Starting phenix.real_space_refine on Thu Jul 2 20:15:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vb2_64913/07_2026/9vb2_64913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vb2_64913/07_2026/9vb2_64913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vb2_64913/07_2026/9vb2_64913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vb2_64913/07_2026/9vb2_64913.map" model { file = "/net/cci-nas-00/data/ceres_data/9vb2_64913/07_2026/9vb2_64913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vb2_64913/07_2026/9vb2_64913.cif" } resolution = 3.08 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= -0.009 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 6376 2.51 5 N 1710 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 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: 10040 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2416 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2794 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 346} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1761 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.18 Number of scatterers: 10040 At special positions: 0 Unit cell: (103.75, 121.733, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 2 15.00 O 1886 8.00 N 1710 7.00 C 6376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.01 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.15 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.07 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: 0.67 Conformation dependent library (CDL) restraints added in 267.4 milliseconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 15 sheets defined 41.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'R' and resid 51 through 55 Processing helix chain 'R' and resid 59 through 62 Processing helix chain 'R' and resid 63 through 89 Processing helix chain 'R' and resid 100 through 119 removed outlier: 3.886A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 127 removed outlier: 3.577A pdb=" N GLU R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.596A pdb=" N GLY R 140 " --> pdb=" O PHE R 136 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP R 149 " --> pdb=" O TYR R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.767A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 206 Proline residue: R 202 - end of helix removed outlier: 3.569A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 273 removed outlier: 3.688A pdb=" N SER R 253 " --> pdb=" O MET R 249 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN R 256 " --> pdb=" O ILE R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 329 Proline residue: R 318 - end of helix removed outlier: 3.717A pdb=" N LEU R 324 " --> pdb=" O HIS R 320 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS R 327 " --> pdb=" O ARG R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 350 removed outlier: 3.564A pdb=" N ASP R 340 " --> pdb=" O PRO R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 367 removed outlier: 3.910A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) Proline residue: R 361 - end of helix removed outlier: 4.371A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 375 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.560A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 69 through 91 removed outlier: 3.967A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.762A pdb=" N ASP A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 135 through 142 removed outlier: 3.623A pdb=" N ARG A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 4.143A pdb=" N ASP A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.730A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.264A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.625A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 329 through 347 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.556A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.719A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.051A 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 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 8.390A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.675A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.702A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.517A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.622A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 148 through 151 Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.651A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 208 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.441A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.392A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.816A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.123A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.564A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1443 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: 1.41 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1892 1.33 - 1.45: 2751 1.45 - 1.58: 5504 1.58 - 1.71: 6 1.71 - 1.83: 98 Bond restraints: 10251 Sorted by residual: bond pdb=" CG HIS B 54 " pdb=" CD2 HIS B 54 " ideal model delta sigma weight residual 1.354 1.286 0.068 1.10e-02 8.26e+03 3.80e+01 bond pdb=" CA SER R 330 " pdb=" CB SER R 330 " ideal model delta sigma weight residual 1.529 1.430 0.099 1.64e-02 3.72e+03 3.68e+01 bond pdb=" CA SER B 74 " pdb=" CB SER B 74 " ideal model delta sigma weight residual 1.532 1.436 0.096 1.68e-02 3.54e+03 3.29e+01 bond pdb=" CA SER B 161 " pdb=" CB SER B 161 " ideal model delta sigma weight residual 1.530 1.443 0.087 1.52e-02 4.33e+03 3.28e+01 bond pdb=" C5 GDP A 401 " pdb=" C4 GDP A 401 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 10246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 11335 2.73 - 5.47: 2242 5.47 - 8.20: 274 8.20 - 10.93: 45 10.93 - 13.67: 9 Bond angle restraints: 13905 Sorted by residual: angle pdb=" C TYR A 287 " pdb=" CA TYR A 287 " pdb=" CB TYR A 287 " ideal model delta sigma weight residual 110.44 121.94 -11.50 9.00e-01 1.23e+00 1.63e+02 angle pdb=" CA PHE R 371 " pdb=" CB PHE R 371 " pdb=" CG PHE R 371 " ideal model delta sigma weight residual 113.80 123.27 -9.47 1.00e+00 1.00e+00 8.97e+01 angle pdb=" N VAL R 250 " pdb=" CA VAL R 250 " pdb=" CB VAL R 250 " ideal model delta sigma weight residual 110.65 120.50 -9.85 1.13e+00 7.83e-01 7.60e+01 angle pdb=" CD ARG A 178 " pdb=" NE ARG A 178 " pdb=" CZ ARG A 178 " ideal model delta sigma weight residual 124.40 134.36 -9.96 1.40e+00 5.10e-01 5.06e+01 angle pdb=" N VAL R 159 " pdb=" CA VAL R 159 " pdb=" CB VAL R 159 " ideal model delta sigma weight residual 110.54 120.20 -9.66 1.36e+00 5.41e-01 5.05e+01 ... (remaining 13900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 5731 27.95 - 55.89: 308 55.89 - 83.84: 29 83.84 - 111.78: 4 111.78 - 139.73: 1 Dihedral angle restraints: 6073 sinusoidal: 2331 harmonic: 3742 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -174.55 88.55 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 166.17 -73.17 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" O2B GDP A 401 " pdb=" O3A GDP A 401 " pdb=" PB GDP A 401 " pdb=" PA GDP A 401 " ideal model delta sinusoidal sigma weight residual -180.00 -40.27 -139.73 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 6070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1150 0.132 - 0.265: 364 0.265 - 0.397: 55 0.397 - 0.530: 10 0.530 - 0.662: 2 Chirality restraints: 1581 Sorted by residual: chirality pdb=" CG LEU R 118 " pdb=" CB LEU R 118 " pdb=" CD1 LEU R 118 " pdb=" CD2 LEU R 118 " both_signs ideal model delta sigma weight residual False -2.59 -1.93 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA SER R 330 " pdb=" N SER R 330 " pdb=" C SER R 330 " pdb=" CB SER R 330 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" CA HIS R 343 " pdb=" N HIS R 343 " pdb=" C HIS R 343 " pdb=" CB HIS R 343 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.47e+00 ... (remaining 1578 not shown) Planarity restraints: 1759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 182 " 0.918 9.50e-02 1.11e+02 4.12e-01 1.03e+02 pdb=" NE ARG R 182 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG R 182 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG R 182 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 182 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 303 " -0.583 9.50e-02 1.11e+02 2.69e-01 9.16e+01 pdb=" NE ARG R 303 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG R 303 " 0.129 2.00e-02 2.50e+03 pdb=" NH1 ARG R 303 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG R 303 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 148 " 0.612 9.50e-02 1.11e+02 2.81e-01 8.92e+01 pdb=" NE ARG R 148 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG R 148 " -0.121 2.00e-02 2.50e+03 pdb=" NH1 ARG R 148 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG R 148 " 0.057 2.00e-02 2.50e+03 ... (remaining 1756 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1889 2.82 - 3.34: 10176 3.34 - 3.86: 16536 3.86 - 4.38: 20102 4.38 - 4.90: 33434 Nonbonded interactions: 82137 Sorted by model distance: nonbonded pdb=" NE2 HIS B 54 " pdb=" O ALA B 56 " model vdw 2.306 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 74 " model vdw 2.333 3.120 nonbonded pdb=" O ILE R 192 " pdb=" OG SER R 196 " model vdw 2.336 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.338 3.040 nonbonded pdb=" O SER D 52 " pdb=" NH1 ARG D 72 " model vdw 2.355 3.120 ... (remaining 82132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.220 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.012 0.121 10254 Z= 0.748 Angle : 2.215 13.668 13911 Z= 1.494 Chirality : 0.129 0.662 1581 Planarity : 0.021 0.412 1759 Dihedral : 16.684 139.728 3652 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.86 % Allowed : 12.84 % Favored : 81.30 % Cbeta Deviations : 2.40 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.20), residues: 1269 helix: -1.80 (0.20), residues: 478 sheet: -1.11 (0.30), residues: 248 loop : -1.45 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.122 0.010 ARG R 303 TYR 0.069 0.008 TYR A 167 PHE 0.045 0.007 PHE A 259 TRP 0.067 0.010 TRP B 99 HIS 0.060 0.007 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.75 (10251) covalent geometry : angle 2.21222 / 1.49 (13905) SS BOND : bond 0.07358 / 5.14 ( 3) SS BOND : angle 6.18923 / 3.69 ( 6) hydrogen bonds : bond 0.20968 / 14.54 ( 499) hydrogen bonds : angle 8.41940 / 6.09 ( 1443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 322 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 GLU cc_start: 0.8803 (tp30) cc_final: 0.8443 (tp30) REVERT: R 245 PHE cc_start: 0.5809 (t80) cc_final: 0.5148 (t80) REVERT: R 267 VAL cc_start: 0.7122 (OUTLIER) cc_final: 0.6158 (p) REVERT: R 304 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8155 (t) REVERT: A 54 LYS cc_start: 0.9034 (ptpt) cc_final: 0.8731 (ptmm) REVERT: A 68 GLN cc_start: 0.9585 (mt0) cc_final: 0.9195 (mt0) REVERT: A 78 ILE cc_start: 0.9583 (mm) cc_final: 0.9317 (mp) REVERT: A 86 ARG cc_start: 0.9413 (ttm170) cc_final: 0.9053 (tmm160) REVERT: A 240 MET cc_start: 0.7793 (mtt) cc_final: 0.7049 (mtt) REVERT: A 272 ASP cc_start: 0.9005 (t70) cc_final: 0.8443 (t0) REVERT: A 340 THR cc_start: 0.8889 (m) cc_final: 0.8604 (p) REVERT: B 6 GLN cc_start: 0.9544 (tt0) cc_final: 0.9055 (tm-30) REVERT: B 12 GLU cc_start: 0.9250 (tp30) cc_final: 0.9001 (tm-30) REVERT: B 19 ARG cc_start: 0.9306 (ttm110) cc_final: 0.8988 (ttp-110) REVERT: B 23 LYS cc_start: 0.9227 (ttmm) cc_final: 0.9019 (tptp) REVERT: B 59 TYR cc_start: 0.9158 (m-10) cc_final: 0.8937 (m-80) REVERT: B 223 THR cc_start: 0.9069 (p) cc_final: 0.8863 (p) REVERT: C 18 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7692 (tp-100) REVERT: C 22 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8832 (mt-10) REVERT: D 73 ASP cc_start: 0.6345 (t0) cc_final: 0.5734 (t70) REVERT: D 93 MET cc_start: 0.8274 (tpp) cc_final: 0.7928 (tpp) REVERT: D 118 THR cc_start: 0.8290 (m) cc_final: 0.7555 (p) REVERT: D 232 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8312 (ttpp) outliers start: 63 outliers final: 15 residues processed: 358 average time/residue: 0.0990 time to fit residues: 47.3817 Evaluate side-chains 235 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LYS Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain D residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 373 HIS ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 91 HIS B 183 HIS B 239 ASN B 259 GLN B 311 HIS B 340 ASN D 39 GLN D 159 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.120594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086396 restraints weight = 20531.619| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.13 r_work: 0.3084 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10254 Z= 0.161 Angle : 0.721 9.073 13911 Z= 0.382 Chirality : 0.046 0.167 1581 Planarity : 0.005 0.079 1759 Dihedral : 8.425 136.964 1443 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 5.12 % Allowed : 16.84 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.72 (0.22), residues: 1269 helix: 0.46 (0.22), residues: 481 sheet: -0.64 (0.29), residues: 295 loop : -1.20 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 268 TYR 0.025 0.002 TYR L 11 PHE 0.027 0.002 PHE R 345 TRP 0.030 0.002 TRP R 334 HIS 0.018 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (10251) covalent geometry : angle 0.72085 / 0.38 (13905) SS BOND : bond 0.00370 / 0.23 ( 3) SS BOND : angle 1.28242 / 0.80 ( 6) hydrogen bonds : bond 0.05213 / 3.64 ( 499) hydrogen bonds : angle 5.22134 / 3.77 ( 1443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 GLU cc_start: 0.8747 (tp30) cc_final: 0.8219 (tm-30) REVERT: R 218 HIS cc_start: 0.7092 (t-90) cc_final: 0.6694 (t70) REVERT: R 300 HIS cc_start: 0.6636 (t70) cc_final: 0.6389 (t70) REVERT: A 25 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7909 (tm-30) REVERT: A 54 LYS cc_start: 0.8498 (ptpt) cc_final: 0.8275 (ptmm) REVERT: A 174 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8868 (p) REVERT: A 216 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8319 (pt0) REVERT: A 245 GLU cc_start: 0.8930 (tp30) cc_final: 0.8395 (mm-30) REVERT: A 272 ASP cc_start: 0.8531 (t70) cc_final: 0.8233 (t0) REVERT: A 276 GLU cc_start: 0.8337 (mp0) cc_final: 0.8075 (pm20) REVERT: A 349 LYS cc_start: 0.8543 (mttm) cc_final: 0.8234 (mmtt) REVERT: B 4 LEU cc_start: 0.8695 (pp) cc_final: 0.8450 (pp) REVERT: B 10 GLU cc_start: 0.8932 (tp30) cc_final: 0.8723 (tp30) REVERT: B 12 GLU cc_start: 0.9133 (tp30) cc_final: 0.8805 (tm-30) REVERT: B 19 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8399 (ttp-110) REVERT: B 59 TYR cc_start: 0.9102 (m-10) cc_final: 0.8686 (m-80) REVERT: B 135 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9053 (t) REVERT: B 284 LEU cc_start: 0.8948 (pt) cc_final: 0.8424 (mp) REVERT: C 14 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8669 (mmmm) REVERT: C 16 VAL cc_start: 0.9399 (p) cc_final: 0.8989 (m) REVERT: C 18 GLN cc_start: 0.8361 (tp-100) cc_final: 0.7684 (tp-100) REVERT: C 20 LYS cc_start: 0.9432 (ttmt) cc_final: 0.9070 (ptpp) REVERT: C 22 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8609 (mt-10) REVERT: D 46 GLU cc_start: 0.7484 (tp30) cc_final: 0.7150 (tt0) REVERT: D 93 MET cc_start: 0.8079 (tpp) cc_final: 0.7760 (tpp) REVERT: D 118 THR cc_start: 0.8384 (m) cc_final: 0.8075 (t) REVERT: D 125 ASP cc_start: 0.8714 (m-30) cc_final: 0.8458 (m-30) REVERT: D 134 SER cc_start: 0.8324 (t) cc_final: 0.8018 (t) outliers start: 55 outliers final: 30 residues processed: 246 average time/residue: 0.0974 time to fit residues: 32.2227 Evaluate side-chains 212 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 331 ASP Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.070027 restraints weight = 20650.580| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.01 r_work: 0.2787 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10254 Z= 0.244 Angle : 0.748 9.159 13911 Z= 0.391 Chirality : 0.047 0.184 1581 Planarity : 0.005 0.046 1759 Dihedral : 7.868 140.323 1427 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.21 % Allowed : 16.93 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.51 (0.22), residues: 1269 helix: 0.63 (0.22), residues: 482 sheet: -0.32 (0.31), residues: 268 loop : -1.20 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.020 0.002 TYR A 74 PHE 0.027 0.002 PHE R 345 TRP 0.014 0.002 TRP A 131 HIS 0.016 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (10251) covalent geometry : angle 0.74665 / 0.39 (13905) SS BOND : bond 0.01405 / 0.97 ( 3) SS BOND : angle 2.47978 / 1.78 ( 6) hydrogen bonds : bond 0.05248 / 3.62 ( 499) hydrogen bonds : angle 5.18128 / 3.76 ( 1443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 134 TRP cc_start: 0.5297 (t-100) cc_final: 0.4788 (t-100) REVERT: R 165 GLU cc_start: 0.9146 (tp30) cc_final: 0.8479 (tm-30) REVERT: R 203 MET cc_start: 0.5413 (tpp) cc_final: 0.4874 (tpp) REVERT: R 207 MET cc_start: 0.6171 (mmm) cc_final: 0.5958 (mmm) REVERT: R 218 HIS cc_start: 0.7540 (t-90) cc_final: 0.7291 (t70) REVERT: R 332 GLU cc_start: 0.9514 (pm20) cc_final: 0.9298 (pm20) REVERT: L 11 TYR cc_start: 0.5675 (p90) cc_final: 0.4913 (p90) REVERT: A 25 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7973 (tm-30) REVERT: A 54 LYS cc_start: 0.8665 (ptpt) cc_final: 0.8423 (ptmm) REVERT: A 88 MET cc_start: 0.9274 (mtp) cc_final: 0.8809 (mtp) REVERT: A 139 CYS cc_start: 0.9732 (t) cc_final: 0.9175 (p) REVERT: A 245 GLU cc_start: 0.9182 (tp30) cc_final: 0.8545 (mm-30) REVERT: A 349 LYS cc_start: 0.8779 (mttm) cc_final: 0.8417 (mttp) REVERT: B 12 GLU cc_start: 0.9309 (tp30) cc_final: 0.8768 (tm-30) REVERT: B 16 ASN cc_start: 0.8486 (t0) cc_final: 0.8190 (m-40) REVERT: B 19 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8071 (ttp80) REVERT: B 42 ARG cc_start: 0.8628 (mtp-110) cc_final: 0.8312 (ttp-110) REVERT: B 46 ARG cc_start: 0.8747 (mpt90) cc_final: 0.8384 (mtp85) REVERT: B 217 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8209 (pmt) REVERT: C 14 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8843 (mmmm) REVERT: C 32 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8236 (tptm) REVERT: C 36 ASP cc_start: 0.8822 (m-30) cc_final: 0.8382 (m-30) REVERT: C 47 GLU cc_start: 0.8630 (pm20) cc_final: 0.8355 (pm20) REVERT: D 73 ASP cc_start: 0.7826 (t0) cc_final: 0.7100 (t0) REVERT: D 118 THR cc_start: 0.8823 (m) cc_final: 0.8423 (p) REVERT: D 128 MET cc_start: 0.9166 (mmm) cc_final: 0.8767 (mmm) REVERT: D 148 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8133 (mtm110) REVERT: D 190 ARG cc_start: 0.8531 (mtp180) cc_final: 0.8098 (mtp180) REVERT: D 218 MET cc_start: 0.9353 (ttp) cc_final: 0.8879 (ttt) outliers start: 56 outliers final: 30 residues processed: 236 average time/residue: 0.0940 time to fit residues: 29.7269 Evaluate side-chains 194 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 131 HIS A 68 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 213 HIS D 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.070693 restraints weight = 20603.138| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.02 r_work: 0.2810 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10254 Z= 0.147 Angle : 0.634 8.412 13911 Z= 0.327 Chirality : 0.043 0.152 1581 Planarity : 0.004 0.041 1759 Dihedral : 7.297 138.930 1425 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.74 % Allowed : 19.16 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1269 helix: 0.95 (0.23), residues: 483 sheet: -0.04 (0.31), residues: 267 loop : -1.12 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.015 0.002 TYR A 74 PHE 0.026 0.002 PHE R 345 TRP 0.012 0.001 TRP B 339 HIS 0.013 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (10251) covalent geometry : angle 0.63282 / 0.33 (13905) SS BOND : bond 0.00991 / 0.70 ( 3) SS BOND : angle 2.10496 / 1.80 ( 6) hydrogen bonds : bond 0.04379 / 3.04 ( 499) hydrogen bonds : angle 4.85526 / 3.51 ( 1443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.368 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 GLU cc_start: 0.9132 (tp30) cc_final: 0.8527 (tm-30) REVERT: R 175 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8237 (mptt) REVERT: R 203 MET cc_start: 0.5674 (tpp) cc_final: 0.4836 (tpp) REVERT: R 207 MET cc_start: 0.6894 (mmm) cc_final: 0.6217 (mmm) REVERT: R 209 GLU cc_start: 0.6228 (pp20) cc_final: 0.5635 (pm20) REVERT: R 218 HIS cc_start: 0.7686 (t-90) cc_final: 0.7414 (t70) REVERT: R 325 MET cc_start: 0.8657 (ttm) cc_final: 0.8339 (ttp) REVERT: A 88 MET cc_start: 0.9193 (mtp) cc_final: 0.8858 (mtp) REVERT: A 139 CYS cc_start: 0.9709 (t) cc_final: 0.9302 (p) REVERT: A 141 ASN cc_start: 0.9539 (m-40) cc_final: 0.9302 (m-40) REVERT: A 180 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8543 (mmmm) REVERT: A 216 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: A 245 GLU cc_start: 0.9139 (tp30) cc_final: 0.8519 (mm-30) REVERT: A 349 LYS cc_start: 0.8725 (mttm) cc_final: 0.8441 (mmtt) REVERT: B 12 GLU cc_start: 0.9272 (tp30) cc_final: 0.8752 (tm-30) REVERT: B 16 ASN cc_start: 0.8374 (t0) cc_final: 0.8057 (m-40) REVERT: B 19 ARG cc_start: 0.8806 (ttm110) cc_final: 0.8150 (ttp80) REVERT: B 46 ARG cc_start: 0.8824 (mpt90) cc_final: 0.8543 (mtp85) REVERT: B 59 TYR cc_start: 0.9055 (m-80) cc_final: 0.8473 (m-80) REVERT: B 61 MET cc_start: 0.9534 (ppp) cc_final: 0.8904 (ppp) REVERT: B 217 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8493 (pmt) REVERT: C 32 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8240 (tptm) REVERT: C 36 ASP cc_start: 0.8865 (m-30) cc_final: 0.8426 (m-30) REVERT: C 47 GLU cc_start: 0.8589 (pm20) cc_final: 0.8387 (pm20) REVERT: D 73 ASP cc_start: 0.8091 (t0) cc_final: 0.7609 (t0) REVERT: D 118 THR cc_start: 0.8902 (m) cc_final: 0.8516 (p) REVERT: D 148 ARG cc_start: 0.8292 (ttp80) cc_final: 0.8006 (mtm110) REVERT: D 218 MET cc_start: 0.9217 (ttp) cc_final: 0.8787 (ttt) outliers start: 51 outliers final: 33 residues processed: 213 average time/residue: 0.0985 time to fit residues: 28.1580 Evaluate side-chains 197 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 110 ASN D 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.104464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.071281 restraints weight = 20593.591| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.01 r_work: 0.2821 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10254 Z= 0.125 Angle : 0.618 11.788 13911 Z= 0.317 Chirality : 0.042 0.148 1581 Planarity : 0.004 0.044 1759 Dihedral : 6.989 138.389 1425 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.63 % Allowed : 21.49 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.03 (0.23), residues: 1269 helix: 1.08 (0.23), residues: 478 sheet: 0.06 (0.31), residues: 270 loop : -0.95 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 96 TYR 0.014 0.001 TYR A 74 PHE 0.024 0.001 PHE R 345 TRP 0.012 0.001 TRP B 297 HIS 0.011 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10251) covalent geometry : angle 0.61750 / 0.32 (13905) SS BOND : bond 0.02087 / 1.48 ( 3) SS BOND : angle 1.75663 / 1.49 ( 6) hydrogen bonds : bond 0.04052 / 2.81 ( 499) hydrogen bonds : angle 4.67718 / 3.36 ( 1443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 GLU cc_start: 0.9144 (tp30) cc_final: 0.8497 (tm-30) REVERT: R 175 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8110 (mppt) REVERT: R 203 MET cc_start: 0.5618 (tpp) cc_final: 0.4836 (tpp) REVERT: R 207 MET cc_start: 0.6751 (mmm) cc_final: 0.6122 (mmm) REVERT: R 209 GLU cc_start: 0.6106 (pp20) cc_final: 0.5351 (pm20) REVERT: R 218 HIS cc_start: 0.7728 (t-90) cc_final: 0.7451 (t70) REVERT: R 325 MET cc_start: 0.8657 (ttm) cc_final: 0.8392 (ttp) REVERT: A 139 CYS cc_start: 0.9693 (t) cc_final: 0.9314 (p) REVERT: A 141 ASN cc_start: 0.9546 (m-40) cc_final: 0.9342 (m110) REVERT: A 180 LYS cc_start: 0.8811 (mmmm) cc_final: 0.8566 (mmmm) REVERT: A 216 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8620 (pt0) REVERT: A 245 GLU cc_start: 0.9194 (tp30) cc_final: 0.8565 (mm-30) REVERT: A 349 LYS cc_start: 0.8837 (mttm) cc_final: 0.8445 (mmtt) REVERT: B 12 GLU cc_start: 0.9321 (tp30) cc_final: 0.8897 (tm-30) REVERT: B 19 ARG cc_start: 0.8698 (ttm110) cc_final: 0.8424 (ttp-110) REVERT: B 42 ARG cc_start: 0.8649 (mtp-110) cc_final: 0.8174 (ttp-110) REVERT: B 46 ARG cc_start: 0.8787 (mpt90) cc_final: 0.8489 (mtp85) REVERT: B 54 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.6824 (t-170) REVERT: B 59 TYR cc_start: 0.8813 (m-80) cc_final: 0.8468 (m-80) REVERT: B 217 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8372 (pmt) REVERT: C 32 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8129 (tptm) REVERT: C 36 ASP cc_start: 0.8817 (m-30) cc_final: 0.8362 (m-30) REVERT: D 73 ASP cc_start: 0.8125 (t0) cc_final: 0.7632 (t0) REVERT: D 118 THR cc_start: 0.8925 (m) cc_final: 0.8537 (p) REVERT: D 148 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7917 (mtm110) REVERT: D 218 MET cc_start: 0.9319 (ttp) cc_final: 0.8852 (ttt) REVERT: D 232 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7710 (ttpp) REVERT: D 234 GLU cc_start: 0.7911 (mp0) cc_final: 0.7468 (pm20) outliers start: 39 outliers final: 25 residues processed: 212 average time/residue: 0.0991 time to fit residues: 28.4356 Evaluate side-chains 199 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 331 ASP Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.101694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.068461 restraints weight = 20753.157| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.01 r_work: 0.2766 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10254 Z= 0.158 Angle : 0.647 10.427 13911 Z= 0.331 Chirality : 0.043 0.188 1581 Planarity : 0.004 0.043 1759 Dihedral : 6.822 137.091 1423 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.09 % Allowed : 21.77 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1269 helix: 1.08 (0.23), residues: 481 sheet: 0.12 (0.32), residues: 264 loop : -1.02 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 372 TYR 0.014 0.001 TYR A 74 PHE 0.026 0.001 PHE R 345 TRP 0.012 0.001 TRP R 134 HIS 0.012 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10251) covalent geometry : angle 0.64570 / 0.33 (13905) SS BOND : bond 0.01058 / 0.74 ( 3) SS BOND : angle 2.04743 / 1.72 ( 6) hydrogen bonds : bond 0.04215 / 2.94 ( 499) hydrogen bonds : angle 4.72036 / 3.41 ( 1443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.267 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6964 (t80) REVERT: R 165 GLU cc_start: 0.9159 (tp30) cc_final: 0.8495 (tm-30) REVERT: R 175 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8075 (mppt) REVERT: R 187 LYS cc_start: 0.8506 (mtpm) cc_final: 0.8291 (tttm) REVERT: R 203 MET cc_start: 0.5844 (tpp) cc_final: 0.4981 (tpp) REVERT: R 207 MET cc_start: 0.6968 (mmm) cc_final: 0.6467 (mmm) REVERT: R 209 GLU cc_start: 0.5649 (pp20) cc_final: 0.5133 (pm20) REVERT: R 218 HIS cc_start: 0.7792 (t-90) cc_final: 0.7536 (t70) REVERT: R 347 MET cc_start: 0.8354 (mmm) cc_final: 0.8131 (mtt) REVERT: A 139 CYS cc_start: 0.9614 (t) cc_final: 0.9290 (p) REVERT: A 180 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8631 (mmmm) REVERT: A 216 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8664 (pt0) REVERT: A 245 GLU cc_start: 0.9228 (tp30) cc_final: 0.8654 (mm-30) REVERT: A 349 LYS cc_start: 0.8809 (mttm) cc_final: 0.8486 (mmtt) REVERT: B 12 GLU cc_start: 0.9327 (tp30) cc_final: 0.8785 (tm-30) REVERT: B 19 ARG cc_start: 0.8717 (ttm110) cc_final: 0.8368 (ttp-110) REVERT: B 46 ARG cc_start: 0.8841 (mpt90) cc_final: 0.8515 (mtp85) REVERT: B 217 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8350 (pmt) REVERT: C 13 ARG cc_start: 0.9179 (mtm110) cc_final: 0.8724 (ptt-90) REVERT: C 29 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8583 (mmmm) REVERT: C 32 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8154 (tptm) REVERT: C 36 ASP cc_start: 0.8830 (m-30) cc_final: 0.8344 (m-30) REVERT: D 73 ASP cc_start: 0.8202 (t0) cc_final: 0.7734 (t0) REVERT: D 118 THR cc_start: 0.9058 (m) cc_final: 0.8587 (p) REVERT: D 148 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7889 (mtm110) REVERT: D 218 MET cc_start: 0.9343 (ttp) cc_final: 0.8872 (ttt) REVERT: D 232 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7915 (ttmm) REVERT: D 234 GLU cc_start: 0.7776 (mp0) cc_final: 0.7574 (pm20) outliers start: 44 outliers final: 32 residues processed: 207 average time/residue: 0.1064 time to fit residues: 29.6387 Evaluate side-chains 194 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 331 ASP Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 89 optimal weight: 0.0770 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.103866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.071265 restraints weight = 20464.950| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.99 r_work: 0.2832 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10254 Z= 0.117 Angle : 0.625 10.680 13911 Z= 0.317 Chirality : 0.041 0.160 1581 Planarity : 0.004 0.055 1759 Dihedral : 6.712 138.194 1423 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.00 % Allowed : 21.95 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.19 (0.23), residues: 1269 helix: 1.19 (0.24), residues: 483 sheet: 0.28 (0.32), residues: 262 loop : -0.93 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.022 0.001 TYR R 70 PHE 0.024 0.001 PHE R 345 TRP 0.012 0.001 TRP B 297 HIS 0.010 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10251) covalent geometry : angle 0.62448 / 0.32 (13905) SS BOND : bond 0.00568 / 0.38 ( 3) SS BOND : angle 1.42687 / 1.15 ( 6) hydrogen bonds : bond 0.03832 / 2.68 ( 499) hydrogen bonds : angle 4.56726 / 3.29 ( 1443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.233 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6914 (t80) REVERT: R 112 ASP cc_start: 0.7941 (t0) cc_final: 0.7202 (t70) REVERT: R 165 GLU cc_start: 0.9148 (tp30) cc_final: 0.8503 (tm-30) REVERT: R 175 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8118 (mppt) REVERT: R 203 MET cc_start: 0.6095 (tpp) cc_final: 0.5311 (tpp) REVERT: R 207 MET cc_start: 0.6868 (mmm) cc_final: 0.6385 (mmm) REVERT: R 209 GLU cc_start: 0.5837 (pp20) cc_final: 0.5255 (pm20) REVERT: R 218 HIS cc_start: 0.7762 (t-90) cc_final: 0.7522 (t70) REVERT: A 139 CYS cc_start: 0.9544 (t) cc_final: 0.9219 (p) REVERT: A 178 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.6830 (ttt90) REVERT: A 216 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: A 245 GLU cc_start: 0.9227 (tp30) cc_final: 0.8639 (mm-30) REVERT: A 349 LYS cc_start: 0.8806 (mttm) cc_final: 0.8448 (mmtt) REVERT: B 12 GLU cc_start: 0.9301 (tp30) cc_final: 0.8771 (tp30) REVERT: B 19 ARG cc_start: 0.8863 (ttm110) cc_final: 0.8541 (ttm110) REVERT: B 29 THR cc_start: 0.9452 (p) cc_final: 0.9202 (t) REVERT: B 46 ARG cc_start: 0.8854 (mpt90) cc_final: 0.8551 (mtp85) REVERT: B 54 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7315 (t-170) REVERT: B 61 MET cc_start: 0.9485 (ppp) cc_final: 0.8788 (ppp) REVERT: B 217 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8398 (pmt) REVERT: C 29 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8282 (mmmm) REVERT: C 32 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8213 (tptm) REVERT: C 36 ASP cc_start: 0.8803 (m-30) cc_final: 0.8317 (m-30) REVERT: D 73 ASP cc_start: 0.8209 (t0) cc_final: 0.7754 (t0) REVERT: D 118 THR cc_start: 0.9067 (m) cc_final: 0.8509 (p) REVERT: D 148 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7918 (mtm110) REVERT: D 207 LEU cc_start: 0.8784 (tt) cc_final: 0.8492 (mp) REVERT: D 218 MET cc_start: 0.9310 (ttp) cc_final: 0.8861 (ttt) REVERT: D 232 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8002 (ttmm) REVERT: D 234 GLU cc_start: 0.7724 (mp0) cc_final: 0.7475 (pm20) outliers start: 43 outliers final: 27 residues processed: 201 average time/residue: 0.1006 time to fit residues: 27.1366 Evaluate side-chains 191 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.065548 restraints weight = 20582.497| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.96 r_work: 0.2704 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10254 Z= 0.210 Angle : 0.680 10.706 13911 Z= 0.347 Chirality : 0.045 0.178 1581 Planarity : 0.004 0.044 1759 Dihedral : 6.797 136.143 1419 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.28 % Allowed : 22.23 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.08 (0.23), residues: 1269 helix: 1.10 (0.24), residues: 492 sheet: 0.32 (0.34), residues: 247 loop : -1.05 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.023 0.002 TYR R 70 PHE 0.023 0.002 PHE R 345 TRP 0.015 0.002 TRP A 131 HIS 0.014 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (10251) covalent geometry : angle 0.67813 / 0.35 (13905) SS BOND : bond 0.01356 / 0.96 ( 3) SS BOND : angle 2.28710 / 1.87 ( 6) hydrogen bonds : bond 0.04208 / 2.94 ( 499) hydrogen bonds : angle 4.69919 / 3.41 ( 1443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.361 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7190 (t80) REVERT: R 165 GLU cc_start: 0.9159 (tp30) cc_final: 0.8468 (tm-30) REVERT: R 175 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8076 (mppt) REVERT: R 203 MET cc_start: 0.6579 (tpp) cc_final: 0.5685 (tpp) REVERT: R 207 MET cc_start: 0.7245 (mmm) cc_final: 0.6494 (mmm) REVERT: R 209 GLU cc_start: 0.6033 (pp20) cc_final: 0.5349 (pm20) REVERT: R 218 HIS cc_start: 0.7623 (t-90) cc_final: 0.7378 (t70) REVERT: R 325 MET cc_start: 0.9063 (ttp) cc_final: 0.8843 (ppp) REVERT: A 216 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: A 245 GLU cc_start: 0.9271 (tp30) cc_final: 0.8657 (mm-30) REVERT: A 349 LYS cc_start: 0.8806 (mttm) cc_final: 0.8355 (mmtm) REVERT: B 12 GLU cc_start: 0.9313 (tp30) cc_final: 0.8765 (tp30) REVERT: B 19 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8556 (ttm110) REVERT: B 29 THR cc_start: 0.9421 (p) cc_final: 0.9206 (t) REVERT: B 46 ARG cc_start: 0.8829 (mpt90) cc_final: 0.8446 (mtp85) REVERT: B 59 TYR cc_start: 0.9248 (m-80) cc_final: 0.8838 (m-80) REVERT: B 217 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8367 (pmt) REVERT: C 13 ARG cc_start: 0.9120 (mtm110) cc_final: 0.8827 (ptp90) REVERT: C 29 LYS cc_start: 0.8890 (mmtm) cc_final: 0.8300 (mmmm) REVERT: C 32 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8193 (tptm) REVERT: C 36 ASP cc_start: 0.8800 (m-30) cc_final: 0.8327 (m-30) REVERT: D 73 ASP cc_start: 0.8272 (t0) cc_final: 0.7841 (t0) REVERT: D 148 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7948 (mtm110) REVERT: D 218 MET cc_start: 0.9363 (ttp) cc_final: 0.8937 (ttt) REVERT: D 232 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8039 (ttmm) REVERT: D 234 GLU cc_start: 0.7764 (mp0) cc_final: 0.7503 (pm20) outliers start: 46 outliers final: 40 residues processed: 195 average time/residue: 0.0951 time to fit residues: 24.9663 Evaluate side-chains 200 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 331 ASP Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 256 ASN A 188 HIS B 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.099854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.067069 restraints weight = 20443.755| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.99 r_work: 0.2741 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10254 Z= 0.144 Angle : 0.648 11.140 13911 Z= 0.329 Chirality : 0.043 0.184 1581 Planarity : 0.004 0.055 1759 Dihedral : 6.742 138.559 1419 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.19 % Allowed : 22.98 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.23 (0.23), residues: 1269 helix: 1.25 (0.24), residues: 486 sheet: 0.42 (0.33), residues: 253 loop : -1.00 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 96 TYR 0.019 0.001 TYR R 70 PHE 0.022 0.001 PHE R 345 TRP 0.013 0.001 TRP A 131 HIS 0.011 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10251) covalent geometry : angle 0.64688 / 0.33 (13905) SS BOND : bond 0.00844 / 0.57 ( 3) SS BOND : angle 1.76421 / 1.41 ( 6) hydrogen bonds : bond 0.03901 / 2.72 ( 499) hydrogen bonds : angle 4.63566 / 3.34 ( 1443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.273 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7322 (t80) REVERT: R 123 GLU cc_start: 0.7975 (tt0) cc_final: 0.7187 (tt0) REVERT: R 165 GLU cc_start: 0.9158 (tp30) cc_final: 0.8469 (tm-30) REVERT: R 175 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8101 (mppt) REVERT: R 203 MET cc_start: 0.6747 (tpp) cc_final: 0.5956 (tpp) REVERT: R 207 MET cc_start: 0.6959 (mmm) cc_final: 0.6200 (mmm) REVERT: R 209 GLU cc_start: 0.5995 (pp20) cc_final: 0.5457 (pm20) REVERT: R 218 HIS cc_start: 0.7563 (t-90) cc_final: 0.7322 (t70) REVERT: R 325 MET cc_start: 0.9173 (ttp) cc_final: 0.8918 (ppp) REVERT: A 216 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8664 (pt0) REVERT: A 245 GLU cc_start: 0.9243 (tp30) cc_final: 0.8615 (mm-30) REVERT: A 349 LYS cc_start: 0.8764 (mttm) cc_final: 0.8312 (mmtm) REVERT: B 12 GLU cc_start: 0.9314 (tp30) cc_final: 0.8829 (tm-30) REVERT: B 19 ARG cc_start: 0.8818 (ttm110) cc_final: 0.8552 (ttm110) REVERT: B 42 ARG cc_start: 0.8767 (mtp-110) cc_final: 0.8305 (ttp-110) REVERT: B 46 ARG cc_start: 0.8774 (mpt90) cc_final: 0.8400 (mtp85) REVERT: B 217 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8434 (pmt) REVERT: C 29 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8335 (mmmm) REVERT: C 32 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8249 (tptm) REVERT: C 36 ASP cc_start: 0.8768 (m-30) cc_final: 0.8291 (m-30) REVERT: D 73 ASP cc_start: 0.8229 (t0) cc_final: 0.7798 (t0) REVERT: D 148 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7950 (mtm110) REVERT: D 218 MET cc_start: 0.9358 (ttp) cc_final: 0.8787 (ttt) REVERT: D 232 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8205 (ttmm) REVERT: D 234 GLU cc_start: 0.7716 (mp0) cc_final: 0.7462 (pm20) outliers start: 45 outliers final: 31 residues processed: 196 average time/residue: 0.1134 time to fit residues: 29.6948 Evaluate side-chains 188 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 9.9990 chunk 70 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.065143 restraints weight = 20499.328| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.98 r_work: 0.2697 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.7697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10254 Z= 0.185 Angle : 0.688 11.771 13911 Z= 0.349 Chirality : 0.044 0.174 1581 Planarity : 0.004 0.079 1759 Dihedral : 6.726 136.670 1417 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.53 % Allowed : 23.53 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.20 (0.23), residues: 1269 helix: 1.21 (0.24), residues: 485 sheet: 0.39 (0.33), residues: 255 loop : -0.98 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 268 TYR 0.021 0.002 TYR B 59 PHE 0.022 0.002 PHE R 345 TRP 0.030 0.002 TRP A 131 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (10251) covalent geometry : angle 0.68683 / 0.35 (13905) SS BOND : bond 0.01175 / 0.83 ( 3) SS BOND : angle 2.11028 / 1.70 ( 6) hydrogen bonds : bond 0.04134 / 2.88 ( 499) hydrogen bonds : angle 4.71038 / 3.39 ( 1443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.282 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7927 (t80) REVERT: R 123 GLU cc_start: 0.8695 (tt0) cc_final: 0.8108 (mt-10) REVERT: R 165 GLU cc_start: 0.9159 (tp30) cc_final: 0.8465 (tm-30) REVERT: R 175 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8100 (mmmm) REVERT: R 203 MET cc_start: 0.6790 (tpp) cc_final: 0.6007 (tpp) REVERT: R 207 MET cc_start: 0.7586 (mmm) cc_final: 0.6781 (mmm) REVERT: R 209 GLU cc_start: 0.6048 (pp20) cc_final: 0.5320 (pm20) REVERT: R 218 HIS cc_start: 0.7598 (t-90) cc_final: 0.7378 (t70) REVERT: R 238 GLN cc_start: 0.8370 (tt0) cc_final: 0.7358 (pt0) REVERT: R 325 MET cc_start: 0.9113 (ttp) cc_final: 0.8837 (ppp) REVERT: A 216 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8664 (pt0) REVERT: A 245 GLU cc_start: 0.9243 (tp30) cc_final: 0.8652 (mm-30) REVERT: A 349 LYS cc_start: 0.8764 (mttm) cc_final: 0.8229 (mmtm) REVERT: B 12 GLU cc_start: 0.9327 (tp30) cc_final: 0.8842 (tm-30) REVERT: B 19 ARG cc_start: 0.8814 (ttm110) cc_final: 0.8547 (ttm110) REVERT: B 42 ARG cc_start: 0.8727 (mtp-110) cc_final: 0.8255 (ttp-110) REVERT: B 46 ARG cc_start: 0.8746 (mpt90) cc_final: 0.8330 (mtp85) REVERT: B 54 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7412 (t-90) REVERT: B 61 MET cc_start: 0.9548 (ppp) cc_final: 0.8824 (ppp) REVERT: B 217 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8396 (pmt) REVERT: C 13 ARG cc_start: 0.9195 (mtm110) cc_final: 0.8964 (ptp90) REVERT: C 29 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8364 (mmmm) REVERT: C 32 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8290 (tptm) REVERT: C 36 ASP cc_start: 0.8787 (m-30) cc_final: 0.8352 (m-30) REVERT: D 73 ASP cc_start: 0.8266 (t0) cc_final: 0.7844 (t0) REVERT: D 148 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7956 (mtm110) REVERT: D 218 MET cc_start: 0.9378 (ttp) cc_final: 0.8798 (ttt) REVERT: D 232 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8207 (ttmm) REVERT: D 234 GLU cc_start: 0.7688 (mp0) cc_final: 0.7401 (pm20) outliers start: 38 outliers final: 33 residues processed: 189 average time/residue: 0.1003 time to fit residues: 25.5315 Evaluate side-chains 193 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 TYR Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 224 CYS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.065295 restraints weight = 20614.133| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.96 r_work: 0.2707 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10254 Z= 0.168 Angle : 0.678 11.573 13911 Z= 0.342 Chirality : 0.044 0.229 1581 Planarity : 0.004 0.046 1759 Dihedral : 6.695 137.799 1417 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.63 % Allowed : 23.81 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.24 (0.23), residues: 1269 helix: 1.27 (0.24), residues: 485 sheet: 0.38 (0.33), residues: 255 loop : -0.97 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.016 0.001 TYR R 70 PHE 0.021 0.001 PHE R 345 TRP 0.021 0.002 TRP A 131 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (10251) covalent geometry : angle 0.67723 / 0.34 (13905) SS BOND : bond 0.01039 / 0.73 ( 3) SS BOND : angle 2.02281 / 1.61 ( 6) hydrogen bonds : bond 0.03995 / 2.76 ( 499) hydrogen bonds : angle 4.65711 / 3.34 ( 1443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.96 seconds wall clock time: 37 minutes 12.55 seconds (2232.55 seconds total)