Starting phenix.real_space_refine on Tue Mar 3 20:21:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vdm_31923/03_2026/7vdm_31923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdm_31923/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vdm_31923/03_2026/7vdm_31923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdm_31923/03_2026/7vdm_31923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vdm_31923/03_2026/7vdm_31923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdm_31923/03_2026/7vdm_31923.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.05, per 1000 atoms: 0.24 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 261.6 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: 0.30 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: 1.25 Time building geometry restraints manager: 0.92 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: 4730 17.86 - 35.72: 390 35.72 - 53.57: 52 53.57 - 71.43: 18 71.43 - 89.29: 5 Dihedral angle restraints: 5195 sinusoidal: 2035 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 5192 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: 0.430 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 13.650 89.286 3148 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 covalent geometry : bond 0.00774 ( 8752) covalent geometry : angle 1.29141 (11865) SS BOND : bond 0.01678 ( 3) SS BOND : angle 3.09962 ( 6) hydrogen bonds : bond 0.14579 ( 418) hydrogen bonds : angle 6.90710 ( 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 : 0.312 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: 0.6773 time to fit residues: 102.1370 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 : 0.306 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.181011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144949 restraints weight = 9290.204| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.73 r_work: 0.3398 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1527 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= 0.126 Angle : 0.622 12.651 11871 Z= 0.319 Chirality : 0.042 0.163 1351 Planarity : 0.005 0.074 1486 Dihedral : 6.357 71.087 1250 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.04 % Allowed : 10.75 % 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: -1.10 (0.24), residues: 1078 helix: 0.20 (0.26), residues: 364 sheet: -0.66 (0.29), residues: 293 loop : -1.51 (0.28), residues: 421 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 0.011 0.001 PHE B 199 TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8752) covalent geometry : angle 0.62132 (11865) SS BOND : bond 0.00760 ( 3) SS BOND : angle 1.46316 ( 6) hydrogen bonds : bond 0.04204 ( 418) hydrogen bonds : angle 4.78854 ( 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: 19 poor density : 113 time to evaluate : 0.288 Fit side-chains REVERT: A 24 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.6925 (ptp-110) REVERT: A 306 GLN cc_start: 0.6905 (mm110) cc_final: 0.6514 (mm110) REVERT: B 19 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7062 (ttp-170) REVERT: B 87 THR cc_start: 0.8365 (p) cc_final: 0.8090 (m) REVERT: B 323 ASP cc_start: 0.7817 (m-30) cc_final: 0.7402 (m-30) REVERT: G 38 MET cc_start: 0.7832 (ttp) cc_final: 0.7481 (ttp) REVERT: R 222 TYR cc_start: 0.6359 (p90) cc_final: 0.5955 (p90) outliers start: 19 outliers final: 7 residues processed: 124 average time/residue: 0.6934 time to fit residues: 90.5699 Evaluate side-chains 108 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 308 GLU 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: 0.0870 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144550 restraints weight = 9278.620| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.78 r_work: 0.3375 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8755 Z= 0.129 Angle : 0.587 9.817 11871 Z= 0.301 Chirality : 0.041 0.161 1351 Planarity : 0.004 0.068 1486 Dihedral : 5.611 70.249 1243 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.58 % Allowed : 12.90 % Favored : 84.52 % 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: -0.41 (0.25), residues: 1078 helix: 1.05 (0.27), residues: 369 sheet: -0.50 (0.30), residues: 290 loop : -1.21 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.023 0.002 TYR R 222 PHE 0.011 0.001 PHE A 223 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8752) covalent geometry : angle 0.58483 (11865) SS BOND : bond 0.00792 ( 3) SS BOND : angle 2.27110 ( 6) hydrogen bonds : bond 0.03900 ( 418) hydrogen bonds : angle 4.50085 ( 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 143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.336 Fit side-chains REVERT: A 251 ASP cc_start: 0.8021 (t0) cc_final: 0.7818 (t0) REVERT: A 306 GLN cc_start: 0.6907 (mm110) cc_final: 0.6527 (mm110) REVERT: A 349 LYS cc_start: 0.8453 (ttmp) cc_final: 0.8017 (ttpm) REVERT: B 19 ARG cc_start: 0.7434 (ttp80) cc_final: 0.7114 (ttp-170) REVERT: B 34 THR cc_start: 0.7552 (m) cc_final: 0.7223 (p) REVERT: B 323 ASP cc_start: 0.7620 (m-30) cc_final: 0.7161 (m-30) REVERT: G 38 MET cc_start: 0.7886 (ttp) cc_final: 0.7556 (ttp) REVERT: S 201 THR cc_start: 0.7959 (m) cc_final: 0.7482 (p) REVERT: R 222 TYR cc_start: 0.6491 (p90) cc_final: 0.6053 (p90) outliers start: 24 outliers final: 11 residues processed: 137 average time/residue: 0.5849 time to fit residues: 85.2908 Evaluate side-chains 115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.180183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144263 restraints weight = 9310.166| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.86 r_work: 0.3350 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8755 Z= 0.140 Angle : 0.595 9.481 11871 Z= 0.306 Chirality : 0.042 0.158 1351 Planarity : 0.004 0.061 1486 Dihedral : 5.570 69.744 1243 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.01 % Allowed : 14.95 % 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: -0.09 (0.26), residues: 1078 helix: 1.42 (0.28), residues: 368 sheet: -0.42 (0.31), residues: 285 loop : -1.05 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 61 TYR 0.021 0.002 TYR R 222 PHE 0.011 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8752) covalent geometry : angle 0.59219 (11865) SS BOND : bond 0.01377 ( 3) SS BOND : angle 2.77877 ( 6) hydrogen bonds : bond 0.03879 ( 418) hydrogen bonds : angle 4.40647 ( 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: 28 poor density : 110 time to evaluate : 0.410 Fit side-chains REVERT: A 243 MET cc_start: 0.7470 (mmt) cc_final: 0.7267 (tpp) REVERT: A 306 GLN cc_start: 0.6929 (mm110) cc_final: 0.6488 (mm110) REVERT: A 349 LYS cc_start: 0.8430 (ttmp) cc_final: 0.7974 (ttpm) REVERT: B 19 ARG cc_start: 0.7413 (ttp80) cc_final: 0.7089 (ttp-170) REVERT: B 170 ASP cc_start: 0.8352 (t0) cc_final: 0.8145 (t70) REVERT: B 323 ASP cc_start: 0.7614 (m-30) cc_final: 0.7128 (m-30) REVERT: G 38 MET cc_start: 0.7830 (ttp) cc_final: 0.7501 (ttp) REVERT: R 222 TYR cc_start: 0.6591 (p90) cc_final: 0.5986 (p90) outliers start: 28 outliers final: 11 residues processed: 128 average time/residue: 0.6027 time to fit residues: 81.9147 Evaluate side-chains 119 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 S residue 7 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.177138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140602 restraints weight = 9299.104| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.08 r_work: 0.3290 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8755 Z= 0.172 Angle : 0.628 11.229 11871 Z= 0.322 Chirality : 0.043 0.154 1351 Planarity : 0.004 0.058 1486 Dihedral : 5.722 69.691 1243 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.44 % Allowed : 16.45 % Favored : 80.11 % 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: 0.01 (0.26), residues: 1078 helix: 1.67 (0.28), residues: 361 sheet: -0.36 (0.30), residues: 295 loop : -1.14 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 61 TYR 0.018 0.002 TYR R 222 PHE 0.013 0.001 PHE A 223 TRP 0.012 0.001 TRP S 36 HIS 0.015 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8752) covalent geometry : angle 0.62511 (11865) SS BOND : bond 0.01665 ( 3) SS BOND : angle 2.96274 ( 6) hydrogen bonds : bond 0.04164 ( 418) hydrogen bonds : angle 4.49445 ( 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 142 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.296 Fit side-chains REVERT: A 306 GLN cc_start: 0.6915 (mm110) cc_final: 0.6354 (mm110) REVERT: A 349 LYS cc_start: 0.8460 (ttmp) cc_final: 0.8013 (ttpm) REVERT: B 19 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7162 (ttm110) REVERT: B 323 ASP cc_start: 0.7786 (m-30) cc_final: 0.7290 (m-30) REVERT: G 38 MET cc_start: 0.7952 (ttp) cc_final: 0.7624 (ttp) REVERT: S 76 LYS cc_start: 0.7579 (tptp) cc_final: 0.7336 (tptp) outliers start: 32 outliers final: 17 residues processed: 135 average time/residue: 0.6119 time to fit residues: 87.6856 Evaluate side-chains 118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 127 VAL 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 209 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.178914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143157 restraints weight = 9270.485| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.82 r_work: 0.3350 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8755 Z= 0.134 Angle : 0.592 10.778 11871 Z= 0.301 Chirality : 0.042 0.156 1351 Planarity : 0.004 0.055 1486 Dihedral : 5.499 70.745 1243 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.69 % Allowed : 18.28 % 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: 0.17 (0.26), residues: 1078 helix: 1.80 (0.28), residues: 363 sheet: -0.28 (0.30), residues: 290 loop : -1.06 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 61 TYR 0.016 0.002 TYR R 222 PHE 0.010 0.001 PHE A 196 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8752) covalent geometry : angle 0.59040 (11865) SS BOND : bond 0.01232 ( 3) SS BOND : angle 2.23512 ( 6) hydrogen bonds : bond 0.03803 ( 418) hydrogen bonds : angle 4.35813 ( 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 137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.345 Fit side-chains REVERT: A 24 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.6903 (ptp-110) REVERT: A 243 MET cc_start: 0.7493 (mmt) cc_final: 0.7113 (tpp) REVERT: A 306 GLN cc_start: 0.6904 (mm110) cc_final: 0.6367 (mm110) REVERT: A 349 LYS cc_start: 0.8463 (ttmp) cc_final: 0.8037 (ttpm) REVERT: B 19 ARG cc_start: 0.7476 (ttp80) cc_final: 0.7159 (ttm110) REVERT: B 323 ASP cc_start: 0.7711 (m-30) cc_final: 0.7266 (m-30) REVERT: G 38 MET cc_start: 0.7908 (ttp) cc_final: 0.7643 (ttp) REVERT: S 76 LYS cc_start: 0.7649 (tptp) cc_final: 0.7437 (tptp) outliers start: 25 outliers final: 15 residues processed: 132 average time/residue: 0.5981 time to fit residues: 83.9232 Evaluate side-chains 118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 69 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN A 333 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.143445 restraints weight = 9311.051| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.87 r_work: 0.3332 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2337 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= 0.145 Angle : 0.601 10.346 11871 Z= 0.305 Chirality : 0.042 0.157 1351 Planarity : 0.004 0.054 1486 Dihedral : 5.503 70.864 1243 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.33 % Allowed : 18.39 % Favored : 78.28 % 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: 0.21 (0.26), residues: 1078 helix: 1.84 (0.28), residues: 363 sheet: -0.23 (0.30), residues: 290 loop : -1.06 (0.29), residues: 425 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 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8752) covalent geometry : angle 0.59884 (11865) SS BOND : bond 0.01327 ( 3) SS BOND : angle 2.21733 ( 6) hydrogen bonds : bond 0.03834 ( 418) hydrogen bonds : angle 4.36125 ( 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 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.359 Fit side-chains REVERT: A 243 MET cc_start: 0.7465 (mmt) cc_final: 0.7156 (tpp) REVERT: A 306 GLN cc_start: 0.6944 (mm110) cc_final: 0.6446 (mm110) REVERT: A 349 LYS cc_start: 0.8440 (ttmp) cc_final: 0.7990 (ttpm) REVERT: B 19 ARG cc_start: 0.7418 (ttp80) cc_final: 0.7110 (ttp-170) REVERT: B 42 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.7305 (ttm-80) REVERT: B 234 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: B 323 ASP cc_start: 0.7700 (m-30) cc_final: 0.7245 (m-30) REVERT: S 76 LYS cc_start: 0.7620 (tptp) cc_final: 0.7386 (tptp) REVERT: S 83 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5255 (mmt) REVERT: R 52 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6630 (mt) REVERT: R 233 LEU cc_start: 0.8493 (tm) cc_final: 0.8085 (tp) outliers start: 31 outliers final: 16 residues processed: 130 average time/residue: 0.6451 time to fit residues: 88.9400 Evaluate side-chains 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 83 MET Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 ASN A 331 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.182728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146955 restraints weight = 9200.613| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.76 r_work: 0.3368 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8755 Z= 0.116 Angle : 0.568 9.440 11871 Z= 0.287 Chirality : 0.041 0.163 1351 Planarity : 0.004 0.059 1486 Dihedral : 5.306 72.312 1243 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.37 % Allowed : 19.35 % Favored : 78.28 % 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: 0.35 (0.26), residues: 1078 helix: 2.00 (0.28), residues: 363 sheet: -0.16 (0.31), residues: 290 loop : -1.00 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 61 TYR 0.013 0.001 TYR S 94 PHE 0.009 0.001 PHE R 104 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8752) covalent geometry : angle 0.56646 (11865) SS BOND : bond 0.00996 ( 3) SS BOND : angle 1.74364 ( 6) hydrogen bonds : bond 0.03476 ( 418) hydrogen bonds : angle 4.22601 ( 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 135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.314 Fit side-chains REVERT: A 306 GLN cc_start: 0.6928 (mm110) cc_final: 0.6386 (mm110) REVERT: A 349 LYS cc_start: 0.8430 (ttmp) cc_final: 0.7984 (ttpm) REVERT: B 19 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7026 (ttp-110) REVERT: B 234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8349 (m-80) outliers start: 22 outliers final: 14 residues processed: 128 average time/residue: 0.6010 time to fit residues: 81.8763 Evaluate side-chains 118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 234 PHE Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 83 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 28 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 241 ASN A 255 ASN B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144488 restraints weight = 9187.486| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.75 r_work: 0.3342 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8755 Z= 0.141 Angle : 0.605 10.346 11871 Z= 0.304 Chirality : 0.042 0.160 1351 Planarity : 0.004 0.057 1486 Dihedral : 5.403 71.802 1243 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.80 % Allowed : 19.25 % Favored : 77.96 % 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: 0.36 (0.26), residues: 1078 helix: 2.00 (0.28), residues: 363 sheet: -0.16 (0.31), residues: 290 loop : -1.00 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 61 TYR 0.014 0.002 TYR S 94 PHE 0.012 0.001 PHE A 196 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8752) covalent geometry : angle 0.60248 (11865) SS BOND : bond 0.01353 ( 3) SS BOND : angle 2.65588 ( 6) hydrogen bonds : bond 0.03721 ( 418) hydrogen bonds : angle 4.29309 ( 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 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.392 Fit side-chains REVERT: A 243 MET cc_start: 0.7527 (mmt) cc_final: 0.7310 (tpp) REVERT: A 245 GLU cc_start: 0.6550 (tp30) cc_final: 0.6191 (mp0) REVERT: A 306 GLN cc_start: 0.6976 (mm110) cc_final: 0.6397 (mm110) REVERT: A 349 LYS cc_start: 0.8441 (ttmp) cc_final: 0.7993 (ttpm) REVERT: B 19 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7061 (ttm110) REVERT: B 234 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: B 267 ASP cc_start: 0.8246 (m-30) cc_final: 0.7904 (m-30) REVERT: B 323 ASP cc_start: 0.7704 (m-30) cc_final: 0.7228 (m-30) REVERT: S 83 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.5258 (mmt) REVERT: R 52 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6510 (mt) REVERT: R 233 LEU cc_start: 0.8469 (tm) cc_final: 0.8054 (tp) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 0.6368 time to fit residues: 87.8115 Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 83 MET Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain R residue 52 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 ASN A 331 ASN B 175 GLN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.182711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146446 restraints weight = 9141.922| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.81 r_work: 0.3379 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8755 Z= 0.106 Angle : 0.568 10.255 11871 Z= 0.283 Chirality : 0.041 0.166 1351 Planarity : 0.003 0.049 1486 Dihedral : 5.185 73.371 1243 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.61 % Allowed : 20.00 % Favored : 78.39 % 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: 0.46 (0.26), residues: 1078 helix: 2.13 (0.28), residues: 366 sheet: -0.28 (0.31), residues: 283 loop : -0.86 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 168 TYR 0.011 0.001 TYR R 113 PHE 0.010 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8752) covalent geometry : angle 0.56595 (11865) SS BOND : bond 0.00915 ( 3) SS BOND : angle 2.09747 ( 6) hydrogen bonds : bond 0.03293 ( 418) hydrogen bonds : angle 4.15255 ( 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 132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 204 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6815 (tp-100) REVERT: A 245 GLU cc_start: 0.6508 (tp30) cc_final: 0.6165 (mp0) REVERT: A 306 GLN cc_start: 0.6934 (mm110) cc_final: 0.6270 (mm110) REVERT: A 349 LYS cc_start: 0.8434 (ttmp) cc_final: 0.7980 (ttpm) REVERT: B 19 ARG cc_start: 0.7347 (ttp80) cc_final: 0.7040 (ttm110) REVERT: B 34 THR cc_start: 0.7493 (m) cc_final: 0.7253 (p) REVERT: B 234 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: B 267 ASP cc_start: 0.8211 (m-30) cc_final: 0.7828 (m-30) REVERT: S 83 MET cc_start: 0.6516 (mmt) cc_final: 0.6269 (mpp) REVERT: R 52 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6512 (mt) REVERT: R 233 LEU cc_start: 0.8444 (tm) cc_final: 0.8022 (tp) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 0.5835 time to fit residues: 79.5364 Evaluate side-chains 122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN 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 153 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 52 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.182267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144934 restraints weight = 9251.694| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.86 r_work: 0.3374 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8755 Z= 0.151 Angle : 0.926 59.200 11871 Z= 0.522 Chirality : 0.048 0.889 1351 Planarity : 0.003 0.048 1486 Dihedral : 5.196 73.374 1243 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.04 % Allowed : 20.54 % Favored : 77.42 % 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: 0.50 (0.26), residues: 1078 helix: 2.26 (0.28), residues: 360 sheet: -0.26 (0.31), residues: 287 loop : -0.89 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 168 TYR 0.012 0.001 TYR R 222 PHE 0.010 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8752) covalent geometry : angle 0.92473 (11865) SS BOND : bond 0.00962 ( 3) SS BOND : angle 2.03479 ( 6) hydrogen bonds : bond 0.03297 ( 418) hydrogen bonds : angle 4.15873 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.13 seconds wall clock time: 59 minutes 32.96 seconds (3572.96 seconds total)