Starting phenix.real_space_refine on Thu Mar 5 00:29:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7onj_12996/03_2026/7onj_12996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7onj_12996/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7onj_12996/03_2026/7onj_12996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7onj_12996/03_2026/7onj_12996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7onj_12996/03_2026/7onj_12996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7onj_12996/03_2026/7onj_12996.map" } 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-5986/lib/python3.9/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: 262 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: 262 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: 262 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: 262 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: 262 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: 262 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: 262 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: 3.95, per 1000 atoms: 0.23 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: 1.49 Conformation dependent library (CDL) restraints added in 646.2 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: 0.49 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: 2.95 Time building geometry restraints manager: 1.89 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 - 28.71: 11543 28.71 - 57.42: 609 57.42 - 86.14: 175 86.14 - 114.85: 238 114.85 - 143.56: 126 Dihedral angle restraints: 12691 sinusoidal: 7434 harmonic: 5257 Sorted by residual: dihedral pdb=" C3 PEE B 303 " pdb=" C1 PEE B 303 " pdb=" C2 PEE B 303 " pdb=" O3P PEE B 303 " ideal model delta sinusoidal sigma weight residual 62.73 -80.83 143.56 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 PEE E 303 " pdb=" C1 PEE E 303 " pdb=" C2 PEE E 303 " pdb=" O3P PEE E 303 " ideal model delta sinusoidal sigma weight residual 62.73 -80.76 143.49 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 PEE A 301 " pdb=" C1 PEE A 301 " pdb=" C2 PEE A 301 " pdb=" O3P PEE A 301 " ideal model delta sinusoidal sigma weight residual 62.73 -80.75 143.48 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 12688 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: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.110 Find NCS groups from input model: 0.420 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:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 27.956 143.559 9303 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 covalent geometry : bond 0.00935 (16905) covalent geometry : angle 0.85704 (22701) hydrogen bonds : bond 0.10857 ( 1082) hydrogen bonds : angle 5.34626 ( 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 : 0.542 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: 0.7996 time to fit residues: 268.5017 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 : 0.562 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 92 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.080879 restraints weight = 19006.072| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.43 r_work: 0.2628 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1436 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= 0.156 Angle : 0.671 7.930 22701 Z= 0.299 Chirality : 0.050 0.387 2926 Planarity : 0.003 0.031 2450 Dihedral : 25.386 147.682 6180 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.62 % Allowed : 8.56 % Favored : 89.82 % 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: 1.87 (0.17), residues: 1820 helix: 2.15 (0.14), residues: 1043 sheet: 0.36 (0.35), residues: 175 loop : -0.06 (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 covalent geometry : bond 0.00332 (16905) covalent geometry : angle 0.67093 (22701) hydrogen bonds : bond 0.04841 ( 1082) hydrogen bonds : angle 4.35156 ( 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 287 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7949 (ttp-110) REVERT: A 47 MET cc_start: 0.8683 (mtt) cc_final: 0.8410 (mtm) REVERT: A 149 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8931 (mp10) REVERT: G 88 ARG cc_start: 0.8671 (mmm160) cc_final: 0.8384 (mmt-90) REVERT: B 46 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7920 (ttp80) REVERT: B 54 ARG cc_start: 0.8281 (mtm110) cc_final: 0.8076 (mtm-85) REVERT: B 59 ARG cc_start: 0.7932 (mmt90) cc_final: 0.7647 (mpt-90) REVERT: B 62 ASP cc_start: 0.8438 (t70) cc_final: 0.8150 (t70) REVERT: C 54 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8170 (mtp180) REVERT: C 88 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8435 (mmt-90) REVERT: D 59 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7620 (mmt90) REVERT: E 47 MET cc_start: 0.8649 (mtm) cc_final: 0.8387 (mtm) REVERT: F 203 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8228 (tm-30) outliers start: 24 outliers final: 4 residues processed: 268 average time/residue: 0.8750 time to fit residues: 252.4918 Evaluate side-chains 260 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 254 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain D 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: 0.7980 chunk 174 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN G 92 GLN G 112 GLN G 276 ASN B 112 GLN B 210 GLN C 92 GLN D 112 GLN E 112 GLN F 92 GLN F 112 GLN F 210 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.080735 restraints weight = 19255.266| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.46 r_work: 0.2665 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16905 Z= 0.142 Angle : 0.670 9.413 22701 Z= 0.293 Chirality : 0.045 0.299 2926 Planarity : 0.003 0.032 2450 Dihedral : 21.725 138.618 6174 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.89 % Allowed : 9.50 % Favored : 88.61 % 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: 2.46 (0.18), residues: 1820 helix: 2.79 (0.15), residues: 1043 sheet: 0.36 (0.27), residues: 280 loop : -0.15 (0.22), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 59 TYR 0.006 0.001 TYR B 75 PHE 0.012 0.001 PHE E 277 TRP 0.003 0.001 TRP C 251 Details of bonding type rmsd covalent geometry : bond 0.00309 (16905) covalent geometry : angle 0.66995 (22701) hydrogen bonds : bond 0.04538 ( 1082) hydrogen bonds : angle 4.17980 ( 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 294 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7945 (ttp-110) REVERT: A 47 MET cc_start: 0.8699 (mtt) cc_final: 0.8445 (mtm) REVERT: A 59 ARG cc_start: 0.8052 (mmt90) cc_final: 0.7509 (mmt90) REVERT: A 149 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8883 (mp10) REVERT: G 88 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8374 (mmt-90) REVERT: G 149 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8859 (mp10) REVERT: G 197 ASP cc_start: 0.8695 (t0) cc_final: 0.8492 (t70) REVERT: G 278 LYS cc_start: 0.8310 (mttt) cc_final: 0.7916 (mttt) REVERT: B 46 ARG cc_start: 0.8209 (ttp-170) cc_final: 0.7976 (ttp80) REVERT: C 59 ARG cc_start: 0.8164 (mmt90) cc_final: 0.7959 (mpt-90) REVERT: C 88 ARG cc_start: 0.8731 (mmm160) cc_final: 0.8490 (mmt-90) REVERT: D 59 ARG cc_start: 0.7985 (mmt90) cc_final: 0.7593 (mmt90) REVERT: F 59 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7726 (mmt90) outliers start: 28 outliers final: 9 residues processed: 272 average time/residue: 0.8346 time to fit residues: 245.1133 Evaluate side-chains 250 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 239 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN 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 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 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: 0.6980 chunk 92 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 210 GLN G 92 GLN G 112 GLN G 210 GLN B 112 GLN B 210 GLN C 92 GLN C 112 GLN C 210 GLN D 30 ASN D 112 GLN E 30 ASN E 112 GLN F 92 GLN F 112 GLN F 203 GLN F 207 ASN F 210 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.083046 restraints weight = 18978.768| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.47 r_work: 0.2702 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16905 Z= 0.122 Angle : 0.640 7.052 22701 Z= 0.275 Chirality : 0.047 0.366 2926 Planarity : 0.003 0.032 2450 Dihedral : 19.919 136.214 6174 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.89 % Allowed : 10.11 % Favored : 88.01 % 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: 2.72 (0.18), residues: 1820 helix: 3.11 (0.15), residues: 1043 sheet: 0.34 (0.27), residues: 280 loop : -0.23 (0.22), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 59 TYR 0.006 0.001 TYR G 75 PHE 0.017 0.001 PHE B 277 TRP 0.002 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00256 (16905) covalent geometry : angle 0.63960 (22701) hydrogen bonds : bond 0.04050 ( 1082) hydrogen bonds : angle 4.07363 ( 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 294 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8209 (ttp-170) cc_final: 0.8003 (ttp-110) REVERT: A 59 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7352 (mmt90) REVERT: A 149 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8957 (mp10) REVERT: G 88 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8402 (mmt-90) REVERT: G 278 LYS cc_start: 0.8347 (mttt) cc_final: 0.7927 (mttt) REVERT: B 46 ARG cc_start: 0.8165 (ttp-170) cc_final: 0.7934 (ttp80) REVERT: C 88 ARG cc_start: 0.8552 (mmm160) cc_final: 0.8338 (mmt-90) REVERT: D 59 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7540 (mmt90) REVERT: D 210 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8754 (mt0) REVERT: E 46 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7416 (tpm170) REVERT: E 88 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8349 (mmt-90) REVERT: F 59 ARG cc_start: 0.8085 (mmt90) cc_final: 0.7571 (mmt90) outliers start: 28 outliers final: 7 residues processed: 271 average time/residue: 0.8828 time to fit residues: 257.6259 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 : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain G residue 89 VAL 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 29 VAL Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 30 ASN B 30 ASN B 112 GLN C 30 ASN C 92 GLN D 30 ASN E 30 ASN F 92 GLN F 112 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.082115 restraints weight = 18974.367| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.49 r_work: 0.2686 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16905 Z= 0.137 Angle : 0.621 7.445 22701 Z= 0.274 Chirality : 0.045 0.328 2926 Planarity : 0.003 0.031 2450 Dihedral : 19.523 133.264 6174 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.16 % Allowed : 10.85 % 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: 2.78 (0.18), residues: 1820 helix: 3.18 (0.15), residues: 1043 sheet: 0.40 (0.27), residues: 280 loop : -0.27 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 46 TYR 0.005 0.001 TYR B 75 PHE 0.011 0.001 PHE E 277 TRP 0.003 0.001 TRP G 240 Details of bonding type rmsd covalent geometry : bond 0.00300 (16905) covalent geometry : angle 0.62126 (22701) hydrogen bonds : bond 0.04230 ( 1082) hydrogen bonds : angle 4.09073 ( 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 280 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7723 (ttp80) REVERT: A 149 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8951 (mp10) REVERT: G 88 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8354 (mmt-90) REVERT: G 149 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: G 278 LYS cc_start: 0.8347 (mttt) cc_final: 0.7892 (mttt) REVERT: B 46 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7948 (ttp80) REVERT: B 60 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8398 (mmtm) REVERT: C 88 ARG cc_start: 0.8621 (mmm160) cc_final: 0.8375 (mmt-90) REVERT: D 59 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7541 (mmt90) REVERT: D 210 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8790 (mt0) REVERT: E 30 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7710 (m110) REVERT: E 46 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7429 (tpm170) REVERT: E 88 ARG cc_start: 0.8754 (mmm160) cc_final: 0.8324 (mmt-90) REVERT: F 149 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8525 (mp10) outliers start: 32 outliers final: 8 residues processed: 260 average time/residue: 0.8970 time to fit residues: 250.8329 Evaluate side-chains 257 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 245 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 149 GLN 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 30 ASN Chi-restraints excluded: chain E residue 89 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN G 30 ASN G 112 GLN B 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 92 GLN C 112 GLN C 210 GLN D 30 ASN D 112 GLN E 30 ASN E 112 GLN F 92 GLN F 112 GLN F 210 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.081447 restraints weight = 18860.428| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.49 r_work: 0.2683 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16905 Z= 0.153 Angle : 0.618 7.285 22701 Z= 0.276 Chirality : 0.046 0.346 2926 Planarity : 0.003 0.023 2450 Dihedral : 19.214 132.509 6174 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.75 % Allowed : 11.52 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.18), residues: 1820 helix: 3.17 (0.15), residues: 1043 sheet: 0.43 (0.27), residues: 280 loop : -0.30 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 88 TYR 0.007 0.001 TYR B 75 PHE 0.012 0.001 PHE B 277 TRP 0.004 0.001 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00342 (16905) covalent geometry : angle 0.61849 (22701) hydrogen bonds : bond 0.04363 ( 1082) hydrogen bonds : angle 4.13107 ( 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 274 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7712 (ttp80) REVERT: A 149 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8947 (mp10) REVERT: G 46 ARG cc_start: 0.8048 (ttp-110) cc_final: 0.7726 (ttp80) REVERT: G 88 ARG cc_start: 0.8709 (mmm160) cc_final: 0.8395 (mmt-90) REVERT: G 149 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: G 278 LYS cc_start: 0.8369 (mttt) cc_final: 0.7926 (mttt) REVERT: B 46 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7958 (ttp80) REVERT: B 60 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8405 (mmtm) REVERT: C 88 ARG cc_start: 0.8712 (mmm160) cc_final: 0.8462 (mmt-90) REVERT: D 59 ARG cc_start: 0.7952 (mmt90) cc_final: 0.7479 (mmt90) REVERT: D 210 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8790 (mt0) REVERT: E 46 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7441 (tpm170) REVERT: E 88 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8404 (mmt-90) REVERT: F 149 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8514 (mp10) outliers start: 26 outliers final: 9 residues processed: 258 average time/residue: 0.9047 time to fit residues: 250.7661 Evaluate side-chains 258 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 149 GLN 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 150 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 149 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 124 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 143 optimal weight: 0.0980 chunk 154 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 30 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 276 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN F 92 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 210 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.079969 restraints weight = 19011.504| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.48 r_work: 0.2644 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16905 Z= 0.186 Angle : 0.641 7.387 22701 Z= 0.290 Chirality : 0.048 0.349 2926 Planarity : 0.003 0.020 2450 Dihedral : 18.986 131.836 6174 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.22 % Allowed : 11.05 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.18), residues: 1820 helix: 3.07 (0.15), residues: 1043 sheet: 0.54 (0.27), residues: 280 loop : -0.33 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 88 TYR 0.007 0.001 TYR B 75 PHE 0.014 0.002 PHE E 277 TRP 0.004 0.001 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00427 (16905) covalent geometry : angle 0.64148 (22701) hydrogen bonds : bond 0.04755 ( 1082) hydrogen bonds : angle 4.24578 ( 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 286 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.497 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: 0.7695 (ttp80) REVERT: A 149 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8885 (mp10) REVERT: G 46 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7711 (ttp80) REVERT: G 88 ARG cc_start: 0.8807 (mmm160) cc_final: 0.8516 (mmt-90) REVERT: G 278 LYS cc_start: 0.8369 (mttt) cc_final: 0.7999 (mttt) REVERT: B 46 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7970 (ttp80) REVERT: B 60 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8397 (mmtm) REVERT: D 30 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7911 (m110) REVERT: D 210 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8809 (mt0) REVERT: E 88 ARG cc_start: 0.8780 (mmm160) cc_final: 0.8467 (mmt-90) REVERT: F 149 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8462 (mp10) outliers start: 33 outliers final: 11 residues processed: 263 average time/residue: 0.8995 time to fit residues: 254.3508 Evaluate side-chains 261 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 247 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 149 GLN 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 30 ASN 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 150 ILE Chi-restraints excluded: chain E residue 220 GLU 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: 3.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 30 ASN G 112 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 30 ASN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 30 ASN D 112 GLN E 30 ASN E 112 GLN F 30 ASN F 92 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.080980 restraints weight = 18979.826| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.46 r_work: 0.2681 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16905 Z= 0.145 Angle : 0.605 7.049 22701 Z= 0.272 Chirality : 0.047 0.368 2926 Planarity : 0.003 0.034 2450 Dihedral : 18.546 132.046 6174 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.89 % Allowed : 11.66 % Favored : 86.46 % 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: 2.75 (0.19), residues: 1820 helix: 3.16 (0.15), residues: 1043 sheet: 0.49 (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 A 88 TYR 0.005 0.001 TYR A 75 PHE 0.016 0.001 PHE B 277 TRP 0.004 0.001 TRP B 240 Details of bonding type rmsd covalent geometry : bond 0.00322 (16905) covalent geometry : angle 0.60458 (22701) hydrogen bonds : bond 0.04337 ( 1082) hydrogen bonds : angle 4.16554 ( 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 278 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7779 (ttp80) REVERT: A 149 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8919 (mp10) REVERT: G 46 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7764 (ttp80) REVERT: G 88 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8498 (mmt-90) REVERT: G 278 LYS cc_start: 0.8397 (mttt) cc_final: 0.8024 (mttt) REVERT: B 46 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7968 (ttp80) REVERT: D 210 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8785 (mt0) REVERT: E 46 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7524 (tpm170) REVERT: E 88 ARG cc_start: 0.8774 (mmm160) cc_final: 0.8440 (mmt-90) outliers start: 28 outliers final: 11 residues processed: 259 average time/residue: 0.9133 time to fit residues: 253.8182 Evaluate side-chains 263 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 251 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 149 GLN 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 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 150 ILE 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: 0.9980 chunk 171 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 30 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 112 GLN F 92 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.080572 restraints weight = 19160.759| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.47 r_work: 0.2649 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16905 Z= 0.155 Angle : 0.604 7.309 22701 Z= 0.276 Chirality : 0.047 0.394 2926 Planarity : 0.003 0.061 2450 Dihedral : 18.061 132.978 6174 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.75 % Allowed : 11.99 % 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: 2.77 (0.19), residues: 1820 helix: 3.16 (0.15), residues: 1043 sheet: 0.51 (0.27), residues: 280 loop : -0.34 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 88 TYR 0.005 0.001 TYR B 75 PHE 0.015 0.002 PHE E 277 TRP 0.004 0.001 TRP G 240 Details of bonding type rmsd covalent geometry : bond 0.00348 (16905) covalent geometry : angle 0.60415 (22701) hydrogen bonds : bond 0.04488 ( 1082) hydrogen bonds : angle 4.18086 ( 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 274 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7768 (ttp80) REVERT: A 149 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8950 (mp10) REVERT: G 46 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7759 (ttp80) REVERT: G 88 ARG cc_start: 0.8792 (mmm160) cc_final: 0.8532 (mmt-90) REVERT: G 278 LYS cc_start: 0.8421 (mttt) cc_final: 0.8047 (mttt) REVERT: B 46 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7915 (ttp80) REVERT: B 60 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8377 (mmtm) REVERT: D 210 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8810 (mt0) REVERT: E 30 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7726 (m110) REVERT: E 88 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8372 (mmt-90) outliers start: 26 outliers final: 12 residues processed: 254 average time/residue: 0.9173 time to fit residues: 250.0695 Evaluate side-chains 262 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 248 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 149 GLN 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 D residue 220 GLU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain F residue 35 LEU 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: 0.9980 chunk 31 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 30 ASN G 112 GLN B 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 30 ASN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 112 GLN E 112 GLN F 92 GLN F 210 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.081463 restraints weight = 19002.261| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.45 r_work: 0.2696 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2480 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= 0.127 Angle : 0.577 7.305 22701 Z= 0.263 Chirality : 0.046 0.432 2926 Planarity : 0.003 0.032 2450 Dihedral : 17.756 132.888 6174 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.28 % Allowed : 12.94 % Favored : 85.78 % 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 (0.19), residues: 1820 helix: 3.25 (0.15), residues: 1043 sheet: 0.42 (0.27), residues: 280 loop : -0.34 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 88 TYR 0.009 0.001 TYR A 75 PHE 0.016 0.001 PHE G 277 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00274 (16905) covalent geometry : angle 0.57710 (22701) hydrogen bonds : bond 0.04181 ( 1082) hydrogen bonds : angle 4.11828 ( 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 269 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8176 (ttp-170) cc_final: 0.7753 (ttp80) REVERT: G 46 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7758 (ttp80) REVERT: G 88 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8513 (mmt-90) REVERT: G 278 LYS cc_start: 0.8459 (mttt) cc_final: 0.8068 (mttt) REVERT: B 46 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7901 (ttp80) REVERT: B 60 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8383 (mmtm) REVERT: B 273 MET cc_start: 0.9243 (ttm) cc_final: 0.8759 (tpp) REVERT: C 59 ARG cc_start: 0.8103 (mmt90) cc_final: 0.7783 (mpt-90) REVERT: C 88 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8461 (mmt-90) REVERT: D 30 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7736 (m110) REVERT: D 210 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8800 (mt0) REVERT: E 46 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7546 (tpm170) REVERT: E 88 ARG cc_start: 0.8734 (mmm160) cc_final: 0.8423 (mmt-90) outliers start: 19 outliers final: 10 residues processed: 255 average time/residue: 0.9039 time to fit residues: 247.6237 Evaluate side-chains 261 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 35 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 30 ASN 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 150 ILE Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 12 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 210 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 30 ASN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 112 GLN E 30 ASN E 112 GLN F 92 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.081901 restraints weight = 19066.376| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.45 r_work: 0.2674 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16905 Z= 0.153 Angle : 0.773 59.198 22701 Z= 0.421 Chirality : 0.046 0.432 2926 Planarity : 0.003 0.030 2450 Dihedral : 17.753 132.898 6174 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.42 % Allowed : 12.74 % Favored : 85.85 % Cbeta Deviations : 0.06 % 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: 2.82 (0.19), residues: 1820 helix: 3.24 (0.15), residues: 1043 sheet: 0.42 (0.27), residues: 280 loop : -0.34 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 88 TYR 0.007 0.001 TYR A 75 PHE 0.012 0.001 PHE G 277 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00302 (16905) covalent geometry : angle 0.77291 (22701) hydrogen bonds : bond 0.04188 ( 1082) hydrogen bonds : angle 4.12318 ( 3183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6915.92 seconds wall clock time: 118 minutes 19.12 seconds (7099.12 seconds total)