK or name CBL or name CBP or name CBQ or nam \ e CBR or name CBS or name CBT or name CCF or name CCH or name CCJ or name CCL or \ name CCM or name CCQ or name O1 or name OAL or name OAN or name OAP or name OBV \ or name OBX or name OCB)))) } 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: 0.010 Normalize map: mean=0, sd=1: 1.150 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.890 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 0.048 16905 Z= 0.420 Angle : 0.857 11.017 22701 Z= 0.378 Chirality : 0.052 0.271 2926 Planarity : 0.004 0.021 2450 Dihedral : 18.326 138.562 6265 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.47 % Allowed : 3.77 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 1820 helix: -0.33 (0.11), residues: 1043 sheet: 0.31 (0.29), residues: 294 loop : 0.43 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 184 TYR 0.010 0.002 TYR G 75 PHE 0.013 0.002 PHE E 127 TRP 0.005 0.001 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00935 / 0.42 (16905) covalent geometry : angle 0.85704 / 0.38 (22701) hydrogen bonds : bond 0.10857 / 7.53 ( 1082) hydrogen bonds : angle 5.34626 / 3.89 ( 3183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 308 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7397 (ttm170) REVERT: A 47 MET cc_start: 0.7933 (mtt) cc_final: 0.7720 (mtm) REVERT: G 197 ASP cc_start: 0.8513 (t0) cc_final: 0.8266 (t70) REVERT: G 247 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8762 (tp-100) REVERT: G 278 LYS cc_start: 0.8230 (mttt) cc_final: 0.7831 (mttt) REVERT: B 46 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7478 (ttp80) REVERT: B 54 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7793 (mtm-85) REVERT: C 278 LYS cc_start: 0.8112 (mttt) cc_final: 0.7857 (mttt) REVERT: D 46 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7321 (ttp-170) REVERT: D 59 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7755 (mmt90) REVERT: D 220 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8459 (pt0) REVERT: D 221 MET cc_start: 0.9153 (mtp) cc_final: 0.8904 (mtp) REVERT: F 54 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7817 (mtm-85) REVERT: F 221 MET cc_start: 0.9128 (mtp) cc_final: 0.8807 (mtp) outliers start: 7 outliers final: 1 residues processed: 310 average time/residue: 0.7783 time to fit residues: 262.4496 Evaluate side-chains 248 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain D residue 220 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN G 92 GLN B 112 GLN B 210 GLN C 92 GLN C 210 GLN D 210 GLN E 210 GLN F 92 GLN F 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.080574 restraints weight = 18939.774| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.46 r_work: 0.2620 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16905 Z= 0.147 Angle : 0.520 4.818 22701 Z= 0.263 Chirality : 0.040 0.155 2926 Planarity : 0.003 0.029 2450 Dihedral : 20.617 141.026 3142 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.62 % Allowed : 8.49 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.17), residues: 1820 helix: 2.13 (0.14), residues: 1043 sheet: 0.36 (0.35), residues: 175 loop : -0.08 (0.21), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.006 0.001 TYR C 27 PHE 0.013 0.001 PHE B 178 TRP 0.004 0.001 TRP G 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (16905) covalent geometry : angle 0.52025 / 0.26 (22701) hydrogen bonds : bond 0.04900 / 3.36 ( 1082) hydrogen bonds : angle 4.36444 / 3.20 ( 3183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8132 (ttp-170) cc_final: 0.7924 (ttp-110) REVERT: A 47 MET cc_start: 0.8671 (mtt) cc_final: 0.8394 (mtm) REVERT: A 60 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8387 (mmmm) REVERT: A 149 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8926 (mp10) REVERT: G 88 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8367 (mmt-90) REVERT: G 278 LYS cc_start: 0.8285 (mttt) cc_final: 0.7983 (mttt) REVERT: B 46 ARG cc_start: 0.8140 (ttp-170) cc_final: 0.7901 (ttp80) REVERT: B 54 ARG cc_start: 0.8257 (mtm110) cc_final: 0.8047 (mtm-85) REVERT: B 62 ASP cc_start: 0.8437 (t70) cc_final: 0.8150 (t70) REVERT: C 54 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.8161 (mtp180) REVERT: C 88 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8421 (mmt-90) REVERT: C 278 LYS cc_start: 0.8229 (mttt) cc_final: 0.8007 (mttt) REVERT: D 59 ARG cc_start: 0.7986 (mmt90) cc_final: 0.7767 (mmm-85) REVERT: E 47 MET cc_start: 0.8629 (mtm) cc_final: 0.8361 (mtm) REVERT: F 203 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8249 (tm-30) outliers start: 24 outliers final: 3 residues processed: 268 average time/residue: 0.8402 time to fit residues: 243.1180 Evaluate side-chains 258 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 253 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 203 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 49 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN G 92 GLN G 276 ASN B 210 GLN C 92 GLN F 92 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.080343 restraints weight = 19113.903| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.47 r_work: 0.2670 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16905 Z= 0.137 Angle : 0.480 5.027 22701 Z= 0.247 Chirality : 0.039 0.140 2926 Planarity : 0.003 0.028 2450 Dihedral : 19.891 139.667 3136 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.68 % Allowed : 9.43 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.18), residues: 1820 helix: 2.78 (0.15), residues: 1043 sheet: 0.61 (0.35), residues: 175 loop : -0.23 (0.20), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.006 0.001 TYR B 75 PHE 0.011 0.001 PHE E 277 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16905) covalent geometry : angle 0.48043 / 0.25 (22701) hydrogen bonds : bond 0.04631 / 3.18 ( 1082) hydrogen bonds : angle 4.20383 / 3.08 ( 3183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8210 (ttp-170) cc_final: 0.8003 (ttp-110) REVERT: A 47 MET cc_start: 0.8677 (mtt) cc_final: 0.8421 (mtm) REVERT: G 88 ARG cc_start: 0.8708 (mmm160) cc_final: 0.8427 (mmt-90) REVERT: G 197 ASP cc_start: 0.8723 (t0) cc_final: 0.8519 (t70) REVERT: B 46 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.8000 (ttp80) REVERT: B 54 ARG cc_start: 0.8309 (mtm110) cc_final: 0.8030 (mtm-85) REVERT: B 59 ARG cc_start: 0.8004 (mmt90) cc_final: 0.7799 (mpt-90) REVERT: D 59 ARG cc_start: 0.8026 (mmt90) cc_final: 0.7601 (mmt90) REVERT: F 203 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8493 (tm-30) REVERT: F 278 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8170 (mttt) outliers start: 25 outliers final: 10 residues processed: 267 average time/residue: 0.8620 time to fit residues: 248.8483 Evaluate side-chains 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 240 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 203 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN G 92 GLN B 210 GLN C 92 GLN C 210 GLN F 92 GLN F 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.080312 restraints weight = 18906.961| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.49 r_work: 0.2623 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16905 Z= 0.149 Angle : 0.486 4.720 22701 Z= 0.248 Chirality : 0.039 0.137 2926 Planarity : 0.003 0.028 2450 Dihedral : 19.515 137.089 3136 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.75 % Allowed : 10.58 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.18), residues: 1820 helix: 2.97 (0.15), residues: 1043 sheet: 0.44 (0.27), residues: 280 loop : -0.27 (0.22), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.006 0.001 TYR B 75 PHE 0.013 0.001 PHE B 277 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16905) covalent geometry : angle 0.48555 / 0.25 (22701) hydrogen bonds : bond 0.04632 / 3.17 ( 1082) hydrogen bonds : angle 4.20048 / 3.08 ( 3183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7923 (ttp-110) REVERT: A 47 MET cc_start: 0.8698 (mtt) cc_final: 0.8456 (mtm) REVERT: G 88 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8408 (mmt-90) REVERT: G 161 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8924 (mtmm) REVERT: G 278 LYS cc_start: 0.8264 (mttt) cc_final: 0.7816 (mttt) REVERT: B 46 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7932 (ttp80) REVERT: B 59 ARG cc_start: 0.7955 (mmt90) cc_final: 0.7733 (mpt-90) REVERT: C 161 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8942 (mtmt) REVERT: D 46 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7946 (ttp-170) REVERT: D 59 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7439 (mmt90) REVERT: D 210 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8561 (mt0) REVERT: F 203 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8394 (tm-30) outliers start: 26 outliers final: 11 residues processed: 250 average time/residue: 0.8872 time to fit residues: 239.2454 Evaluate side-chains 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 238 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 149 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 116 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN A 210 GLN B 210 GLN C 92 GLN D 30 ASN F 92 GLN F 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.081717 restraints weight = 18882.029| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.49 r_work: 0.2641 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16905 Z= 0.126 Angle : 0.463 4.677 22701 Z= 0.236 Chirality : 0.039 0.130 2926 Planarity : 0.003 0.026 2450 Dihedral : 18.787 131.644 3136 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.75 % Allowed : 10.58 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.18), residues: 1820 helix: 3.17 (0.15), residues: 1043 sheet: 0.42 (0.27), residues: 280 loop : -0.28 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 46 TYR 0.006 0.001 TYR G 75 PHE 0.015 0.001 PHE E 277 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (16905) covalent geometry : angle 0.46261 / 0.24 (22701) hydrogen bonds : bond 0.04320 / 2.96 ( 1082) hydrogen bonds : angle 4.10388 / 3.01 ( 3183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7886 (ttp-110) REVERT: A 47 MET cc_start: 0.8692 (mtt) cc_final: 0.8443 (mtm) REVERT: G 88 ARG cc_start: 0.8700 (mmm160) cc_final: 0.8468 (mmt-90) REVERT: G 278 LYS cc_start: 0.8298 (mttt) cc_final: 0.7865 (mttt) REVERT: B 46 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7892 (ttp80) REVERT: B 59 ARG cc_start: 0.7940 (mmt90) cc_final: 0.7723 (mpt-90) REVERT: C 161 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8893 (mttt) REVERT: D 59 ARG cc_start: 0.7866 (mmt90) cc_final: 0.7399 (mmt90) REVERT: D 210 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8743 (mt0) REVERT: E 46 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7389 (tpm170) REVERT: E 88 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8440 (mmt-90) REVERT: E 149 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8911 (mt0) REVERT: F 203 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8249 (tm-30) outliers start: 26 outliers final: 8 residues processed: 253 average time/residue: 0.8737 time to fit residues: 238.4249 Evaluate side-chains 247 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 121 optimal weight: 0.0020 chunk 148 optimal weight: 3.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 210 GLN G 210 GLN B 210 GLN C 92 GLN C 210 GLN E 30 ASN F 92 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.082019 restraints weight = 18775.958| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.48 r_work: 0.2696 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16905 Z= 0.116 Angle : 0.453 4.600 22701 Z= 0.231 Chirality : 0.039 0.126 2926 Planarity : 0.002 0.022 2450 Dihedral : 18.309 126.947 3136 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.62 % Allowed : 10.92 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.18), residues: 1820 helix: 3.26 (0.15), residues: 1043 sheet: 0.42 (0.27), residues: 280 loop : -0.30 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 59 TYR 0.006 0.001 TYR A 75 PHE 0.015 0.001 PHE B 277 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (16905) covalent geometry : angle 0.45325 / 0.23 (22701) hydrogen bonds : bond 0.04158 / 2.85 ( 1082) hydrogen bonds : angle 4.06342 / 2.98 ( 3183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8194 (ttp-170) cc_final: 0.7936 (ttp-110) REVERT: A 47 MET cc_start: 0.8715 (mtt) cc_final: 0.8473 (mtm) REVERT: A 149 GLN cc_start: 0.9082 (mp10) cc_final: 0.8647 (mp10) REVERT: G 278 LYS cc_start: 0.8374 (mttt) cc_final: 0.7949 (mttt) REVERT: B 46 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7896 (ttp80) REVERT: B 59 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7793 (mpt-90) REVERT: C 59 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7769 (mpt-90) REVERT: C 161 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8925 (mttt) REVERT: D 210 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8816 (mt0) REVERT: E 46 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7477 (tpm170) REVERT: E 88 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8526 (mmt-90) REVERT: F 203 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8306 (tm-30) outliers start: 24 outliers final: 8 residues processed: 254 average time/residue: 0.8918 time to fit residues: 244.1122 Evaluate side-chains 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 243 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 124 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 14 optimal weight: 0.0010 chunk 171 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN G 149 GLN C 92 GLN D 276 ASN F 30 ASN F 92 GLN F 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.080954 restraints weight = 19039.357| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.47 r_work: 0.2680 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16905 Z= 0.136 Angle : 0.476 4.686 22701 Z= 0.241 Chirality : 0.039 0.144 2926 Planarity : 0.003 0.028 2450 Dihedral : 18.175 128.420 3136 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.95 % Allowed : 11.05 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.18), residues: 1820 helix: 3.23 (0.15), residues: 1043 sheet: 0.47 (0.27), residues: 280 loop : -0.33 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 88 TYR 0.007 0.001 TYR B 75 PHE 0.010 0.001 PHE G 188 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (16905) covalent geometry : angle 0.47602 / 0.24 (22701) hydrogen bonds : bond 0.04310 / 2.95 ( 1082) hydrogen bonds : angle 4.10724 / 3.01 ( 3183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7964 (ttp-110) REVERT: A 47 MET cc_start: 0.8685 (mtt) cc_final: 0.8447 (mtm) REVERT: G 161 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9018 (mtmm) REVERT: G 278 LYS cc_start: 0.8389 (mttt) cc_final: 0.7987 (mttt) REVERT: B 46 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7923 (ttp80) REVERT: B 59 ARG cc_start: 0.8056 (mmt90) cc_final: 0.7844 (mpt-90) REVERT: C 161 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8950 (mttt) REVERT: D 210 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8833 (mt0) REVERT: E 46 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7496 (tpm170) REVERT: E 149 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8930 (mt0) REVERT: F 149 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8626 (mp10) REVERT: F 203 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8201 (tm-30) outliers start: 29 outliers final: 9 residues processed: 249 average time/residue: 0.8933 time to fit residues: 239.6366 Evaluate side-chains 254 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 149 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 chunk 93 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN G 210 GLN B 210 GLN C 92 GLN F 92 GLN F 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.082382 restraints weight = 18971.821| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.47 r_work: 0.2710 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16905 Z= 0.105 Angle : 0.452 4.615 22701 Z= 0.229 Chirality : 0.039 0.122 2926 Planarity : 0.002 0.022 2450 Dihedral : 17.892 127.503 3136 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.08 % Allowed : 11.99 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.19), residues: 1820 helix: 3.31 (0.15), residues: 1043 sheet: 0.41 (0.27), residues: 280 loop : -0.36 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 88 TYR 0.007 0.001 TYR A 75 PHE 0.013 0.001 PHE E 277 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (16905) covalent geometry : angle 0.45240 / 0.23 (22701) hydrogen bonds : bond 0.03989 / 2.73 ( 1082) hydrogen bonds : angle 4.03670 / 2.96 ( 3183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8681 (mtt) cc_final: 0.8448 (mtm) REVERT: G 161 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9005 (mtmm) REVERT: G 278 LYS cc_start: 0.8423 (mttt) cc_final: 0.8021 (mttt) REVERT: B 46 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7907 (ttp80) REVERT: B 59 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7729 (mpt-90) REVERT: C 59 ARG cc_start: 0.8060 (mmt90) cc_final: 0.7752 (mpt-90) REVERT: E 46 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7464 (tpm170) REVERT: F 203 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8168 (tm-30) outliers start: 16 outliers final: 7 residues processed: 252 average time/residue: 0.8413 time to fit residues: 228.2255 Evaluate side-chains 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 243 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 0.6980 chunk 171 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 GLN F 92 GLN F 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.082008 restraints weight = 19188.191| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.47 r_work: 0.2695 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16905 Z= 0.120 Angle : 0.466 4.653 22701 Z= 0.236 Chirality : 0.039 0.125 2926 Planarity : 0.003 0.025 2450 Dihedral : 17.731 128.281 3136 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.08 % Allowed : 12.67 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.19), residues: 1820 helix: 3.31 (0.15), residues: 1043 sheet: 0.44 (0.27), residues: 280 loop : -0.37 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 88 TYR 0.009 0.001 TYR A 75 PHE 0.010 0.001 PHE G 277 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (16905) covalent geometry : angle 0.46613 / 0.24 (22701) hydrogen bonds : bond 0.04123 / 2.82 ( 1082) hydrogen bonds : angle 4.05006 / 2.97 ( 3183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8723 (mtt) cc_final: 0.8486 (mtm) REVERT: G 278 LYS cc_start: 0.8420 (mttt) cc_final: 0.8026 (mttt) REVERT: B 46 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7910 (ttp80) REVERT: B 59 ARG cc_start: 0.8041 (mmt90) cc_final: 0.7751 (mpt-90) REVERT: C 59 ARG cc_start: 0.8088 (mmt90) cc_final: 0.7771 (mpt-90) REVERT: E 46 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7474 (tpm170) REVERT: E 149 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8954 (mt0) REVERT: F 149 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: F 203 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8208 (tm-30) outliers start: 16 outliers final: 9 residues processed: 244 average time/residue: 0.8586 time to fit residues: 225.5373 Evaluate side-chains 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 240 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 149 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 112 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 149 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 GLN F 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.081524 restraints weight = 19027.934| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.46 r_work: 0.2681 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16905 Z= 0.127 Angle : 0.467 4.780 22701 Z= 0.237 Chirality : 0.039 0.126 2926 Planarity : 0.003 0.038 2450 Dihedral : 17.611 129.905 3136 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.74 % Allowed : 13.27 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.19), residues: 1820 helix: 3.32 (0.15), residues: 1043 sheet: 0.46 (0.27), residues: 280 loop : -0.36 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 88 TYR 0.008 0.001 TYR A 75 PHE 0.013 0.001 PHE E 277 TRP 0.003 0.001 TRP G 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16905) covalent geometry : angle 0.46725 / 0.24 (22701) hydrogen bonds : bond 0.04215 / 2.88 ( 1082) hydrogen bonds : angle 4.07084 / 2.98 ( 3183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 242 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8710 (mtt) cc_final: 0.8472 (mtm) REVERT: G 278 LYS cc_start: 0.8435 (mttt) cc_final: 0.8049 (mttt) REVERT: B 46 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7908 (ttp80) REVERT: B 59 ARG cc_start: 0.8046 (mmt90) cc_final: 0.7749 (mpt-90) REVERT: C 59 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7758 (mpt-90) REVERT: E 46 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7553 (tpm170) REVERT: E 149 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8957 (mt0) REVERT: F 149 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: F 203 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8243 (tm-30) outliers start: 11 outliers final: 8 residues processed: 242 average time/residue: 0.8908 time to fit residues: 232.0426 Evaluate side-chains 252 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 242 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 149 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 12 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 GLN F 92 GLN F 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.081528 restraints weight = 19106.740| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.47 r_work: 0.2683 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16905 Z= 0.123 Angle : 0.464 5.393 22701 Z= 0.236 Chirality : 0.039 0.125 2926 Planarity : 0.003 0.027 2450 Dihedral : 17.431 131.028 3136 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.81 % Allowed : 13.27 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.19), residues: 1820 helix: 3.34 (0.15), residues: 1043 sheet: 0.47 (0.27), residues: 280 loop : -0.35 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 88 TYR 0.008 0.001 TYR A 75 PHE 0.014 0.001 PHE G 277 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16905) covalent geometry : angle 0.46442 / 0.24 (22701) hydrogen bonds : bond 0.04185 / 2.86 ( 1082) hydrogen bonds : angle 4.05835 / 2.97 ( 3183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6768.31 seconds wall clock time: 115 minutes 54.25 seconds (6954.25 seconds total)