Starting phenix.real_space_refine on Wed Mar 4 20:36:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ooa_13008/03_2026/7ooa_13008.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ooa_13008/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ooa_13008/03_2026/7ooa_13008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ooa_13008/03_2026/7ooa_13008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ooa_13008/03_2026/7ooa_13008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ooa_13008/03_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-5986/lib/python3.9/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: 133 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: 133 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: 133 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: 133 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: 133 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: 133 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: 133 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 3.91, per 1000 atoms: 0.25 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: 1.56 Conformation dependent library (CDL) restraints added in 589.4 milliseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 56.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 20 through 59 removed outlier: 4.186A 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: 2.47 Time building geometry restraints manager: 1.95 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: 10339 25.55 - 51.11: 301 51.11 - 76.66: 112 76.66 - 102.22: 84 102.22 - 127.77: 140 Dihedral angle restraints: 10976 sinusoidal: 5719 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 10973 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: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 21.922 127.771 7588 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 covalent geometry : bond 0.00518 (15813) covalent geometry : angle 0.66233 (21301) hydrogen bonds : bond 0.09467 ( 1077) hydrogen bonds : angle 5.02574 ( 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 : 0.502 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: 0.8690 time to fit residues: 254.4626 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 : 0.505 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3210 r_free = 0.3210 target = 0.114304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.087864 restraints weight = 17474.408| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.16 r_work: 0.2671 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15813 Z= 0.215 Angle : 0.650 8.133 21301 Z= 0.309 Chirality : 0.045 0.178 2681 Planarity : 0.004 0.024 2450 Dihedral : 20.084 125.978 4463 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.29 % Allowed : 9.37 % Favored : 88.34 % 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: 2.26 (0.18), residues: 1820 helix: 2.86 (0.15), residues: 1029 sheet: 0.05 (0.32), residues: 175 loop : -0.48 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 184 TYR 0.011 0.002 TYR D 75 PHE 0.021 0.003 PHE B 178 TRP 0.005 0.001 TRP D 251 Details of bonding type rmsd covalent geometry : bond 0.00510 (15813) covalent geometry : angle 0.64962 (21301) hydrogen bonds : bond 0.05176 ( 1077) hydrogen bonds : angle 4.44696 ( 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 259 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.555 Fit side-chains REVERT: C 210 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: D 46 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7754 (ttp-110) REVERT: E 210 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: G 92 GLN cc_start: 0.8834 (mt0) cc_final: 0.8593 (mt0) REVERT: G 210 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7826 (mp10) outliers start: 34 outliers final: 7 residues processed: 236 average time/residue: 0.8683 time to fit residues: 219.0444 Evaluate side-chains 217 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 0.0170 chunk 164 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN 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 = 0.3259 r_free = 0.3259 target = 0.118149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.091740 restraints weight = 17653.247| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.18 r_work: 0.2734 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15813 Z= 0.104 Angle : 0.490 7.434 21301 Z= 0.240 Chirality : 0.040 0.123 2681 Planarity : 0.003 0.034 2450 Dihedral : 15.907 123.318 4461 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.68 % Allowed : 10.92 % Favored : 87.40 % 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: 2.55 (0.18), residues: 1820 helix: 3.21 (0.15), residues: 1029 sheet: 0.13 (0.35), residues: 175 loop : -0.57 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 59 TYR 0.007 0.001 TYR D 75 PHE 0.018 0.002 PHE B 277 TRP 0.005 0.001 TRP A 251 Details of bonding type rmsd covalent geometry : bond 0.00205 (15813) covalent geometry : angle 0.49002 (21301) hydrogen bonds : bond 0.04130 ( 1077) hydrogen bonds : angle 4.08219 ( 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 262 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.462 Fit side-chains REVERT: A 112 GLN cc_start: 0.8108 (tt0) cc_final: 0.7893 (tt0) REVERT: A 210 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: B 59 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7591 (mmt90) REVERT: C 149 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8532 (mm110) REVERT: C 273 MET cc_start: 0.8869 (tpp) cc_final: 0.8294 (tpp) REVERT: D 46 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7650 (ttp-110) REVERT: D 54 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7193 (mtp180) REVERT: D 155 MET cc_start: 0.9506 (ptp) cc_final: 0.9270 (ptm) REVERT: G 47 MET cc_start: 0.8599 (mtm) cc_final: 0.8338 (mtm) REVERT: G 92 GLN cc_start: 0.8748 (mt0) cc_final: 0.8506 (mt0) outliers start: 25 outliers final: 3 residues processed: 244 average time/residue: 0.8593 time to fit residues: 224.0831 Evaluate side-chains 212 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 195 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 63 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN D 92 GLN D 210 GLN F 112 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 = 0.3240 r_free = 0.3240 target = 0.116655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.090345 restraints weight = 17552.746| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.17 r_work: 0.2710 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: 0.8575 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15813 Z= 0.121 Angle : 0.469 4.514 21301 Z= 0.241 Chirality : 0.040 0.132 2681 Planarity : 0.003 0.030 2450 Dihedral : 15.092 123.643 4459 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 2.29 % Allowed : 11.59 % Favored : 86.12 % 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: 2.58 (0.18), residues: 1820 helix: 3.25 (0.15), residues: 1029 sheet: 0.12 (0.34), residues: 175 loop : -0.57 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 59 TYR 0.010 0.001 TYR D 75 PHE 0.015 0.002 PHE E 277 TRP 0.002 0.001 TRP A 251 Details of bonding type rmsd covalent geometry : bond 0.00265 (15813) covalent geometry : angle 0.46904 (21301) hydrogen bonds : bond 0.04277 ( 1077) hydrogen bonds : angle 4.07409 ( 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 257 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.442 Fit side-chains REVERT: A 112 GLN cc_start: 0.8141 (tt0) cc_final: 0.7918 (tt0) REVERT: A 210 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: B 59 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7553 (mmt90) REVERT: C 105 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8471 (tt) REVERT: C 149 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8586 (mm110) REVERT: C 273 MET cc_start: 0.8734 (tpp) cc_final: 0.8190 (tpp) REVERT: D 46 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7580 (ttp-110) REVERT: D 50 ASN cc_start: 0.8762 (m-40) cc_final: 0.8519 (m110) REVERT: D 54 ARG cc_start: 0.7605 (mtp180) cc_final: 0.7204 (mtp180) REVERT: D 155 MET cc_start: 0.9519 (ptp) cc_final: 0.9291 (ptm) REVERT: E 210 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: G 210 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7789 (mp10) outliers start: 34 outliers final: 7 residues processed: 235 average time/residue: 0.8869 time to fit residues: 222.6559 Evaluate side-chains 219 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 213 ASP 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 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 210 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 34 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3209 r_free = 0.3209 target = 0.114290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.087994 restraints weight = 17596.847| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.17 r_work: 0.2670 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1810 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= 0.190 Angle : 0.534 4.831 21301 Z= 0.274 Chirality : 0.042 0.139 2681 Planarity : 0.004 0.030 2450 Dihedral : 15.158 123.129 4459 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 1.95 % Allowed : 13.21 % 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: 2.98 (0.15), residues: 1029 sheet: 0.02 (0.33), residues: 175 loop : -0.55 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 59 TYR 0.013 0.002 TYR B 75 PHE 0.016 0.002 PHE B 178 TRP 0.004 0.001 TRP B 251 Details of bonding type rmsd covalent geometry : bond 0.00453 (15813) covalent geometry : angle 0.53431 (21301) hydrogen bonds : bond 0.04830 ( 1077) hydrogen bonds : angle 4.27599 ( 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 247 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.415 Fit side-chains REVERT: A 112 GLN cc_start: 0.8261 (tt0) cc_final: 0.8043 (tt0) REVERT: A 181 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 210 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: B 59 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7634 (mmt90) REVERT: C 61 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8237 (mt) REVERT: C 88 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7866 (tpt90) REVERT: C 105 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8475 (tt) REVERT: C 149 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8617 (mm110) REVERT: C 273 MET cc_start: 0.8761 (tpp) cc_final: 0.8235 (tpp) REVERT: D 46 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7707 (ttp-110) REVERT: D 50 ASN cc_start: 0.8806 (m-40) cc_final: 0.8595 (m110) REVERT: D 54 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7240 (mtp180) REVERT: E 210 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: G 47 MET cc_start: 0.8690 (mtm) cc_final: 0.8411 (mtm) REVERT: G 210 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.7743 (mp10) outliers start: 29 outliers final: 6 residues processed: 236 average time/residue: 0.8940 time to fit residues: 225.1707 Evaluate side-chains 222 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN F 112 GLN F 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.089359 restraints weight = 17514.465| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.13 r_work: 0.2698 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15813 Z= 0.140 Angle : 0.474 4.738 21301 Z= 0.248 Chirality : 0.040 0.132 2681 Planarity : 0.003 0.027 2450 Dihedral : 14.851 121.520 4459 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 2.29 % Allowed : 13.01 % Favored : 84.70 % 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: 2.40 (0.18), residues: 1820 helix: 3.07 (0.15), residues: 1029 sheet: 0.01 (0.33), residues: 175 loop : -0.59 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 59 TYR 0.011 0.001 TYR B 75 PHE 0.015 0.002 PHE E 277 TRP 0.003 0.001 TRP D 240 Details of bonding type rmsd covalent geometry : bond 0.00319 (15813) covalent geometry : angle 0.47415 (21301) hydrogen bonds : bond 0.04455 ( 1077) hydrogen bonds : angle 4.16555 ( 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 252 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.531 Fit side-chains REVERT: A 112 GLN cc_start: 0.8180 (tt0) cc_final: 0.7958 (tt0) REVERT: A 210 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: B 59 ARG cc_start: 0.7852 (mmt-90) cc_final: 0.7603 (mmt90) REVERT: C 88 ARG cc_start: 0.8073 (tpp80) cc_final: 0.7855 (tpt90) REVERT: C 105 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8474 (tt) REVERT: C 149 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8618 (mm110) REVERT: C 273 MET cc_start: 0.8768 (tpp) cc_final: 0.8215 (tpp) REVERT: D 46 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7830 (ttp-110) REVERT: D 54 ARG cc_start: 0.7583 (mtp180) cc_final: 0.7190 (mtp180) REVERT: E 210 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: G 47 MET cc_start: 0.8692 (mtm) cc_final: 0.8418 (mtm) REVERT: G 210 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: G 273 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8110 (ttm) outliers start: 34 outliers final: 9 residues processed: 235 average time/residue: 0.8768 time to fit residues: 219.9431 Evaluate side-chains 223 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 169 LYS Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain E residue 29 VAL 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 273 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 171 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN C 30 ASN D 92 GLN F 112 GLN F 149 GLN F 210 GLN G 30 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.087231 restraints weight = 17503.452| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.17 r_work: 0.2658 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15813 Z= 0.207 Angle : 0.556 4.992 21301 Z= 0.285 Chirality : 0.043 0.141 2681 Planarity : 0.004 0.034 2450 Dihedral : 15.132 122.046 4459 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.36 % Allowed : 12.94 % Favored : 84.70 % 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: 2.18 (0.18), residues: 1820 helix: 2.83 (0.15), residues: 1029 sheet: -0.01 (0.33), residues: 175 loop : -0.59 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 59 TYR 0.014 0.002 TYR B 75 PHE 0.017 0.002 PHE B 178 TRP 0.005 0.001 TRP B 251 Details of bonding type rmsd covalent geometry : bond 0.00495 (15813) covalent geometry : angle 0.55596 (21301) hydrogen bonds : bond 0.04997 ( 1077) hydrogen bonds : angle 4.33326 ( 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 251 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.476 Fit side-chains REVERT: A 112 GLN cc_start: 0.8245 (tt0) cc_final: 0.8028 (tt0) REVERT: A 210 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: B 59 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7560 (mmt90) REVERT: C 273 MET cc_start: 0.8766 (tpp) cc_final: 0.8208 (tpp) REVERT: D 46 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7808 (ttp-110) REVERT: E 35 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8208 (mm) REVERT: E 210 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: G 47 MET cc_start: 0.8710 (mtm) cc_final: 0.8435 (mtm) REVERT: G 210 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: G 273 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8117 (ttm) outliers start: 35 outliers final: 10 residues processed: 236 average time/residue: 0.8808 time to fit residues: 222.0433 Evaluate side-chains 224 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 C residue 169 LYS Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain E residue 29 VAL 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 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: 0.9990 chunk 99 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 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 = 0.3229 r_free = 0.3229 target = 0.116204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.089865 restraints weight = 17607.830| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.18 r_work: 0.2701 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15813 Z= 0.115 Angle : 0.454 4.706 21301 Z= 0.239 Chirality : 0.040 0.144 2681 Planarity : 0.003 0.033 2450 Dihedral : 14.490 119.881 4459 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 1.55 % Allowed : 13.95 % Favored : 84.50 % 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: 2.41 (0.18), residues: 1820 helix: 3.12 (0.15), residues: 1029 sheet: -0.01 (0.33), residues: 175 loop : -0.65 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 59 TYR 0.007 0.001 TYR D 75 PHE 0.014 0.002 PHE C 277 TRP 0.003 0.001 TRP A 251 Details of bonding type rmsd covalent geometry : bond 0.00242 (15813) covalent geometry : angle 0.45362 (21301) hydrogen bonds : bond 0.04263 ( 1077) hydrogen bonds : angle 4.12060 ( 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 246 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.429 Fit side-chains REVERT: A 112 GLN cc_start: 0.8151 (tt0) cc_final: 0.7905 (tt0) REVERT: B 59 ARG cc_start: 0.7775 (mmt-90) cc_final: 0.7518 (mmt90) REVERT: C 149 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8544 (mm110) REVERT: C 273 MET cc_start: 0.8716 (tpp) cc_final: 0.8178 (tpp) REVERT: D 54 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7143 (mtp180) REVERT: E 35 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8182 (mm) REVERT: E 210 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: E 260 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8360 (mm-30) REVERT: G 210 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.7654 (mp10) outliers start: 23 outliers final: 8 residues processed: 235 average time/residue: 0.8751 time to fit residues: 219.8023 Evaluate side-chains 220 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 278 LYS 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 F residue 88 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 105 LEU 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: 1.9990 chunk 85 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 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 = 0.3220 r_free = 0.3220 target = 0.115571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.089536 restraints weight = 17523.586| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.13 r_work: 0.2700 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15813 Z= 0.130 Angle : 0.472 4.825 21301 Z= 0.248 Chirality : 0.040 0.144 2681 Planarity : 0.003 0.030 2450 Dihedral : 14.323 120.709 4459 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.48 % Allowed : 14.08 % Favored : 84.43 % 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: 2.40 (0.18), residues: 1820 helix: 3.10 (0.15), residues: 1029 sheet: 0.00 (0.33), 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 0.008 0.001 TYR D 75 PHE 0.014 0.002 PHE G 277 TRP 0.003 0.001 TRP D 240 Details of bonding type rmsd covalent geometry : bond 0.00291 (15813) covalent geometry : angle 0.47216 (21301) hydrogen bonds : bond 0.04364 ( 1077) hydrogen bonds : angle 4.14017 ( 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 234 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.526 Fit side-chains REVERT: A 112 GLN cc_start: 0.8153 (tt0) cc_final: 0.7922 (tt0) REVERT: B 59 ARG cc_start: 0.7783 (mmt-90) cc_final: 0.7529 (mmt90) REVERT: C 149 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8563 (mm110) REVERT: C 273 MET cc_start: 0.8750 (tpp) cc_final: 0.8185 (tpp) REVERT: C 278 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7232 (mtpt) REVERT: D 54 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7120 (mtp180) REVERT: E 35 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8223 (mm) REVERT: E 210 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: E 260 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8380 (mm-30) REVERT: G 210 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7739 (mp10) outliers start: 22 outliers final: 7 residues processed: 223 average time/residue: 0.8821 time to fit residues: 209.9771 Evaluate side-chains 219 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 278 LYS 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 F residue 88 ARG Chi-restraints excluded: chain F residue 89 VAL 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: 3.9990 chunk 86 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3226 r_free = 0.3226 target = 0.116054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.090023 restraints weight = 17453.415| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.13 r_work: 0.2707 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15813 Z= 0.121 Angle : 0.460 4.760 21301 Z= 0.243 Chirality : 0.040 0.143 2681 Planarity : 0.003 0.032 2450 Dihedral : 14.046 120.448 4459 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.28 % Allowed : 14.08 % Favored : 84.64 % 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: 2.41 (0.18), residues: 1820 helix: 3.12 (0.15), residues: 1029 sheet: -0.02 (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 B 75 PHE 0.014 0.002 PHE B 178 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd covalent geometry : bond 0.00265 (15813) covalent geometry : angle 0.46020 (21301) hydrogen bonds : bond 0.04252 ( 1077) hydrogen bonds : angle 4.10587 ( 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 233 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.948 Fit side-chains REVERT: A 112 GLN cc_start: 0.8144 (tt0) cc_final: 0.7912 (tt0) REVERT: B 59 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7426 (mmt90) REVERT: C 273 MET cc_start: 0.8749 (tpp) cc_final: 0.8160 (tpp) REVERT: C 278 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7129 (mtpt) REVERT: D 54 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7114 (mtp180) REVERT: E 35 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8212 (mm) REVERT: E 210 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: E 260 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8369 (mm-30) REVERT: F 273 MET cc_start: 0.8929 (ttm) cc_final: 0.8414 (ttm) REVERT: G 210 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.7760 (mp10) outliers start: 19 outliers final: 8 residues processed: 224 average time/residue: 0.8927 time to fit residues: 213.5429 Evaluate side-chains 220 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 278 LYS 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 F residue 88 ARG Chi-restraints excluded: chain F residue 89 VAL 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: 1.9990 chunk 177 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3227 r_free = 0.3227 target = 0.116130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.089865 restraints weight = 17345.285| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.16 r_work: 0.2698 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15813 Z= 0.125 Angle : 0.468 4.919 21301 Z= 0.246 Chirality : 0.041 0.153 2681 Planarity : 0.003 0.032 2450 Dihedral : 13.878 121.234 4459 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.48 % Allowed : 13.88 % Favored : 84.64 % 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: 2.40 (0.18), residues: 1820 helix: 3.11 (0.15), residues: 1029 sheet: -0.01 (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 0.007 0.001 TYR D 75 PHE 0.014 0.002 PHE B 178 TRP 0.002 0.001 TRP D 240 Details of bonding type rmsd covalent geometry : bond 0.00277 (15813) covalent geometry : angle 0.46761 (21301) hydrogen bonds : bond 0.04287 ( 1077) hydrogen bonds : angle 4.11475 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5520.38 seconds wall clock time: 94 minutes 30.60 seconds (5670.60 seconds total)