Starting phenix.real_space_refine on Fri Jul 3 21:00:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ooa_13008/07_2026/7ooa_13008.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ooa_13008/07_2026/7ooa_13008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ooa_13008/07_2026/7ooa_13008.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ooa_13008/07_2026/7ooa_13008.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ooa_13008/07_2026/7ooa_13008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ooa_13008/07_2026/7ooa_13008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ooa_13008/07_2026/7ooa_13008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ooa_13008/07_2026/7ooa_13008.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 10171 2.51 5 N 2450 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15610 Number of models: 1 Model: "" Number of chains: 14 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: "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: "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: "A" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "B" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "C" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "D" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "E" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "F" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "G" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 3.52, per 1000 atoms: 0.23 Number of scatterers: 15610 At special positions: 0 Unit cell: (98.9055, 98.9055, 138.255, 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 2940 8.00 N 2450 7.00 C 10171 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: 1.38 Conformation dependent library (CDL) restraints added in 650.3 milliseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 56.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 Processing helix chain 'A' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 20 through 59 removed outlier: 4.185A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 89 Processing helix chain 'B' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 89 Processing helix chain 'C' and resid 92 through 128 removed outlier: 5.366A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 89 Processing helix chain 'D' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 89 Processing helix chain 'E' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 89 Processing helix chain 'F' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 20 through 59 removed outlier: 4.185A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 89 Processing helix chain 'G' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 removed outlier: 3.571A pdb=" N GLY G 173 " --> pdb=" O LYS G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.713A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.746A 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: 6.617A 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: 8.212A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N MET G 273 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ARG G 279 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LYS G 278 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.618A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.618A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 3168 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: 2.60 Time building geometry restraints manager: 1.79 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: 2311 1.32 - 1.44: 3961 1.44 - 1.56: 9443 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 15813 Sorted by residual: bond pdb=" C4 PEE G 303 " pdb=" O4P PEE G 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C4 PEE B 303 " pdb=" O4P PEE B 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C4 PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C4 PEE C 303 " pdb=" O4P PEE C 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 15808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 20966 2.43 - 4.85: 321 4.85 - 7.28: 7 7.28 - 9.71: 0 9.71 - 12.13: 7 Bond angle restraints: 21301 Sorted by residual: angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O3P PEE D 303 " pdb=" P PEE D 303 " pdb=" O4P PEE D 303 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O3P PEE G 303 " pdb=" P PEE G 303 " pdb=" O4P PEE G 303 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3P PEE C 303 " pdb=" P PEE C 303 " pdb=" O4P PEE C 303 " ideal model delta sigma weight residual 92.91 105.03 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 92.91 105.03 -12.12 3.00e+00 1.11e-01 1.63e+01 ... (remaining 21296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.55: 8981 25.55 - 51.11: 154 51.11 - 76.66: 35 76.66 - 102.22: 14 102.22 - 127.77: 42 Dihedral angle restraints: 9226 sinusoidal: 3969 harmonic: 5257 Sorted by residual: dihedral pdb=" C12 PEE E 303 " pdb=" C10 PEE E 303 " pdb=" C11 PEE E 303 " pdb=" O4 PEE E 303 " ideal model delta sinusoidal sigma weight residual -19.47 -147.24 127.77 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C12 PEE A 301 " pdb=" C10 PEE A 301 " pdb=" C11 PEE A 301 " pdb=" O4 PEE A 301 " ideal model delta sinusoidal sigma weight residual -19.47 -147.21 127.74 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C12 PEE D 303 " pdb=" C10 PEE D 303 " pdb=" C11 PEE D 303 " pdb=" O4 PEE D 303 " ideal model delta sinusoidal sigma weight residual -19.47 -147.21 127.74 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 9223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2074 0.050 - 0.100: 474 0.100 - 0.150: 98 0.150 - 0.199: 18 0.199 - 0.249: 17 Chirality restraints: 2681 Sorted by residual: chirality pdb=" C2 PEE C 303 " pdb=" C1 PEE C 303 " pdb=" C3 PEE C 303 " pdb=" O2 PEE C 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 PEE A 301 " pdb=" C1 PEE A 301 " pdb=" C3 PEE A 301 " pdb=" O2 PEE A 301 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.55e+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 -2.58 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2678 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 270 " 0.012 5.00e-02 4.00e+02 1.87e-02 5.60e-01 pdb=" N PRO D 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 270 " 0.012 5.00e-02 4.00e+02 1.87e-02 5.58e-01 pdb=" N PRO E 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO E 271 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 271 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 270 " 0.012 5.00e-02 4.00e+02 1.85e-02 5.50e-01 pdb=" N PRO F 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " 0.010 5.00e-02 4.00e+02 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2897 2.78 - 3.31: 14785 3.31 - 3.84: 25988 3.84 - 4.37: 30771 4.37 - 4.90: 54493 Nonbonded interactions: 128934 Sorted by model distance: nonbonded pdb=" OD2 ASP B 159 " pdb=" NZ LYS B 161 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP E 159 " pdb=" NZ LYS E 161 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP D 159 " pdb=" NZ LYS D 161 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP G 159 " pdb=" NZ LYS G 161 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP A 159 " pdb=" NZ LYS A 161 " model vdw 2.256 3.120 ... (remaining 128929 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 302 or (resid 305 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name CAA or name CAB or n \ ame 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 CBP or name CBQ or name CBR or name CBS or n \ ame CBT or name CCF or name CCH or name CCJ or name CCL or name CCM or name CCQ \ or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name OAL or \ name OAN or name OAP or name OBV or name OBX or name OCB)))) selection = (chain 'B' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'C' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'D' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'E' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'F' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'G' and (resid 19 through 280 or (resid 302 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 305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.170 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.005 0.041 15813 Z= 0.249 Angle : 0.662 12.132 21301 Z= 0.289 Chirality : 0.047 0.249 2681 Planarity : 0.003 0.019 2450 Dihedral : 15.269 127.771 5838 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 2.71 (0.18), residues: 1820 helix: 3.13 (0.15), residues: 1029 sheet: 0.82 (0.29), residues: 280 loop : -0.53 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 184 TYR 0.006 0.001 TYR E 75 PHE 0.012 0.002 PHE G 178 TRP 0.002 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.25 (15813) covalent geometry : angle 0.66233 / 0.29 (21301) hydrogen bonds : bond 0.09467 / 6.59 ( 1077) hydrogen bonds : angle 5.02574 / 3.73 ( 3168) *********************** 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 274 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.552 Fit side-chains REVERT: A 105 LEU cc_start: 0.8773 (tp) cc_final: 0.8553 (tp) REVERT: B 92 GLN cc_start: 0.8454 (mt0) cc_final: 0.8233 (mt0) REVERT: C 54 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6997 (mtm-85) REVERT: C 149 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8162 (mm110) REVERT: D 75 TYR cc_start: 0.8614 (m-10) cc_final: 0.8359 (m-80) REVERT: E 75 TYR cc_start: 0.8712 (m-10) cc_final: 0.8464 (m-80) REVERT: G 92 GLN cc_start: 0.8355 (mt0) cc_final: 0.8085 (mt0) outliers start: 0 outliers final: 2 residues processed: 274 average time/residue: 0.8861 time to fit residues: 260.4556 Evaluate side-chains 210 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain G residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 276 ASN C 276 ASN D 92 GLN D 112 GLN F 92 GLN F 112 GLN F 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.087799 restraints weight = 17466.749| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.12 r_work: 0.2674 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15813 Z= 0.215 Angle : 0.577 4.724 21301 Z= 0.293 Chirality : 0.043 0.140 2681 Planarity : 0.004 0.026 2450 Dihedral : 17.297 123.743 2713 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.43 % Allowed : 9.30 % Favored : 88.27 % 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: 2.21 (0.18), residues: 1820 helix: 2.82 (0.15), residues: 1029 sheet: -0.00 (0.32), residues: 175 loop : -0.49 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 184 TYR 0.011 0.002 TYR D 75 PHE 0.020 0.003 PHE B 178 TRP 0.005 0.001 TRP D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (15813) covalent geometry : angle 0.57676 / 0.29 (21301) hydrogen bonds : bond 0.05213 / 3.62 ( 1077) hydrogen bonds : angle 4.44566 / 3.29 ( 3168) *********************** 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 263 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.490 Fit side-chains REVERT: A 149 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8856 (mm-40) REVERT: C 59 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7849 (mmt90) REVERT: C 210 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: D 46 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7698 (ttp-110) REVERT: E 210 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: G 92 GLN cc_start: 0.8819 (mt0) cc_final: 0.8587 (mt0) REVERT: G 210 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.7850 (mp10) outliers start: 36 outliers final: 7 residues processed: 239 average time/residue: 0.7890 time to fit residues: 202.4909 Evaluate side-chains 215 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 129 optimal weight: 7.9990 chunk 164 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 112 GLN F 112 GLN F 149 GLN F 210 GLN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.088868 restraints weight = 17644.444| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.19 r_work: 0.2686 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15813 Z= 0.140 Angle : 0.473 4.596 21301 Z= 0.248 Chirality : 0.041 0.130 2681 Planarity : 0.003 0.028 2450 Dihedral : 16.530 120.038 2711 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.22 % Allowed : 10.98 % Favored : 86.79 % 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: 2.36 (0.18), residues: 1820 helix: 3.00 (0.15), residues: 1029 sheet: 0.04 (0.33), residues: 175 loop : -0.53 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 59 TYR 0.009 0.001 TYR B 75 PHE 0.019 0.002 PHE B 277 TRP 0.002 0.001 TRP D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15813) covalent geometry : angle 0.47298 / 0.25 (21301) hydrogen bonds : bond 0.04620 / 3.21 ( 1077) hydrogen bonds : angle 4.25303 / 3.15 ( 3168) *********************** 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 263 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.471 Fit side-chains REVERT: A 112 GLN cc_start: 0.8256 (tt0) cc_final: 0.8049 (tt0) REVERT: A 149 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8870 (mm-40) REVERT: A 210 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: B 59 ARG cc_start: 0.7880 (mmt-90) cc_final: 0.7628 (mmt90) REVERT: C 88 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7821 (tpt90) REVERT: C 149 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8592 (mm110) REVERT: C 273 MET cc_start: 0.8943 (tpp) cc_final: 0.8257 (tpp) REVERT: D 46 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7665 (ttp-110) REVERT: D 61 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8214 (mt) REVERT: D 155 MET cc_start: 0.9523 (ptp) cc_final: 0.9281 (ptm) REVERT: E 210 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: F 155 MET cc_start: 0.9469 (ptp) cc_final: 0.9240 (ptm) REVERT: G 47 MET cc_start: 0.8697 (mtm) cc_final: 0.8412 (mtm) REVERT: G 92 GLN cc_start: 0.8785 (mt0) cc_final: 0.8542 (mt0) REVERT: G 210 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7703 (mp10) outliers start: 33 outliers final: 6 residues processed: 243 average time/residue: 0.8321 time to fit residues: 216.6566 Evaluate side-chains 224 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 ASN B 149 GLN D 92 GLN F 112 GLN F 210 GLN G 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.090786 restraints weight = 17619.553| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.17 r_work: 0.2715 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 15813 Z= 0.106 Angle : 0.432 4.545 21301 Z= 0.229 Chirality : 0.040 0.125 2681 Planarity : 0.003 0.036 2450 Dihedral : 15.826 116.324 2711 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.95 % Allowed : 11.73 % Favored : 86.32 % 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: 2.53 (0.18), residues: 1820 helix: 3.21 (0.15), residues: 1029 sheet: 0.10 (0.34), residues: 175 loop : -0.60 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 59 TYR 0.009 0.001 TYR D 75 PHE 0.017 0.002 PHE G 277 TRP 0.002 0.001 TRP C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (15813) covalent geometry : angle 0.43180 / 0.23 (21301) hydrogen bonds : bond 0.04156 / 2.88 ( 1077) hydrogen bonds : angle 4.08361 / 3.02 ( 3168) *********************** 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 262 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.538 Fit side-chains REVERT: A 112 GLN cc_start: 0.8172 (tt0) cc_final: 0.7950 (tt0) REVERT: A 210 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.7575 (mp10) REVERT: B 59 ARG cc_start: 0.7790 (mmt-90) cc_final: 0.7512 (mmt90) REVERT: C 105 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8434 (tt) REVERT: C 149 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8579 (mm110) REVERT: C 273 MET cc_start: 0.8760 (tpp) cc_final: 0.8218 (tpp) REVERT: D 46 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7649 (ttp-110) REVERT: D 54 ARG cc_start: 0.7612 (mtp180) cc_final: 0.7208 (mtp180) REVERT: D 155 MET cc_start: 0.9509 (ptp) cc_final: 0.9280 (ptm) REVERT: E 210 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: F 155 MET cc_start: 0.9469 (ptp) cc_final: 0.9236 (ptm) REVERT: G 47 MET cc_start: 0.8676 (mtm) cc_final: 0.8385 (mtm) REVERT: G 210 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7733 (mp10) outliers start: 29 outliers final: 5 residues processed: 245 average time/residue: 0.8794 time to fit residues: 231.2315 Evaluate side-chains 218 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 112 GLN F 149 GLN F 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.088215 restraints weight = 17670.692| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.17 r_work: 0.2674 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15813 Z= 0.174 Angle : 0.512 4.578 21301 Z= 0.265 Chirality : 0.042 0.136 2681 Planarity : 0.003 0.025 2450 Dihedral : 16.242 116.850 2709 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 2.22 % Allowed : 12.33 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.18), residues: 1820 helix: 3.00 (0.14), residues: 1029 sheet: 0.00 (0.33), residues: 175 loop : -0.57 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 59 TYR 0.013 0.002 TYR B 75 PHE 0.017 0.002 PHE B 277 TRP 0.004 0.001 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (15813) covalent geometry : angle 0.51247 / 0.26 (21301) hydrogen bonds : bond 0.04739 / 3.30 ( 1077) hydrogen bonds : angle 4.25421 / 3.14 ( 3168) *********************** 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 259 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.524 Fit side-chains REVERT: A 112 GLN cc_start: 0.8256 (tt0) cc_final: 0.8039 (tt0) REVERT: A 210 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: B 59 ARG cc_start: 0.7827 (mmt-90) cc_final: 0.7570 (mmt90) REVERT: C 61 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8250 (mt) REVERT: C 88 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7859 (tpt90) REVERT: C 273 MET cc_start: 0.8778 (tpp) cc_final: 0.8214 (tpp) REVERT: D 46 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7661 (ttp-110) REVERT: D 54 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7234 (mtp180) REVERT: E 210 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: F 155 MET cc_start: 0.9484 (ptp) cc_final: 0.9247 (ptm) REVERT: G 47 MET cc_start: 0.8676 (mtm) cc_final: 0.8392 (mtm) REVERT: G 210 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: G 278 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6954 (mtmt) outliers start: 33 outliers final: 9 residues processed: 241 average time/residue: 0.8980 time to fit residues: 231.9161 Evaluate side-chains 232 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 24 optimal weight: 0.0670 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN D 92 GLN F 112 GLN F 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.090654 restraints weight = 17606.917| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.19 r_work: 0.2717 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15813 Z= 0.102 Angle : 0.432 4.562 21301 Z= 0.229 Chirality : 0.040 0.125 2681 Planarity : 0.003 0.034 2450 Dihedral : 15.700 115.741 2709 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.62 % Allowed : 12.94 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.18), residues: 1820 helix: 3.24 (0.15), residues: 1029 sheet: 0.03 (0.34), residues: 175 loop : -0.65 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 59 TYR 0.008 0.001 TYR E 75 PHE 0.016 0.001 PHE B 277 TRP 0.003 0.001 TRP A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (15813) covalent geometry : angle 0.43152 / 0.23 (21301) hydrogen bonds : bond 0.04117 / 2.86 ( 1077) hydrogen bonds : angle 4.06314 / 3.01 ( 3168) *********************** 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 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.377 Fit side-chains REVERT: A 112 GLN cc_start: 0.8140 (tt0) cc_final: 0.7908 (tt0) REVERT: A 210 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: B 59 ARG cc_start: 0.7818 (mmt-90) cc_final: 0.7565 (mmt90) REVERT: B 278 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7101 (mtmt) REVERT: C 88 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7795 (tpt90) REVERT: C 273 MET cc_start: 0.8767 (tpp) cc_final: 0.8180 (tpp) REVERT: D 54 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7168 (mtp180) REVERT: D 155 MET cc_start: 0.9495 (ptp) cc_final: 0.9269 (ptm) REVERT: E 210 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: F 155 MET cc_start: 0.9458 (ptp) cc_final: 0.9218 (ptm) REVERT: G 210 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7625 (mp10) outliers start: 24 outliers final: 6 residues processed: 237 average time/residue: 0.8044 time to fit residues: 204.0692 Evaluate side-chains 223 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 213 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 171 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN D 92 GLN F 112 GLN F 149 GLN F 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.088264 restraints weight = 17521.812| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.17 r_work: 0.2676 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15813 Z= 0.175 Angle : 0.518 4.859 21301 Z= 0.267 Chirality : 0.042 0.138 2681 Planarity : 0.003 0.026 2450 Dihedral : 16.142 116.364 2709 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.02 % Allowed : 13.14 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.18), residues: 1820 helix: 3.01 (0.15), residues: 1029 sheet: -0.02 (0.33), residues: 175 loop : -0.60 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 59 TYR 0.012 0.002 TYR B 75 PHE 0.017 0.002 PHE B 277 TRP 0.004 0.001 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (15813) covalent geometry : angle 0.51767 / 0.27 (21301) hydrogen bonds : bond 0.04711 / 3.27 ( 1077) hydrogen bonds : angle 4.23721 / 3.14 ( 3168) *********************** 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 245 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.530 Fit side-chains REVERT: A 112 GLN cc_start: 0.8228 (tt0) cc_final: 0.8005 (tt0) REVERT: A 210 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: B 59 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7572 (mmt90) REVERT: C 88 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7863 (tpt90) REVERT: C 112 GLN cc_start: 0.8153 (tt0) cc_final: 0.7665 (tm-30) REVERT: C 273 MET cc_start: 0.8767 (tpp) cc_final: 0.8182 (tpp) REVERT: D 54 ARG cc_start: 0.7574 (mtp180) cc_final: 0.7171 (mtp180) REVERT: D 155 MET cc_start: 0.9514 (ptp) cc_final: 0.9282 (ptm) REVERT: E 35 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8189 (mm) REVERT: E 210 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: F 155 MET cc_start: 0.9477 (ptp) cc_final: 0.9245 (ptm) REVERT: G 210 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: G 273 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8114 (ttm) outliers start: 30 outliers final: 8 residues processed: 233 average time/residue: 0.8753 time to fit residues: 218.2533 Evaluate side-chains 225 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 19 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 66 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 112 GLN F 149 GLN F 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.090337 restraints weight = 17690.242| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.19 r_work: 0.2709 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15813 Z= 0.108 Angle : 0.441 4.585 21301 Z= 0.234 Chirality : 0.040 0.139 2681 Planarity : 0.003 0.033 2450 Dihedral : 15.623 116.084 2709 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.48 % Allowed : 13.48 % Favored : 85.04 % 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: 2.50 (0.18), residues: 1820 helix: 3.23 (0.15), residues: 1029 sheet: 0.00 (0.34), residues: 175 loop : -0.66 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 59 TYR 0.006 0.001 TYR D 75 PHE 0.015 0.002 PHE B 277 TRP 0.003 0.001 TRP A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (15813) covalent geometry : angle 0.44116 / 0.23 (21301) hydrogen bonds : bond 0.04129 / 2.86 ( 1077) hydrogen bonds : angle 4.06026 / 3.01 ( 3168) *********************** 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 244 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8145 (tt0) cc_final: 0.7910 (tt0) REVERT: A 210 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7525 (mp10) REVERT: B 59 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.7448 (mmt90) REVERT: C 88 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7815 (tpt90) REVERT: C 112 GLN cc_start: 0.8114 (tt0) cc_final: 0.7595 (tm-30) REVERT: C 273 MET cc_start: 0.8771 (tpp) cc_final: 0.8235 (tpp) REVERT: D 54 ARG cc_start: 0.7508 (mtp180) cc_final: 0.7120 (mtp180) REVERT: D 155 MET cc_start: 0.9521 (ptp) cc_final: 0.9294 (ptm) REVERT: E 35 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8158 (mm) REVERT: E 210 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.7805 (mp10) REVERT: E 260 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8347 (mm-30) REVERT: F 88 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.8005 (tpt90) REVERT: F 155 MET cc_start: 0.9467 (ptp) cc_final: 0.9234 (ptm) REVERT: G 210 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7617 (mp10) outliers start: 22 outliers final: 5 residues processed: 235 average time/residue: 0.8649 time to fit residues: 217.6209 Evaluate side-chains 217 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 170 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 GLN C 30 ASN D 92 GLN F 112 GLN F 149 GLN F 210 GLN G 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.090808 restraints weight = 17600.562| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.19 r_work: 0.2721 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15813 Z= 0.108 Angle : 0.442 4.560 21301 Z= 0.234 Chirality : 0.040 0.135 2681 Planarity : 0.003 0.035 2450 Dihedral : 15.293 116.272 2709 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.68 % Allowed : 13.54 % Favored : 84.77 % 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: 2.51 (0.18), residues: 1820 helix: 3.24 (0.15), residues: 1029 sheet: 0.01 (0.34), residues: 175 loop : -0.65 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 59 TYR 0.005 0.001 TYR B 75 PHE 0.015 0.002 PHE B 277 TRP 0.002 0.001 TRP A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (15813) covalent geometry : angle 0.44212 / 0.23 (21301) hydrogen bonds : bond 0.04094 / 2.83 ( 1077) hydrogen bonds : angle 4.03568 / 2.99 ( 3168) *********************** 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 240 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8113 (tt0) cc_final: 0.7883 (tt0) REVERT: A 210 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: B 59 ARG cc_start: 0.7669 (mmt-90) cc_final: 0.7345 (mmt90) REVERT: C 88 ARG cc_start: 0.8033 (tpp80) cc_final: 0.7796 (tpt90) REVERT: C 112 GLN cc_start: 0.8119 (tt0) cc_final: 0.7672 (tp40) REVERT: C 273 MET cc_start: 0.8788 (tpp) cc_final: 0.8261 (tpp) REVERT: D 54 ARG cc_start: 0.7495 (mtp180) cc_final: 0.7103 (mtp180) REVERT: E 35 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8210 (mm) REVERT: E 210 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: E 260 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8360 (mm-30) REVERT: F 88 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7994 (tpt90) REVERT: G 210 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.7639 (mp10) outliers start: 25 outliers final: 6 residues processed: 229 average time/residue: 0.8754 time to fit residues: 214.4057 Evaluate side-chains 216 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 GLN D 92 GLN F 112 GLN F 149 GLN F 210 GLN G 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.088543 restraints weight = 17543.387| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.18 r_work: 0.2679 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15813 Z= 0.164 Angle : 0.514 5.747 21301 Z= 0.267 Chirality : 0.042 0.156 2681 Planarity : 0.003 0.030 2450 Dihedral : 15.754 117.379 2709 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.21 % Allowed : 13.81 % Favored : 84.97 % 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: 2.33 (0.18), residues: 1820 helix: 3.01 (0.15), residues: 1029 sheet: -0.02 (0.33), residues: 175 loop : -0.60 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 59 TYR 0.009 0.001 TYR B 75 PHE 0.018 0.002 PHE B 178 TRP 0.004 0.001 TRP B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (15813) covalent geometry : angle 0.51442 / 0.27 (21301) hydrogen bonds : bond 0.04599 / 3.19 ( 1077) hydrogen bonds : angle 4.20996 / 3.12 ( 3168) ********************** 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 226 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.597 Fit side-chains REVERT: A 105 LEU cc_start: 0.9055 (tp) cc_final: 0.8846 (tp) REVERT: A 112 GLN cc_start: 0.8203 (tt0) cc_final: 0.7977 (tt0) REVERT: A 210 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: B 59 ARG cc_start: 0.7775 (mmt-90) cc_final: 0.7487 (mmt90) REVERT: C 88 ARG cc_start: 0.8087 (tpp80) cc_final: 0.7871 (tpt90) REVERT: C 112 GLN cc_start: 0.8122 (tt0) cc_final: 0.7632 (tm-30) REVERT: C 273 MET cc_start: 0.8790 (tpp) cc_final: 0.8257 (tpp) REVERT: D 54 ARG cc_start: 0.7461 (mtp180) cc_final: 0.7105 (mtp180) REVERT: E 35 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8172 (mm) REVERT: E 210 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: G 35 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8017 (mm) REVERT: G 210 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.7669 (mp10) outliers start: 18 outliers final: 5 residues processed: 219 average time/residue: 0.8652 time to fit residues: 202.4674 Evaluate side-chains 218 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 16 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 GLN C 149 GLN D 92 GLN F 112 GLN F 149 GLN F 210 GLN G 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.090288 restraints weight = 17413.093| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.17 r_work: 0.2707 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15813 Z= 0.116 Angle : 0.458 4.967 21301 Z= 0.242 Chirality : 0.041 0.161 2681 Planarity : 0.003 0.039 2450 Dihedral : 15.428 116.998 2709 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.28 % Allowed : 13.75 % Favored : 84.97 % 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: 2.45 (0.18), residues: 1820 helix: 3.16 (0.15), residues: 1029 sheet: 0.01 (0.34), residues: 175 loop : -0.64 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 59 TYR 0.010 0.001 TYR E 75 PHE 0.015 0.002 PHE B 277 TRP 0.002 0.001 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15813) covalent geometry : angle 0.45835 / 0.24 (21301) hydrogen bonds : bond 0.04198 / 2.90 ( 1077) hydrogen bonds : angle 4.09280 / 3.03 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5521.94 seconds wall clock time: 94 minutes 50.35 seconds (5690.35 seconds total)