Starting phenix.real_space_refine on Thu Jul 2 18:12:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rkm_24500/07_2026/7rkm_24500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rkm_24500/07_2026/7rkm_24500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rkm_24500/07_2026/7rkm_24500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rkm_24500/07_2026/7rkm_24500.map" model { file = "/net/cci-nas-00/data/ceres_data/7rkm_24500/07_2026/7rkm_24500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rkm_24500/07_2026/7rkm_24500.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rkm_24500/07_2026/7rkm_24500.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rkm_24500/07_2026/7rkm_24500.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 72 5.16 5 C 6056 2.51 5 N 1604 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 9491 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Conformer: "B" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} bond proxies already assigned to first conformer: 2622 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 531 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PCA:plan-2': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2395 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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: 2.48, per 1000 atoms: 0.26 Number of scatterers: 9491 At special positions: 0 Unit cell: (98.4, 134.48, 132.84, 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 72 16.00 O 1759 8.00 N 1604 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.04 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " 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: 0.90 Conformation dependent library (CDL) restraints added in 401.6 milliseconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 36.3% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.701A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.390A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.746A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.784A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.794A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.722A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.625A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.655A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.771A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.870A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.538A pdb=" N VAL L 5 " --> pdb=" O HIS L 2 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR L 6 " --> pdb=" O HIS L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'L' and resid 56 through 67 removed outlier: 3.511A pdb=" N ASP L 60 " --> pdb=" O GLN L 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP L 66 " --> pdb=" O MET L 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 59 Proline residue: R 34 - end of helix removed outlier: 3.610A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 95 removed outlier: 3.556A pdb=" N VAL R 70 " --> pdb=" O CYS R 66 " (cutoff:3.500A) Proline residue: R 87 - end of helix removed outlier: 4.240A pdb=" N ASP R 95 " --> pdb=" O GLN R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 134 Processing helix chain 'R' and resid 140 through 158 removed outlier: 3.799A pdb=" N LEU R 146 " --> pdb=" O LYS R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 164 Processing helix chain 'R' and resid 183 through 195 removed outlier: 4.150A pdb=" N GLU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 218 removed outlier: 3.541A pdb=" N VAL R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 256 removed outlier: 3.787A pdb=" N VAL R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 263 through 292 removed outlier: 3.527A pdb=" N ARG R 267 " --> pdb=" O CYS R 263 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 295 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.082A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.772A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.764A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.779A 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: 4.206A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.945A 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: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.093A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.670A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.445A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.972A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 136 removed outlier: 4.037A pdb=" N GLU D 234 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.657A pdb=" N THR L 11 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 24 through 29 Processing sheet with id=AB6, first strand: chain 'R' and resid 167 through 168 450 hydrogen bonds defined for protein. 1266 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: 1.43 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2923 1.34 - 1.46: 2284 1.46 - 1.58: 4390 1.58 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 9697 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" CB MET B 262 " pdb=" CG MET B 262 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.88e+00 bond pdb=" C ILE R 160 " pdb=" N PRO R 161 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.96e+00 bond pdb=" SD MET B 262 " pdb=" CE MET B 262 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.88e+00 bond pdb=" C ASN R 287 " pdb=" N PRO R 288 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 ... (remaining 9692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 13054 4.60 - 9.19: 84 9.19 - 13.79: 5 13.79 - 18.39: 0 18.39 - 22.99: 1 Bond angle restraints: 13144 Sorted by residual: angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 89.71 22.99 3.00e+00 1.11e-01 5.87e+01 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" CB MET R 174 " pdb=" CG MET R 174 " pdb=" SD MET R 174 " ideal model delta sigma weight residual 112.70 125.74 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 110.49 117.48 -6.99 1.69e+00 3.50e-01 1.71e+01 angle pdb=" N ASN R 287 " pdb=" CA ASN R 287 " pdb=" C ASN R 287 " ideal model delta sigma weight residual 113.16 118.58 -5.42 1.42e+00 4.96e-01 1.46e+01 ... (remaining 13139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5360 17.94 - 35.89: 327 35.89 - 53.83: 67 53.83 - 71.77: 7 71.77 - 89.72: 4 Dihedral angle restraints: 5765 sinusoidal: 2261 harmonic: 3504 Sorted by residual: 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 93.00 158.42 -65.42 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -131.88 45.88 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CA ILE R 259 " pdb=" C ILE R 259 " pdb=" N SER R 260 " pdb=" CA SER R 260 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1248 0.073 - 0.146: 209 0.146 - 0.219: 23 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA ASN R 287 " pdb=" N ASN R 287 " pdb=" C ASN R 287 " pdb=" CB ASN R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR A 324 " pdb=" CA THR A 324 " pdb=" OG1 THR A 324 " pdb=" CG2 THR A 324 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.73e+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 -2.62 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1490 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 57 " -0.014 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP L 57 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP L 57 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 57 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 57 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 44 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE R 44 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE R 44 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 45 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 94 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU R 94 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU R 94 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP R 95 " 0.014 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 447 2.73 - 3.27: 9397 3.27 - 3.81: 15586 3.81 - 4.36: 19326 4.36 - 4.90: 33285 Nonbonded interactions: 78041 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.181 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN R 189 " pdb=" OG1 THR R 252 " model vdw 2.206 3.040 nonbonded pdb=" O LEU R 53 " pdb=" OG1 THR R 57 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.241 3.040 ... (remaining 78036 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.050 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 9704 Z= 0.239 Angle : 0.975 22.986 13158 Z= 0.503 Chirality : 0.060 0.365 1493 Planarity : 0.005 0.042 1654 Dihedral : 12.310 89.718 3480 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.13 (0.24), residues: 1183 helix: 0.52 (0.26), residues: 400 sheet: -1.09 (0.29), residues: 288 loop : -1.52 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 148 TYR 0.024 0.003 TYR A 320 PHE 0.024 0.003 PHE D 68 TRP 0.045 0.002 TRP L 57 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 ( 9697) covalent geometry : angle 0.97002 / 0.50 (13144) SS BOND : bond 0.00562 / 0.29 ( 7) SS BOND : angle 3.06407 / 1.70 ( 14) hydrogen bonds : bond 0.11955 / 7.42 ( 450) hydrogen bonds : angle 6.34443 / 4.42 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.369 Fit side-chains REVERT: A 26 ASP cc_start: 0.7340 (m-30) cc_final: 0.6893 (m-30) REVERT: D 6 GLU cc_start: 0.7503 (mp0) cc_final: 0.7194 (mp0) REVERT: D 127 VAL cc_start: 0.8911 (p) cc_final: 0.8640 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1119 time to fit residues: 27.4019 Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112031 restraints weight = 18737.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110920 restraints weight = 17036.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113032 restraints weight = 16020.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113349 restraints weight = 9908.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114193 restraints weight = 9465.051| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9704 Z= 0.150 Angle : 0.604 7.787 13158 Z= 0.320 Chirality : 0.044 0.183 1493 Planarity : 0.003 0.037 1654 Dihedral : 4.613 25.761 1314 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.87 % Allowed : 8.29 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.89 (0.24), residues: 1183 helix: 0.91 (0.27), residues: 403 sheet: -0.94 (0.29), residues: 283 loop : -1.60 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.029 0.002 TYR R 92 PHE 0.031 0.002 PHE A 334 TRP 0.016 0.001 TRP L 57 HIS 0.005 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9697) covalent geometry : angle 0.60330 / 0.32 (13144) SS BOND : bond 0.00430 / 0.22 ( 7) SS BOND : angle 1.25034 / 0.61 ( 14) hydrogen bonds : bond 0.03863 / 2.58 ( 450) hydrogen bonds : angle 5.15833 / 3.55 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.349 Fit side-chains REVERT: A 26 ASP cc_start: 0.7321 (m-30) cc_final: 0.6906 (m-30) REVERT: A 52 GLN cc_start: 0.7100 (tm-30) cc_final: 0.6804 (tt0) REVERT: A 248 LYS cc_start: 0.8157 (mttm) cc_final: 0.7915 (tptp) REVERT: B 247 ASP cc_start: 0.6898 (t70) cc_final: 0.6671 (t0) REVERT: D 6 GLU cc_start: 0.7317 (mp0) cc_final: 0.7054 (mp0) REVERT: R 191 GLU cc_start: 0.7763 (tt0) cc_final: 0.7542 (tt0) outliers start: 9 outliers final: 5 residues processed: 157 average time/residue: 0.0960 time to fit residues: 20.9827 Evaluate side-chains 142 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 66 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112744 restraints weight = 13981.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113753 restraints weight = 12894.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114743 restraints weight = 9579.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114953 restraints weight = 7744.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115398 restraints weight = 7263.664| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9704 Z= 0.119 Angle : 0.568 7.638 13158 Z= 0.298 Chirality : 0.042 0.224 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.413 24.349 1314 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.54 % Allowed : 10.13 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.69 (0.24), residues: 1183 helix: 1.15 (0.27), residues: 402 sheet: -0.89 (0.29), residues: 285 loop : -1.51 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.029 0.001 TYR R 92 PHE 0.023 0.001 PHE A 334 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9697) covalent geometry : angle 0.56728 / 0.30 (13144) SS BOND : bond 0.00414 / 0.21 ( 7) SS BOND : angle 1.22527 / 0.59 ( 14) hydrogen bonds : bond 0.03570 / 2.40 ( 450) hydrogen bonds : angle 4.87404 / 3.37 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.360 Fit side-chains REVERT: A 26 ASP cc_start: 0.7297 (m-30) cc_final: 0.6884 (m-30) REVERT: A 248 LYS cc_start: 0.8214 (mttm) cc_final: 0.7916 (tptp) REVERT: B 247 ASP cc_start: 0.6767 (t70) cc_final: 0.6511 (t0) REVERT: R 191 GLU cc_start: 0.7759 (tt0) cc_final: 0.7558 (tt0) outliers start: 16 outliers final: 9 residues processed: 163 average time/residue: 0.0900 time to fit residues: 20.5193 Evaluate side-chains 145 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 109 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 HIS L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113885 restraints weight = 22443.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115834 restraints weight = 22285.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117070 restraints weight = 15490.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118962 restraints weight = 8979.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119452 restraints weight = 7125.706| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9704 Z= 0.127 Angle : 0.570 7.548 13158 Z= 0.297 Chirality : 0.042 0.194 1493 Planarity : 0.003 0.042 1654 Dihedral : 4.350 24.751 1314 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.64 % Allowed : 11.09 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.57 (0.24), residues: 1183 helix: 1.25 (0.27), residues: 403 sheet: -0.79 (0.30), residues: 274 loop : -1.46 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 206 TYR 0.031 0.001 TYR R 92 PHE 0.018 0.001 PHE A 334 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9697) covalent geometry : angle 0.56838 / 0.30 (13144) SS BOND : bond 0.00392 / 0.19 ( 7) SS BOND : angle 1.28874 / 0.58 ( 14) hydrogen bonds : bond 0.03463 / 2.33 ( 450) hydrogen bonds : angle 4.71940 / 3.23 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.288 Fit side-chains REVERT: A 26 ASP cc_start: 0.7303 (m-30) cc_final: 0.6878 (m-30) REVERT: A 52 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6293 (tt0) REVERT: B 247 ASP cc_start: 0.6859 (t70) cc_final: 0.6604 (t0) REVERT: R 191 GLU cc_start: 0.7717 (tt0) cc_final: 0.7495 (tt0) outliers start: 17 outliers final: 10 residues processed: 158 average time/residue: 0.0936 time to fit residues: 20.8185 Evaluate side-chains 142 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN L 30 ASN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110918 restraints weight = 22465.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113014 restraints weight = 22926.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114057 restraints weight = 16157.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115954 restraints weight = 9226.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116373 restraints weight = 7211.451| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9704 Z= 0.172 Angle : 0.593 7.755 13158 Z= 0.309 Chirality : 0.044 0.289 1493 Planarity : 0.003 0.041 1654 Dihedral : 4.411 24.201 1314 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.25 % Allowed : 12.44 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.54 (0.24), residues: 1183 helix: 1.27 (0.27), residues: 403 sheet: -0.84 (0.29), residues: 279 loop : -1.40 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 206 TYR 0.032 0.002 TYR R 92 PHE 0.018 0.002 PHE A 334 TRP 0.012 0.001 TRP B 99 HIS 0.006 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9697) covalent geometry : angle 0.59197 / 0.31 (13144) SS BOND : bond 0.00353 / 0.17 ( 7) SS BOND : angle 1.26215 / 0.61 ( 14) hydrogen bonds : bond 0.03616 / 2.42 ( 450) hydrogen bonds : angle 4.78144 / 3.28 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.243 Fit side-chains REVERT: A 26 ASP cc_start: 0.7356 (m-30) cc_final: 0.6917 (m-30) REVERT: B 247 ASP cc_start: 0.6982 (t70) cc_final: 0.6738 (t0) REVERT: R 191 GLU cc_start: 0.7788 (tt0) cc_final: 0.7498 (tt0) outliers start: 13 outliers final: 12 residues processed: 151 average time/residue: 0.0860 time to fit residues: 18.1681 Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 102 optimal weight: 0.0030 chunk 7 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113984 restraints weight = 28353.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118252 restraints weight = 33892.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121577 restraints weight = 11915.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121890 restraints weight = 6990.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122185 restraints weight = 6708.803| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9704 Z= 0.115 Angle : 0.563 8.315 13158 Z= 0.293 Chirality : 0.042 0.251 1493 Planarity : 0.003 0.038 1654 Dihedral : 4.270 24.919 1314 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.45 % Allowed : 12.83 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.45 (0.24), residues: 1183 helix: 1.37 (0.27), residues: 403 sheet: -0.72 (0.30), residues: 274 loop : -1.41 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 206 TYR 0.031 0.001 TYR R 92 PHE 0.017 0.001 PHE R 163 TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 9697) covalent geometry : angle 0.56206 / 0.29 (13144) SS BOND : bond 0.00357 / 0.17 ( 7) SS BOND : angle 0.97381 / 0.46 ( 14) hydrogen bonds : bond 0.03377 / 2.28 ( 450) hydrogen bonds : angle 4.65051 / 3.19 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7296 (m-30) cc_final: 0.6877 (m-30) REVERT: A 52 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6576 (tt0) REVERT: B 247 ASP cc_start: 0.6867 (t70) cc_final: 0.6630 (t0) REVERT: C 25 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8350 (mt) REVERT: R 191 GLU cc_start: 0.7612 (tt0) cc_final: 0.7406 (tt0) outliers start: 15 outliers final: 9 residues processed: 166 average time/residue: 0.1030 time to fit residues: 23.8522 Evaluate side-chains 147 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110292 restraints weight = 13871.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111943 restraints weight = 11405.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112605 restraints weight = 8354.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113175 restraints weight = 6934.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113325 restraints weight = 6348.424| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9704 Z= 0.134 Angle : 0.576 8.656 13158 Z= 0.299 Chirality : 0.042 0.226 1493 Planarity : 0.003 0.042 1654 Dihedral : 4.249 24.867 1314 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.83 % Allowed : 13.69 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.37 (0.24), residues: 1183 helix: 1.44 (0.27), residues: 403 sheet: -0.69 (0.30), residues: 275 loop : -1.36 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 206 TYR 0.030 0.001 TYR R 92 PHE 0.019 0.001 PHE D 68 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9697) covalent geometry : angle 0.57501 / 0.30 (13144) SS BOND : bond 0.00376 / 0.18 ( 7) SS BOND : angle 1.05696 / 0.51 ( 14) hydrogen bonds : bond 0.03403 / 2.28 ( 450) hydrogen bonds : angle 4.64331 / 3.18 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7280 (m-30) cc_final: 0.6853 (m-30) REVERT: C 25 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8337 (mt) REVERT: R 92 TYR cc_start: 0.7763 (t80) cc_final: 0.7543 (t80) REVERT: R 191 GLU cc_start: 0.7783 (tt0) cc_final: 0.7492 (tt0) outliers start: 19 outliers final: 13 residues processed: 156 average time/residue: 0.0920 time to fit residues: 20.3313 Evaluate side-chains 148 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111679 restraints weight = 24170.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116268 restraints weight = 27910.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117383 restraints weight = 11026.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119348 restraints weight = 7883.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120059 restraints weight = 6610.911| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9704 Z= 0.140 Angle : 0.583 8.955 13158 Z= 0.303 Chirality : 0.042 0.213 1493 Planarity : 0.003 0.042 1654 Dihedral : 4.237 25.001 1314 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.45 % Allowed : 13.89 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.33 (0.25), residues: 1183 helix: 1.41 (0.27), residues: 407 sheet: -0.65 (0.30), residues: 274 loop : -1.30 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.030 0.001 TYR R 92 PHE 0.019 0.001 PHE D 68 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9697) covalent geometry : angle 0.58226 / 0.30 (13144) SS BOND : bond 0.00383 / 0.18 ( 7) SS BOND : angle 1.06227 / 0.51 ( 14) hydrogen bonds : bond 0.03437 / 2.29 ( 450) hydrogen bonds : angle 4.63973 / 3.17 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7334 (m-30) cc_final: 0.6896 (m-30) REVERT: A 52 GLN cc_start: 0.6891 (tm-30) cc_final: 0.6419 (tt0) REVERT: A 287 TYR cc_start: 0.7116 (m-80) cc_final: 0.6778 (m-80) REVERT: B 262 MET cc_start: 0.7923 (ttm) cc_final: 0.7685 (ttm) REVERT: C 25 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8339 (mt) REVERT: D 127 VAL cc_start: 0.8981 (p) cc_final: 0.8744 (t) REVERT: R 92 TYR cc_start: 0.7781 (t80) cc_final: 0.7547 (t80) REVERT: R 191 GLU cc_start: 0.7685 (tt0) cc_final: 0.7420 (tt0) outliers start: 15 outliers final: 13 residues processed: 156 average time/residue: 0.0900 time to fit residues: 19.8917 Evaluate side-chains 151 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110871 restraints weight = 23937.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112046 restraints weight = 25167.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113330 restraints weight = 17500.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115406 restraints weight = 9754.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116099 restraints weight = 7306.835| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9704 Z= 0.179 Angle : 0.618 9.131 13158 Z= 0.321 Chirality : 0.043 0.203 1493 Planarity : 0.003 0.043 1654 Dihedral : 4.375 25.085 1314 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.64 % Allowed : 14.08 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.38 (0.24), residues: 1183 helix: 1.33 (0.27), residues: 405 sheet: -0.72 (0.30), residues: 275 loop : -1.26 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 206 TYR 0.030 0.002 TYR R 92 PHE 0.021 0.002 PHE D 68 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 9697) covalent geometry : angle 0.61744 / 0.32 (13144) SS BOND : bond 0.00387 / 0.18 ( 7) SS BOND : angle 1.18472 / 0.57 ( 14) hydrogen bonds : bond 0.03581 / 2.39 ( 450) hydrogen bonds : angle 4.75183 / 3.25 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.306 Fit side-chains REVERT: A 26 ASP cc_start: 0.7404 (m-30) cc_final: 0.7134 (m-30) REVERT: A 287 TYR cc_start: 0.7297 (m-80) cc_final: 0.7079 (m-80) REVERT: B 262 MET cc_start: 0.7983 (ttm) cc_final: 0.7716 (ttm) REVERT: C 25 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8354 (mt) REVERT: D 127 VAL cc_start: 0.9022 (p) cc_final: 0.8737 (t) REVERT: R 254 LYS cc_start: 0.7562 (tmtt) cc_final: 0.6994 (tttt) outliers start: 17 outliers final: 13 residues processed: 162 average time/residue: 0.0925 time to fit residues: 21.0952 Evaluate side-chains 158 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 97 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110193 restraints weight = 16143.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109269 restraints weight = 15352.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111473 restraints weight = 12692.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111859 restraints weight = 8696.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112499 restraints weight = 7819.408| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9704 Z= 0.151 Angle : 0.614 9.676 13158 Z= 0.320 Chirality : 0.043 0.232 1493 Planarity : 0.003 0.044 1654 Dihedral : 4.344 25.151 1314 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.45 % Allowed : 15.04 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1183 helix: 1.33 (0.27), residues: 406 sheet: -0.70 (0.30), residues: 274 loop : -1.23 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 206 TYR 0.035 0.002 TYR R 92 PHE 0.020 0.002 PHE D 68 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9697) covalent geometry : angle 0.61371 / 0.32 (13144) SS BOND : bond 0.00444 / 0.21 ( 7) SS BOND : angle 1.11706 / 0.53 ( 14) hydrogen bonds : bond 0.03515 / 2.34 ( 450) hydrogen bonds : angle 4.71562 / 3.23 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.340 Fit side-chains REVERT: A 26 ASP cc_start: 0.7355 (m-30) cc_final: 0.6962 (m-30) REVERT: A 52 GLN cc_start: 0.6928 (tm-30) cc_final: 0.6374 (tt0) REVERT: C 25 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8360 (mt) REVERT: D 127 VAL cc_start: 0.9015 (p) cc_final: 0.8711 (t) REVERT: R 254 LYS cc_start: 0.7588 (tmtt) cc_final: 0.7037 (tttt) outliers start: 15 outliers final: 14 residues processed: 159 average time/residue: 0.0957 time to fit residues: 21.1601 Evaluate side-chains 157 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110613 restraints weight = 18959.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110317 restraints weight = 15832.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112017 restraints weight = 12404.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112902 restraints weight = 8767.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113873 restraints weight = 8339.209| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9704 Z= 0.154 Angle : 0.615 9.727 13158 Z= 0.321 Chirality : 0.043 0.230 1493 Planarity : 0.003 0.043 1654 Dihedral : 4.340 24.937 1314 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.45 % Allowed : 15.81 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1183 helix: 1.33 (0.27), residues: 406 sheet: -0.75 (0.30), residues: 275 loop : -1.18 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 206 TYR 0.036 0.002 TYR R 92 PHE 0.017 0.002 PHE D 68 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9697) covalent geometry : angle 0.61409 / 0.32 (13144) SS BOND : bond 0.00471 / 0.23 ( 7) SS BOND : angle 1.10240 / 0.52 ( 14) hydrogen bonds : bond 0.03530 / 2.33 ( 450) hydrogen bonds : angle 4.74547 / 3.25 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.47 seconds wall clock time: 30 minutes 46.30 seconds (1846.30 seconds total)