Starting phenix.real_space_refine on Thu Jul 2 11:38:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vdm_31923/07_2026/7vdm_31923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdm_31923/07_2026/7vdm_31923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vdm_31923/07_2026/7vdm_31923.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vdm_31923/07_2026/7vdm_31923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vdm_31923/07_2026/7vdm_31923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdm_31923/07_2026/7vdm_31923.map" model { file = "/net/cci-nas-00/data/ceres_data/7vdm_31923/07_2026/7vdm_31923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdm_31923/07_2026/7vdm_31923.cif" } resolution = 2.98 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= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5486 2.51 5 N 1438 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8563 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1744 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2590 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1749 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2010 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Classifications: {'peptide': 3} Link IDs: {'PTRANS': 1, 'TRANS': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.87, per 1000 atoms: 0.22 Number of scatterers: 8563 At special positions: 0 Unit cell: (118.56, 108.16, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1576 8.00 N 1438 7.00 C 5486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 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: 0.66 Conformation dependent library (CDL) restraints added in 454.3 milliseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 35.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 4.003A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.562A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.567A pdb=" N ASP A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.784A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 removed outlier: 4.049A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.906A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.595A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 removed outlier: 4.366A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.177A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'R' and resid 33 through 57 Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.733A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE R 93 " --> pdb=" O TYR R 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 4.056A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 144 through 169 removed outlier: 3.599A pdb=" N VAL R 148 " --> pdb=" O HIS R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.864A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 238 through 243 Processing helix chain 'R' and resid 245 through 250 removed outlier: 3.625A pdb=" N ILE R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 280 removed outlier: 4.104A pdb=" N VAL R 263 " --> pdb=" O HIS R 259 " (cutoff:3.500A) Proline residue: R 276 - end of helix removed outlier: 3.530A pdb=" N TYR R 279 " --> pdb=" O ASN R 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.605A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.560A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.004A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.507A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.652A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.167A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.471A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.624A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.505A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.732A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.732A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.532A pdb=" N THR S 201 " --> pdb=" O SER S 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.636A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1200 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: 1.30 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 2712 1.35 - 1.48: 2341 1.48 - 1.61: 3611 1.61 - 1.75: 1 1.75 - 1.88: 87 Bond restraints: 8752 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.668 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.20e-02 6.94e+03 2.28e+01 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.54e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.96e+00 bond pdb=" C13 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.550 1.598 -0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 8747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 11691 4.39 - 8.77: 152 8.77 - 13.16: 19 13.16 - 17.55: 1 17.55 - 21.93: 2 Bond angle restraints: 11865 Sorted by residual: angle pdb=" CA LEU R 237 " pdb=" CB LEU R 237 " pdb=" CG LEU R 237 " ideal model delta sigma weight residual 116.30 138.23 -21.93 3.50e+00 8.16e-02 3.93e+01 angle pdb=" C ARG L 1 " pdb=" N PRO L 2 " pdb=" CA PRO L 2 " ideal model delta sigma weight residual 119.84 127.32 -7.48 1.25e+00 6.40e-01 3.58e+01 angle pdb=" CA LEU R 45 " pdb=" CB LEU R 45 " pdb=" CG LEU R 45 " ideal model delta sigma weight residual 116.30 135.77 -19.47 3.50e+00 8.16e-02 3.09e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" N THR B 143 " pdb=" CA THR B 143 " pdb=" C THR B 143 " ideal model delta sigma weight residual 112.47 118.75 -6.28 1.24e+00 6.50e-01 2.56e+01 ... (remaining 11860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4683 17.86 - 35.72: 387 35.72 - 53.57: 49 53.57 - 71.43: 15 71.43 - 89.29: 5 Dihedral angle restraints: 5139 sinusoidal: 1979 harmonic: 3160 Sorted by residual: dihedral pdb=" CA LEU R 237 " pdb=" C LEU R 237 " pdb=" N PRO R 238 " pdb=" CA PRO R 238 " ideal model delta harmonic sigma weight residual 180.00 140.63 39.37 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 162.18 -69.18 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -144.58 -35.42 0 5.00e+00 4.00e-02 5.02e+01 ... (remaining 5136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1051 0.074 - 0.148: 250 0.148 - 0.222: 37 0.222 - 0.295: 10 0.295 - 0.369: 3 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.75 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1348 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 237 " 0.064 5.00e-02 4.00e+02 9.73e-02 1.52e+01 pdb=" N PRO R 238 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO R 238 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 238 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 32 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO R 33 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 275 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO R 276 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 276 " 0.039 5.00e-02 4.00e+02 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1920 2.79 - 3.32: 7073 3.32 - 3.84: 14460 3.84 - 4.37: 16889 4.37 - 4.90: 29299 Nonbonded interactions: 69641 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.261 3.040 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.336 3.040 ... (remaining 69636 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.400 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.008 0.133 8755 Z= 0.351 Angle : 1.293 21.931 11871 Z= 0.678 Chirality : 0.066 0.369 1351 Planarity : 0.008 0.097 1486 Dihedral : 13.537 89.286 3092 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.22 % Allowed : 0.75 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.19 % 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: -2.74 (0.22), residues: 1078 helix: -2.29 (0.20), residues: 363 sheet: -0.82 (0.29), residues: 299 loop : -1.91 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 134 TYR 0.024 0.004 TYR R 222 PHE 0.028 0.003 PHE B 199 TRP 0.020 0.003 TRP B 63 HIS 0.010 0.003 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.35 ( 8752) covalent geometry : angle 1.29141 / 0.68 (11865) SS BOND : bond 0.01678 / 0.87 ( 3) SS BOND : angle 3.09962 / 1.63 ( 6) hydrogen bonds : bond 0.14579 / 8.88 ( 418) hydrogen bonds : angle 6.90710 / 4.80 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.390 Fit side-chains REVERT: A 24 ARG cc_start: 0.7023 (mtm-85) cc_final: 0.6684 (ptp-110) REVERT: A 26 ASP cc_start: 0.7134 (m-30) cc_final: 0.6880 (m-30) outliers start: 2 outliers final: 2 residues processed: 143 average time/residue: 0.6429 time to fit residues: 97.2454 Evaluate side-chains 103 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain L residue 1 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 91 HIS B 175 GLN B 340 ASN G 18 GLN S 182 ASN R 48 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144452 restraints weight = 9293.214| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.77 r_work: 0.3391 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8755 Z= 0.128 Angle : 0.620 12.465 11871 Z= 0.318 Chirality : 0.042 0.180 1351 Planarity : 0.005 0.074 1486 Dihedral : 6.164 71.228 1194 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.94 % Allowed : 10.86 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.24), residues: 1078 helix: 0.12 (0.26), residues: 370 sheet: -0.66 (0.30), residues: 289 loop : -1.45 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.029 0.002 TYR R 222 PHE 0.010 0.001 PHE S 200 TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8752) covalent geometry : angle 0.61962 / 0.32 (11865) SS BOND : bond 0.00717 / 0.37 ( 3) SS BOND : angle 1.46808 / 0.71 ( 6) hydrogen bonds : bond 0.04205 / 2.84 ( 418) hydrogen bonds : angle 4.76459 / 3.26 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.302 Fit side-chains REVERT: A 306 GLN cc_start: 0.6900 (mm110) cc_final: 0.6511 (mm110) REVERT: B 19 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7059 (ttp-170) REVERT: B 87 THR cc_start: 0.8374 (p) cc_final: 0.8094 (m) REVERT: B 323 ASP cc_start: 0.7796 (m-30) cc_final: 0.7386 (m-30) REVERT: R 222 TYR cc_start: 0.6522 (p90) cc_final: 0.6109 (p90) outliers start: 18 outliers final: 6 residues processed: 124 average time/residue: 0.6267 time to fit residues: 82.4248 Evaluate side-chains 107 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 255 ASN A 331 ASN B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.179349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143157 restraints weight = 9280.392| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.87 r_work: 0.3350 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8755 Z= 0.143 Angle : 0.605 9.891 11871 Z= 0.310 Chirality : 0.042 0.166 1351 Planarity : 0.004 0.069 1486 Dihedral : 5.588 69.369 1187 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.23 % Allowed : 12.37 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.25), residues: 1078 helix: 1.02 (0.27), residues: 369 sheet: -0.54 (0.30), residues: 290 loop : -1.22 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 168 TYR 0.024 0.002 TYR R 222 PHE 0.012 0.001 PHE A 223 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8752) covalent geometry : angle 0.60314 / 0.31 (11865) SS BOND : bond 0.00969 / 0.50 ( 3) SS BOND : angle 2.22988 / 1.14 ( 6) hydrogen bonds : bond 0.04033 / 2.73 ( 418) hydrogen bonds : angle 4.53658 / 3.11 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.315 Fit side-chains REVERT: A 251 ASP cc_start: 0.7817 (t0) cc_final: 0.7586 (t0) REVERT: A 306 GLN cc_start: 0.6898 (mm110) cc_final: 0.6508 (mm110) REVERT: A 349 LYS cc_start: 0.8362 (ttmp) cc_final: 0.7963 (ttpm) REVERT: B 19 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6998 (ttp-170) REVERT: B 269 ILE cc_start: 0.7131 (mp) cc_final: 0.6840 (mt) REVERT: B 323 ASP cc_start: 0.7496 (m-30) cc_final: 0.7050 (m-30) REVERT: G 37 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8627 (mp) REVERT: G 38 MET cc_start: 0.7788 (ttp) cc_final: 0.7478 (ttp) REVERT: R 222 TYR cc_start: 0.6295 (p90) cc_final: 0.5886 (p90) outliers start: 30 outliers final: 11 residues processed: 137 average time/residue: 0.5486 time to fit residues: 80.3030 Evaluate side-chains 115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 255 ASN B 142 HIS B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.180763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144783 restraints weight = 9331.440| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.82 r_work: 0.3393 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8755 Z= 0.119 Angle : 0.568 8.553 11871 Z= 0.294 Chirality : 0.041 0.149 1351 Planarity : 0.004 0.060 1486 Dihedral : 5.328 70.320 1187 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.47 % Allowed : 15.48 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1078 helix: 1.45 (0.28), residues: 368 sheet: -0.41 (0.31), residues: 284 loop : -1.00 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 61 TYR 0.020 0.002 TYR R 222 PHE 0.010 0.001 PHE A 196 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8752) covalent geometry : angle 0.56610 / 0.29 (11865) SS BOND : bond 0.01127 / 0.59 ( 3) SS BOND : angle 2.34529 / 1.21 ( 6) hydrogen bonds : bond 0.03662 / 2.49 ( 418) hydrogen bonds : angle 4.34097 / 2.97 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.292 Fit side-chains REVERT: A 306 GLN cc_start: 0.6980 (mm110) cc_final: 0.6553 (mm110) REVERT: A 349 LYS cc_start: 0.8407 (ttmp) cc_final: 0.7974 (ttpm) REVERT: B 34 THR cc_start: 0.7433 (m) cc_final: 0.7160 (p) REVERT: B 219 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7614 (mmm160) REVERT: B 269 ILE cc_start: 0.6990 (mp) cc_final: 0.6761 (mt) REVERT: G 38 MET cc_start: 0.7812 (ttp) cc_final: 0.7516 (ttp) REVERT: R 222 TYR cc_start: 0.6565 (p90) cc_final: 0.5986 (p90) outliers start: 23 outliers final: 13 residues processed: 132 average time/residue: 0.5569 time to fit residues: 78.4003 Evaluate side-chains 121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 278 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 103 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 255 ASN A 331 ASN B 142 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.180035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.144279 restraints weight = 9304.389| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.90 r_work: 0.3368 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8755 Z= 0.125 Angle : 0.563 8.989 11871 Z= 0.290 Chirality : 0.041 0.152 1351 Planarity : 0.004 0.058 1486 Dihedral : 5.255 71.357 1187 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.33 % Allowed : 16.02 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1078 helix: 1.69 (0.28), residues: 368 sheet: -0.36 (0.30), residues: 290 loop : -0.97 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 61 TYR 0.017 0.002 TYR R 222 PHE 0.010 0.001 PHE A 196 TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 8752) covalent geometry : angle 0.56035 / 0.29 (11865) SS BOND : bond 0.01235 / 0.65 ( 3) SS BOND : angle 2.27741 / 1.18 ( 6) hydrogen bonds : bond 0.03636 / 2.48 ( 418) hydrogen bonds : angle 4.27238 / 2.93 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.294 Fit side-chains REVERT: A 306 GLN cc_start: 0.6908 (mm110) cc_final: 0.6467 (mm110) REVERT: A 349 LYS cc_start: 0.8419 (ttmp) cc_final: 0.7991 (ttpm) REVERT: B 19 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6988 (ttp-170) REVERT: B 219 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7639 (mmm160) REVERT: B 267 ASP cc_start: 0.8016 (m-30) cc_final: 0.7715 (m-30) REVERT: G 38 MET cc_start: 0.7824 (ttp) cc_final: 0.7532 (ttp) REVERT: S 76 LYS cc_start: 0.7544 (tptp) cc_final: 0.7266 (tptp) outliers start: 31 outliers final: 18 residues processed: 138 average time/residue: 0.5418 time to fit residues: 80.0156 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 278 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 0.9980 chunk 77 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 255 ASN B 88 ASN B 142 HIS B 340 ASN S 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.179373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143164 restraints weight = 9256.804| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.80 r_work: 0.3354 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8755 Z= 0.134 Angle : 0.592 12.446 11871 Z= 0.299 Chirality : 0.042 0.152 1351 Planarity : 0.004 0.053 1486 Dihedral : 5.245 71.396 1187 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.33 % Allowed : 17.63 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1078 helix: 1.74 (0.28), residues: 369 sheet: -0.29 (0.30), residues: 288 loop : -0.99 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 61 TYR 0.015 0.002 TYR R 222 PHE 0.010 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.014 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8752) covalent geometry : angle 0.59010 / 0.30 (11865) SS BOND : bond 0.01233 / 0.64 ( 3) SS BOND : angle 2.12589 / 1.08 ( 6) hydrogen bonds : bond 0.03679 / 2.50 ( 418) hydrogen bonds : angle 4.26699 / 2.93 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.327 Fit side-chains REVERT: A 23 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 306 GLN cc_start: 0.6890 (mm110) cc_final: 0.6448 (mm110) REVERT: A 349 LYS cc_start: 0.8415 (ttmp) cc_final: 0.7983 (ttpm) REVERT: B 19 ARG cc_start: 0.7260 (ttp80) cc_final: 0.6924 (ttp-170) REVERT: B 219 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7632 (mmm160) REVERT: B 269 ILE cc_start: 0.7076 (mp) cc_final: 0.6790 (mt) REVERT: G 38 MET cc_start: 0.7814 (ttp) cc_final: 0.7529 (ttp) REVERT: R 83 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6567 (mm) outliers start: 31 outliers final: 18 residues processed: 132 average time/residue: 0.5797 time to fit residues: 81.5151 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 255 ASN A 331 ASN B 142 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.183018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146658 restraints weight = 9256.534| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.77 r_work: 0.3347 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8755 Z= 0.141 Angle : 0.604 12.406 11871 Z= 0.304 Chirality : 0.042 0.152 1351 Planarity : 0.004 0.053 1486 Dihedral : 5.276 71.122 1187 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.33 % Allowed : 17.96 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1078 helix: 1.86 (0.28), residues: 363 sheet: -0.28 (0.30), residues: 292 loop : -1.03 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 61 TYR 0.015 0.002 TYR S 94 PHE 0.011 0.001 PHE A 196 TRP 0.011 0.001 TRP B 82 HIS 0.017 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 8752) covalent geometry : angle 0.60193 / 0.30 (11865) SS BOND : bond 0.01304 / 0.68 ( 3) SS BOND : angle 2.23243 / 1.13 ( 6) hydrogen bonds : bond 0.03747 / 2.55 ( 418) hydrogen bonds : angle 4.29108 / 2.95 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.342 Fit side-chains REVERT: A 23 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 245 GLU cc_start: 0.6744 (mp0) cc_final: 0.6476 (mm-30) REVERT: A 255 ASN cc_start: 0.7767 (m-40) cc_final: 0.7235 (m110) REVERT: A 306 GLN cc_start: 0.6835 (mm110) cc_final: 0.6391 (mm110) REVERT: A 308 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: A 312 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7405 (mptt) REVERT: A 349 LYS cc_start: 0.8424 (ttmp) cc_final: 0.7988 (ttpm) REVERT: B 19 ARG cc_start: 0.7247 (ttp80) cc_final: 0.6974 (ttp-170) REVERT: B 219 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7594 (mmm160) REVERT: B 234 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: G 38 MET cc_start: 0.7819 (ttp) cc_final: 0.7467 (ttp) outliers start: 31 outliers final: 19 residues processed: 133 average time/residue: 0.5684 time to fit residues: 80.7393 Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.185464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150019 restraints weight = 9180.219| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.76 r_work: 0.3399 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8755 Z= 0.109 Angle : 0.566 11.693 11871 Z= 0.284 Chirality : 0.041 0.153 1351 Planarity : 0.004 0.057 1486 Dihedral : 5.106 72.615 1187 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.69 % Allowed : 18.39 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1078 helix: 1.94 (0.28), residues: 366 sheet: -0.30 (0.30), residues: 289 loop : -0.88 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 61 TYR 0.012 0.001 TYR S 94 PHE 0.010 0.001 PHE R 104 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8752) covalent geometry : angle 0.56496 / 0.28 (11865) SS BOND : bond 0.00878 / 0.45 ( 3) SS BOND : angle 1.64632 / 0.81 ( 6) hydrogen bonds : bond 0.03357 / 2.30 ( 418) hydrogen bonds : angle 4.16820 / 2.86 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 306 GLN cc_start: 0.6955 (mm110) cc_final: 0.6371 (mm110) REVERT: A 308 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: A 313 ARG cc_start: 0.6751 (mpp80) cc_final: 0.6541 (mtm110) REVERT: A 349 LYS cc_start: 0.8413 (ttmp) cc_final: 0.7983 (ttpm) REVERT: B 19 ARG cc_start: 0.7320 (ttp80) cc_final: 0.7026 (ttp-170) REVERT: B 219 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7673 (mmm160) REVERT: B 234 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: B 269 ILE cc_start: 0.6974 (mp) cc_final: 0.6715 (mt) REVERT: G 38 MET cc_start: 0.7810 (ttp) cc_final: 0.7473 (ttp) REVERT: S 76 LYS cc_start: 0.7720 (tptm) cc_final: 0.7519 (tptp) outliers start: 25 outliers final: 13 residues processed: 133 average time/residue: 0.5507 time to fit residues: 77.9963 Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 278 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.0070 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 110 ASN B 175 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.183350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147161 restraints weight = 9231.244| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.80 r_work: 0.3420 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8755 Z= 0.102 Angle : 0.553 11.321 11871 Z= 0.278 Chirality : 0.041 0.157 1351 Planarity : 0.004 0.061 1486 Dihedral : 5.000 73.329 1187 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.26 % Allowed : 19.14 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1078 helix: 2.10 (0.28), residues: 362 sheet: -0.16 (0.30), residues: 286 loop : -0.94 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 61 TYR 0.011 0.001 TYR R 113 PHE 0.010 0.001 PHE R 104 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 8752) covalent geometry : angle 0.55124 / 0.28 (11865) SS BOND : bond 0.00894 / 0.46 ( 3) SS BOND : angle 1.89809 / 0.96 ( 6) hydrogen bonds : bond 0.03213 / 2.20 ( 418) hydrogen bonds : angle 4.08712 / 2.81 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 245 GLU cc_start: 0.6536 (mp0) cc_final: 0.6229 (tp30) REVERT: A 306 GLN cc_start: 0.6970 (mm110) cc_final: 0.6340 (mm110) REVERT: A 308 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: A 349 LYS cc_start: 0.8408 (ttmp) cc_final: 0.7982 (ttpm) REVERT: B 19 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6989 (ttp-170) REVERT: B 219 ARG cc_start: 0.8172 (mmm160) cc_final: 0.7656 (mmm160) REVERT: B 269 ILE cc_start: 0.6900 (mp) cc_final: 0.6667 (mt) REVERT: G 38 MET cc_start: 0.7747 (ttp) cc_final: 0.7413 (ttp) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 0.5040 time to fit residues: 71.0295 Evaluate side-chains 118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146291 restraints weight = 9232.817| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.84 r_work: 0.3384 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8755 Z= 0.111 Angle : 0.571 12.175 11871 Z= 0.285 Chirality : 0.041 0.157 1351 Planarity : 0.004 0.048 1486 Dihedral : 5.010 73.404 1187 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.94 % Allowed : 19.89 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1078 helix: 2.13 (0.28), residues: 363 sheet: -0.16 (0.30), residues: 288 loop : -0.92 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 61 TYR 0.012 0.001 TYR S 94 PHE 0.010 0.001 PHE R 104 TRP 0.013 0.001 TRP R 154 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8752) covalent geometry : angle 0.56930 / 0.28 (11865) SS BOND : bond 0.00967 / 0.50 ( 3) SS BOND : angle 2.11290 / 1.10 ( 6) hydrogen bonds : bond 0.03324 / 2.26 ( 418) hydrogen bonds : angle 4.09282 / 2.82 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 204 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6835 (tp-100) REVERT: A 306 GLN cc_start: 0.6930 (mm110) cc_final: 0.6317 (mm110) REVERT: A 349 LYS cc_start: 0.8328 (ttmp) cc_final: 0.7941 (ttpm) REVERT: B 19 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6939 (ttp-170) REVERT: B 142 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7745 (t70) REVERT: B 219 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7648 (mmm160) REVERT: B 269 ILE cc_start: 0.7019 (mp) cc_final: 0.6762 (mt) REVERT: G 38 MET cc_start: 0.7678 (ttp) cc_final: 0.7343 (ttp) outliers start: 18 outliers final: 13 residues processed: 123 average time/residue: 0.5614 time to fit residues: 73.4670 Evaluate side-chains 117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 58 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.182311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146280 restraints weight = 9285.210| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.93 r_work: 0.3384 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 8755 Z= 0.168 Angle : 0.926 59.168 11871 Z= 0.524 Chirality : 0.047 0.802 1351 Planarity : 0.004 0.048 1486 Dihedral : 5.027 73.404 1187 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.04 % Allowed : 20.43 % Favored : 77.53 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1078 helix: 2.11 (0.28), residues: 364 sheet: -0.16 (0.30), residues: 288 loop : -0.92 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 61 TYR 0.011 0.001 TYR R 222 PHE 0.010 0.001 PHE R 104 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 8752) covalent geometry : angle 0.92533 / 0.52 (11865) SS BOND : bond 0.01012 / 0.53 ( 3) SS BOND : angle 2.07400 / 1.07 ( 6) hydrogen bonds : bond 0.03331 / 2.27 ( 418) hydrogen bonds : angle 4.09356 / 2.82 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.04 seconds wall clock time: 55 minutes 51.65 seconds (3351.65 seconds total)