Starting phenix.real_space_refine on Sat Jun 14 14:57:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ooa_13008/06_2025/7ooa_13008.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ooa_13008/06_2025/7ooa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ooa_13008/06_2025/7ooa_13008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ooa_13008/06_2025/7ooa_13008.map" model { file = "/net/cci-nas-00/data/ceres_data/7ooa_13008/06_2025/7ooa_13008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ooa_13008/06_2025/7ooa_13008.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.28, per 1000 atoms: 0.59 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: 4.65 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.74 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: 4.71 Time building geometry restraints manager: 5.32 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: 0.02 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: 2.670 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.790 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.060 ------------------------------------------------------------------------------- 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 : 5.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.001 TRP G 251 PHE 0.012 0.002 PHE G 178 TYR 0.006 0.001 TYR E 75 ARG 0.003 0.000 ARG D 184 Details of bonding type rmsd hydrogen bonds : bond 0.09467 ( 1077) hydrogen bonds : angle 5.02574 ( 3168) covalent geometry : bond 0.00518 (15813) covalent geometry : angle 0.66233 (21301) *********************** 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 : 1.837 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: 1.8889 time to fit residues: 554.4934 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 : 1.760 ------------------------------------------------------------------------------- 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 153 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 47 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.090350 restraints weight = 17434.090| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.17 r_work: 0.2711 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1159 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= 0.144 Angle : 0.590 7.855 21301 Z= 0.278 Chirality : 0.043 0.167 2681 Planarity : 0.003 0.033 2450 Dihedral : 18.816 126.785 4463 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 1.89 % Allowed : 9.70 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 1820 helix: 3.13 (0.15), residues: 1029 sheet: 0.10 (0.33), residues: 175 loop : -0.48 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 251 PHE 0.017 0.002 PHE B 178 TYR 0.007 0.001 TYR B 75 ARG 0.005 0.001 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 1077) hydrogen bonds : angle 4.26645 ( 3168) covalent geometry : bond 0.00315 (15813) covalent geometry : angle 0.59043 (21301) *********************** 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 262 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 1.597 Fit side-chains REVERT: A 105 LEU cc_start: 0.8947 (tp) cc_final: 0.8745 (tp) REVERT: B 59 ARG cc_start: 0.7930 (mmt-90) cc_final: 0.7665 (mmt90) REVERT: C 54 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.7165 (mtm-85) REVERT: C 105 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8382 (tt) REVERT: C 149 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8572 (mm110) REVERT: D 46 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7666 (ttp-110) REVERT: D 126 MET cc_start: 0.9299 (ttp) cc_final: 0.8958 (ttp) REVERT: D 155 MET cc_start: 0.9522 (ptp) cc_final: 0.9294 (ptm) REVERT: D 217 LYS cc_start: 0.9288 (mmtp) cc_final: 0.9088 (mmtm) REVERT: F 60 LYS cc_start: 0.8219 (mmtm) cc_final: 0.8005 (mtmm) REVERT: G 92 GLN cc_start: 0.8832 (mt0) cc_final: 0.8568 (mt0) REVERT: G 203 GLN cc_start: 0.8387 (pp30) cc_final: 0.8132 (pp30) outliers start: 28 outliers final: 3 residues processed: 243 average time/residue: 1.8585 time to fit residues: 483.8630 Evaluate side-chains 211 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain G residue 44 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 19 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 134 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 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 = 0.3217 r_free = 0.3217 target = 0.114980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.088962 restraints weight = 17358.797| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.12 r_work: 0.2692 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15813 Z= 0.156 Angle : 0.542 7.254 21301 Z= 0.268 Chirality : 0.041 0.135 2681 Planarity : 0.003 0.029 2450 Dihedral : 16.035 122.522 4461 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 2.43 % Allowed : 10.71 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 1820 helix: 3.05 (0.15), residues: 1029 sheet: 0.02 (0.33), residues: 175 loop : -0.52 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 251 PHE 0.015 0.002 PHE G 277 TYR 0.009 0.001 TYR B 75 ARG 0.004 0.001 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 1077) hydrogen bonds : angle 4.26457 ( 3168) covalent geometry : bond 0.00357 (15813) covalent geometry : angle 0.54221 (21301) *********************** 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 258 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 1.615 Fit side-chains REVERT: A 105 LEU cc_start: 0.8931 (tp) cc_final: 0.8730 (tp) REVERT: A 210 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: B 59 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.7634 (mmt90) REVERT: C 273 MET cc_start: 0.8831 (tpp) cc_final: 0.8188 (tpp) REVERT: D 46 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7690 (ttp-110) REVERT: E 210 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: G 47 MET cc_start: 0.8690 (mtm) cc_final: 0.8403 (mtm) REVERT: G 203 GLN cc_start: 0.8433 (pp30) cc_final: 0.8210 (pp30) REVERT: G 210 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7803 (mp10) outliers start: 36 outliers final: 7 residues processed: 235 average time/residue: 1.8812 time to fit residues: 473.2785 Evaluate side-chains 214 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 112 GLN D 92 GLN D 112 GLN F 112 GLN F 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.090645 restraints weight = 17417.997| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.17 r_work: 0.2715 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15813 Z= 0.111 Angle : 0.452 4.555 21301 Z= 0.234 Chirality : 0.040 0.127 2681 Planarity : 0.003 0.030 2450 Dihedral : 15.078 121.914 4459 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.02 % Allowed : 11.73 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.18), residues: 1820 helix: 3.23 (0.15), residues: 1029 sheet: 0.07 (0.34), residues: 175 loop : -0.55 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 251 PHE 0.016 0.002 PHE G 277 TYR 0.010 0.001 TYR D 75 ARG 0.008 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 1077) hydrogen bonds : angle 4.08958 ( 3168) covalent geometry : bond 0.00236 (15813) covalent geometry : angle 0.45169 (21301) *********************** 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 258 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 1.499 Fit side-chains REVERT: A 105 LEU cc_start: 0.8947 (tp) cc_final: 0.8744 (tp) REVERT: A 112 GLN cc_start: 0.8128 (tt0) cc_final: 0.7927 (tt0) REVERT: A 210 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: B 59 ARG cc_start: 0.7880 (mmt-90) cc_final: 0.7577 (mmt90) REVERT: C 105 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8449 (tt) REVERT: C 149 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8569 (mm110) REVERT: C 273 MET cc_start: 0.8745 (tpp) cc_final: 0.8206 (tpp) REVERT: D 46 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7749 (ttp-110) REVERT: D 54 ARG cc_start: 0.7626 (mtp180) cc_final: 0.7231 (mtp180) REVERT: E 210 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: G 47 MET cc_start: 0.8673 (mtm) cc_final: 0.8380 (mtm) REVERT: G 210 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: G 278 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6847 (mtmt) outliers start: 30 outliers final: 7 residues processed: 239 average time/residue: 1.8384 time to fit residues: 470.3785 Evaluate side-chains 221 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 278 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 30 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 115 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 G 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.116959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.090663 restraints weight = 17696.814| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.18 r_work: 0.2712 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15813 Z= 0.115 Angle : 0.447 4.535 21301 Z= 0.234 Chirality : 0.040 0.130 2681 Planarity : 0.003 0.035 2450 Dihedral : 14.582 122.167 4459 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 2.09 % Allowed : 12.20 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.18), residues: 1820 helix: 3.24 (0.15), residues: 1029 sheet: 0.04 (0.34), residues: 175 loop : -0.59 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 251 PHE 0.014 0.002 PHE E 277 TYR 0.009 0.001 TYR B 75 ARG 0.010 0.000 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 1077) hydrogen bonds : angle 4.07543 ( 3168) covalent geometry : bond 0.00247 (15813) covalent geometry : angle 0.44693 (21301) *********************** 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: 31 poor density : 228 time to evaluate : 1.637 Fit side-chains REVERT: A 105 LEU cc_start: 0.8925 (tp) cc_final: 0.8723 (tp) REVERT: A 112 GLN cc_start: 0.8136 (tt0) cc_final: 0.7912 (tt0) REVERT: A 149 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8862 (mm-40) REVERT: A 210 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: B 59 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7565 (mmt90) REVERT: B 210 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.7636 (mp10) REVERT: C 61 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8261 (mt) REVERT: C 88 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7775 (tpt90) REVERT: C 149 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8562 (mm110) REVERT: C 273 MET cc_start: 0.8764 (tpp) cc_final: 0.8192 (tpp) REVERT: D 54 ARG cc_start: 0.7536 (mtp180) cc_final: 0.7152 (mtp180) REVERT: E 210 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: G 210 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.7780 (mp10) outliers start: 31 outliers final: 8 residues processed: 239 average time/residue: 1.8560 time to fit residues: 475.2056 Evaluate side-chains 223 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 169 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 115 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 121 optimal weight: 0.0020 chunk 44 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.091333 restraints weight = 17448.556| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.17 r_work: 0.2727 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15813 Z= 0.101 Angle : 0.427 5.015 21301 Z= 0.224 Chirality : 0.039 0.127 2681 Planarity : 0.003 0.037 2450 Dihedral : 14.168 121.680 4459 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.75 % Allowed : 12.94 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.18), residues: 1820 helix: 3.31 (0.15), residues: 1029 sheet: 0.08 (0.34), residues: 175 loop : -0.60 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 251 PHE 0.013 0.001 PHE G 277 TYR 0.007 0.001 TYR D 75 ARG 0.009 0.000 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 1077) hydrogen bonds : angle 4.00396 ( 3168) covalent geometry : bond 0.00205 (15813) covalent geometry : angle 0.42703 (21301) *********************** 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 243 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.739 Fit side-chains REVERT: A 105 LEU cc_start: 0.8926 (tp) cc_final: 0.8717 (tp) REVERT: A 112 GLN cc_start: 0.8117 (tt0) cc_final: 0.7890 (tt0) REVERT: A 210 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: B 59 ARG cc_start: 0.7814 (mmt-90) cc_final: 0.7499 (mmt90) REVERT: C 105 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8460 (tt) REVERT: C 149 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8596 (mm110) REVERT: C 273 MET cc_start: 0.8754 (tpp) cc_final: 0.8181 (tpp) REVERT: D 54 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7140 (mtp180) REVERT: D 155 MET cc_start: 0.9488 (ptp) cc_final: 0.9265 (ptm) REVERT: E 35 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8189 (mm) REVERT: E 210 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: E 260 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8320 (mm-30) REVERT: F 88 ARG cc_start: 0.8240 (tpp-160) cc_final: 0.8034 (tpt90) REVERT: G 210 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: G 278 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6964 (mtmt) outliers start: 26 outliers final: 6 residues processed: 229 average time/residue: 1.9035 time to fit residues: 466.4794 Evaluate side-chains 217 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 C residue 105 LEU Chi-restraints excluded: chain C residue 278 LYS 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 Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 149 GLN D 92 GLN F 112 GLN F 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.088851 restraints weight = 17555.448| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.19 r_work: 0.2684 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15813 Z= 0.158 Angle : 0.493 4.942 21301 Z= 0.256 Chirality : 0.041 0.147 2681 Planarity : 0.003 0.033 2450 Dihedral : 14.383 121.986 4459 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.82 % Allowed : 13.01 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.18), residues: 1820 helix: 3.10 (0.15), residues: 1029 sheet: 0.02 (0.33), residues: 175 loop : -0.54 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 251 PHE 0.015 0.002 PHE G 178 TYR 0.010 0.001 TYR B 75 ARG 0.007 0.001 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1077) hydrogen bonds : angle 4.17210 ( 3168) covalent geometry : bond 0.00366 (15813) covalent geometry : angle 0.49267 (21301) *********************** 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 243 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 1.514 Fit side-chains REVERT: A 112 GLN cc_start: 0.8197 (tt0) cc_final: 0.7967 (tt0) REVERT: A 210 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: B 59 ARG cc_start: 0.7850 (mmt-90) cc_final: 0.7512 (mmt90) REVERT: B 210 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: C 88 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7823 (tpt90) REVERT: C 149 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8591 (mm110) REVERT: C 273 MET cc_start: 0.8728 (tpp) cc_final: 0.8150 (tpp) REVERT: D 54 ARG cc_start: 0.7531 (mtp180) cc_final: 0.7136 (mtp180) REVERT: D 61 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8133 (mt) REVERT: E 35 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8196 (mm) REVERT: E 210 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: F 88 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.8074 (tpt90) REVERT: G 210 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: G 278 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6888 (mtmt) outliers start: 27 outliers final: 8 residues processed: 231 average time/residue: 1.9124 time to fit residues: 471.7300 Evaluate side-chains 223 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 220 GLU 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 D residue 61 ILE 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 278 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 144 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.090626 restraints weight = 17478.287| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.19 r_work: 0.2715 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15813 Z= 0.107 Angle : 0.438 4.618 21301 Z= 0.231 Chirality : 0.040 0.127 2681 Planarity : 0.003 0.042 2450 Dihedral : 14.048 120.715 4459 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.62 % Allowed : 13.14 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.18), residues: 1820 helix: 3.25 (0.15), residues: 1029 sheet: 0.05 (0.34), residues: 175 loop : -0.60 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.013 0.001 PHE C 277 TYR 0.007 0.001 TYR D 75 ARG 0.008 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 1077) hydrogen bonds : angle 4.04162 ( 3168) covalent geometry : bond 0.00225 (15813) covalent geometry : angle 0.43778 (21301) *********************** 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 236 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 1.555 Fit side-chains REVERT: A 112 GLN cc_start: 0.8162 (tt0) cc_final: 0.7931 (tt0) REVERT: A 210 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: B 59 ARG cc_start: 0.7868 (mmt-90) cc_final: 0.7551 (mmt90) REVERT: B 278 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7037 (mtmt) REVERT: C 88 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7768 (tpt90) REVERT: C 149 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8602 (mm110) REVERT: C 273 MET cc_start: 0.8737 (tpp) cc_final: 0.8220 (tpp) REVERT: D 54 ARG cc_start: 0.7517 (mtp180) cc_final: 0.7130 (mtp180) REVERT: E 35 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8165 (mm) REVERT: E 210 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: E 260 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8324 (mm-30) REVERT: F 88 ARG cc_start: 0.8241 (tpp-160) cc_final: 0.8035 (tpt90) REVERT: G 210 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: G 278 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6953 (mtmt) outliers start: 24 outliers final: 7 residues processed: 225 average time/residue: 1.9091 time to fit residues: 458.8339 Evaluate side-chains 223 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 54 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN C 112 GLN D 92 GLN F 112 GLN F 149 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 = 0.3220 r_free = 0.3220 target = 0.115357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.089175 restraints weight = 17470.630| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.17 r_work: 0.2691 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1935 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= 0.146 Angle : 0.486 4.963 21301 Z= 0.254 Chirality : 0.041 0.151 2681 Planarity : 0.003 0.038 2450 Dihedral : 14.154 121.133 4459 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.68 % Allowed : 13.21 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.18), residues: 1820 helix: 3.09 (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 TRP 0.004 0.001 TRP B 251 PHE 0.021 0.002 PHE G 277 TYR 0.009 0.001 TYR B 75 ARG 0.009 0.001 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 1077) hydrogen bonds : angle 4.16058 ( 3168) covalent geometry : bond 0.00335 (15813) covalent geometry : angle 0.48606 (21301) *********************** 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 236 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 1.665 Fit side-chains REVERT: A 112 GLN cc_start: 0.8203 (tt0) cc_final: 0.7974 (tt0) REVERT: A 210 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: B 59 ARG cc_start: 0.7858 (mmt-90) cc_final: 0.7529 (mmt90) REVERT: B 210 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7636 (mp10) REVERT: B 278 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7145 (mtmt) REVERT: C 88 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7822 (tpt90) REVERT: C 112 GLN cc_start: 0.8177 (tt0) cc_final: 0.7698 (tm-30) REVERT: C 149 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8881 (mm-40) REVERT: C 273 MET cc_start: 0.8749 (tpp) cc_final: 0.8198 (tpp) REVERT: D 54 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7131 (mtp180) REVERT: D 61 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8151 (mt) REVERT: E 35 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8168 (mm) REVERT: E 210 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: E 260 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8305 (mm-30) REVERT: G 210 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: G 278 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6970 (mtmt) outliers start: 25 outliers final: 7 residues processed: 224 average time/residue: 2.0265 time to fit residues: 486.2740 Evaluate side-chains 223 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 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 D residue 61 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN B 149 GLN D 92 GLN F 112 GLN F 149 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 = 0.3236 r_free = 0.3236 target = 0.116539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.090636 restraints weight = 17582.789| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.14 r_work: 0.2716 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15813 Z= 0.114 Angle : 0.449 4.806 21301 Z= 0.238 Chirality : 0.040 0.132 2681 Planarity : 0.003 0.042 2450 Dihedral : 13.905 121.424 4459 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.35 % Allowed : 13.54 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.18), residues: 1820 helix: 3.18 (0.15), residues: 1029 sheet: 0.02 (0.34), residues: 175 loop : -0.58 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.013 0.002 PHE B 178 TYR 0.006 0.001 TYR B 75 ARG 0.009 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1077) hydrogen bonds : angle 4.07308 ( 3168) covalent geometry : bond 0.00246 (15813) covalent geometry : angle 0.44933 (21301) ********************** 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 234 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 1.649 Fit side-chains REVERT: A 112 GLN cc_start: 0.8157 (tt0) cc_final: 0.7930 (tt0) REVERT: A 210 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: B 59 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7519 (mmt90) REVERT: B 278 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7055 (mtmt) REVERT: C 88 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7792 (tpt90) REVERT: C 112 GLN cc_start: 0.8171 (tt0) cc_final: 0.7698 (tm-30) REVERT: C 273 MET cc_start: 0.8726 (tpp) cc_final: 0.8185 (tpp) REVERT: D 54 ARG cc_start: 0.7528 (mtp180) cc_final: 0.7144 (mtp180) REVERT: E 35 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8205 (mm) REVERT: E 210 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7776 (mp10) REVERT: E 260 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8318 (mm-30) REVERT: G 210 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: G 278 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6937 (mtmt) outliers start: 20 outliers final: 7 residues processed: 224 average time/residue: 1.9155 time to fit residues: 457.5390 Evaluate side-chains 223 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 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 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 113 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 170 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 G 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.091762 restraints weight = 17509.169| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.19 r_work: 0.2732 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15813 Z= 0.100 Angle : 0.431 4.739 21301 Z= 0.229 Chirality : 0.040 0.142 2681 Planarity : 0.003 0.041 2450 Dihedral : 13.499 121.896 4459 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.28 % Allowed : 13.54 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.18), residues: 1820 helix: 3.27 (0.15), residues: 1029 sheet: 1.22 (0.36), residues: 140 loop : -0.77 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 251 PHE 0.011 0.001 PHE C 277 TYR 0.005 0.001 TYR G 75 ARG 0.009 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1077) hydrogen bonds : angle 3.97991 ( 3168) covalent geometry : bond 0.00206 (15813) covalent geometry : angle 0.43098 (21301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11457.98 seconds wall clock time: 196 minutes 25.42 seconds (11785.42 seconds total)