Starting phenix.real_space_refine on Sat Aug 23 01:17:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iul_35725/08_2025/8iul_35725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iul_35725/08_2025/8iul_35725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iul_35725/08_2025/8iul_35725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iul_35725/08_2025/8iul_35725.map" model { file = "/net/cci-nas-00/data/ceres_data/8iul_35725/08_2025/8iul_35725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iul_35725/08_2025/8iul_35725_neut.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5725 2.51 5 N 1551 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9016 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2314 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 5, 'TRANS': 287} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7WT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.24 Number of scatterers: 9016 At special positions: 0 Unit cell: (122.776, 92.288, 128.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1676 8.00 N 1551 7.00 C 5725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 307.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.625A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.594A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.576A pdb=" N PHE A 282 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.591A pdb=" N ALA A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 360 Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.564A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 3.720A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.561A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.693A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.695A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 removed outlier: 3.951A pdb=" N ASP G 47 " --> pdb=" O ALA G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 47' Processing helix chain 'G' and resid 54 through 58 Processing helix chain 'R' and resid 30 through 59 removed outlier: 3.585A pdb=" N VAL R 39 " --> pdb=" O ILE R 35 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY R 40 " --> pdb=" O PHE R 36 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 93 removed outlier: 3.578A pdb=" N GLY R 85 " --> pdb=" O HIS R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 102 Processing helix chain 'R' and resid 106 through 139 removed outlier: 4.470A pdb=" N MET R 115 " --> pdb=" O PHE R 111 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER R 118 " --> pdb=" O CYS R 114 " (cutoff:3.500A) Proline residue: R 122 - end of helix removed outlier: 4.028A pdb=" N GLY R 126 " --> pdb=" O PRO R 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA R 130 " --> pdb=" O GLY R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 148 through 169 Processing helix chain 'R' and resid 170 through 174 removed outlier: 3.889A pdb=" N HIS R 174 " --> pdb=" O ILE R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 233 removed outlier: 3.944A pdb=" N ARG R 199 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 276 removed outlier: 3.587A pdb=" N CYS R 259 " --> pdb=" O MET R 255 " (cutoff:3.500A) Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 282 through 294 removed outlier: 3.545A pdb=" N THR R 286 " --> pdb=" O THR R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 305 removed outlier: 3.877A pdb=" N ILE R 305 " --> pdb=" O PRO R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 323 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.525A pdb=" N LEU A 34 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.533A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.665A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.838A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 180 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.841A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.856A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.666A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.688A pdb=" N ARG E 17 " --> pdb=" O MET E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.072A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.566A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.911A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 178 through 179 removed outlier: 3.585A pdb=" N PHE R 187 " --> pdb=" O LYS R 178 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1272 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: 1.50 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1481 1.31 - 1.44: 2528 1.44 - 1.56: 5090 1.56 - 1.69: 4 1.69 - 1.81: 92 Bond restraints: 9195 Sorted by residual: bond pdb=" C02 7WT R 401 " pdb=" C06 7WT R 401 " ideal model delta sigma weight residual 1.525 1.339 0.186 2.00e-02 2.50e+03 8.66e+01 bond pdb=" C03 7WT R 401 " pdb=" C04 7WT R 401 " ideal model delta sigma weight residual 1.538 1.372 0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C02 7WT R 401 " pdb=" C03 7WT R 401 " ideal model delta sigma weight residual 1.527 1.662 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" CA VAL R 30 " pdb=" C VAL R 30 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.27e-02 6.20e+03 4.20e+01 bond pdb=" N PHE R 31 " pdb=" CA PHE R 31 " ideal model delta sigma weight residual 1.459 1.399 0.060 1.23e-02 6.61e+03 2.41e+01 ... (remaining 9190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 12334 3.14 - 6.29: 78 6.29 - 9.43: 18 9.43 - 12.58: 3 12.58 - 15.72: 2 Bond angle restraints: 12435 Sorted by residual: angle pdb=" N ILE R 298 " pdb=" CA ILE R 298 " pdb=" C ILE R 298 " ideal model delta sigma weight residual 111.67 98.24 13.43 9.50e-01 1.11e+00 2.00e+02 angle pdb=" N ASN R 296 " pdb=" CA ASN R 296 " pdb=" C ASN R 296 " ideal model delta sigma weight residual 113.97 98.25 15.72 1.28e+00 6.10e-01 1.51e+02 angle pdb=" N PHE R 111 " pdb=" CA PHE R 111 " pdb=" C PHE R 111 " ideal model delta sigma weight residual 112.97 102.86 10.11 1.06e+00 8.90e-01 9.09e+01 angle pdb=" N TYR R 92 " pdb=" CA TYR R 92 " pdb=" C TYR R 92 " ideal model delta sigma weight residual 113.50 103.29 10.21 1.23e+00 6.61e-01 6.89e+01 angle pdb=" N LEU R 290 " pdb=" CA LEU R 290 " pdb=" C LEU R 290 " ideal model delta sigma weight residual 111.36 103.15 8.21 1.09e+00 8.42e-01 5.68e+01 ... (remaining 12430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.41: 5392 25.41 - 50.81: 77 50.81 - 76.22: 14 76.22 - 101.63: 2 101.63 - 127.03: 4 Dihedral angle restraints: 5489 sinusoidal: 2170 harmonic: 3319 Sorted by residual: dihedral pdb=" CD ARG A 209 " pdb=" NE ARG A 209 " pdb=" CZ ARG A 209 " pdb=" NH1 ARG A 209 " ideal model delta sinusoidal sigma weight residual 0.00 86.80 -86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" C LEU R 120 " pdb=" N LEU R 120 " pdb=" CA LEU R 120 " pdb=" CB LEU R 120 " ideal model delta harmonic sigma weight residual -122.60 -133.86 11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CA LEU R 120 " pdb=" CB LEU R 120 " ideal model delta harmonic sigma weight residual 122.80 133.92 -11.12 0 2.50e+00 1.60e-01 1.98e+01 ... (remaining 5486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1335 0.108 - 0.216: 56 0.216 - 0.324: 11 0.324 - 0.432: 6 0.432 - 0.540: 3 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA PRO R 122 " pdb=" N PRO R 122 " pdb=" C PRO R 122 " pdb=" CB PRO R 122 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA CYS R 114 " pdb=" N CYS R 114 " pdb=" C CYS R 114 " pdb=" CB CYS R 114 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 1408 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 209 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 209 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 209 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 209 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 121 " 0.104 5.00e-02 4.00e+02 1.51e-01 3.67e+01 pdb=" N PRO R 122 " -0.261 5.00e-02 4.00e+02 pdb=" CA PRO R 122 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO R 122 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 300 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO R 301 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " 0.059 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 189 2.67 - 3.23: 8854 3.23 - 3.79: 13642 3.79 - 4.34: 18934 4.34 - 4.90: 31663 Nonbonded interactions: 73282 Sorted by model distance: nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.116 3.040 nonbonded pdb=" OD1 ASP A 226 " pdb=" OG SER A 228 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASN A 216 " pdb=" NZ LYS B 62 " model vdw 2.146 3.120 nonbonded pdb=" ND2 ASN E 169 " pdb=" OD1 ASN E 171 " model vdw 2.190 3.120 nonbonded pdb=" O ALA A 318 " pdb=" OG SER A 319 " model vdw 2.238 3.040 ... (remaining 73277 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.006 0.186 9196 Z= 0.370 Angle : 0.659 15.725 12437 Z= 0.433 Chirality : 0.058 0.540 1411 Planarity : 0.014 0.492 1572 Dihedral : 9.740 127.032 3342 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.61 % Allowed : 4.48 % Favored : 94.91 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.10 (0.24), residues: 1129 helix: 0.07 (0.25), residues: 418 sheet: -0.53 (0.30), residues: 257 loop : -1.51 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 291 TYR 0.005 0.000 TYR R 92 PHE 0.011 0.001 PHE R 117 TRP 0.003 0.001 TRP R 302 HIS 0.004 0.000 HIS R 81 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 9195) covalent geometry : angle 0.65893 (12435) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.78256 ( 2) hydrogen bonds : bond 0.18501 ( 453) hydrogen bonds : angle 6.83273 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 317 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7006 (m-40) cc_final: 0.6643 (m-40) REVERT: A 227 SER cc_start: 0.7758 (p) cc_final: 0.7519 (p) REVERT: A 298 ASP cc_start: 0.7698 (t0) cc_final: 0.7470 (t0) REVERT: A 310 LYS cc_start: 0.7746 (tptt) cc_final: 0.7331 (tptt) REVERT: A 314 ASP cc_start: 0.6837 (m-30) cc_final: 0.6590 (m-30) REVERT: B 42 ILE cc_start: 0.7703 (tt) cc_final: 0.7460 (pt) REVERT: B 252 ASP cc_start: 0.6133 (t0) cc_final: 0.4766 (t0) REVERT: B 306 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6773 (mmmm) REVERT: E 92 MET cc_start: 0.7731 (ttm) cc_final: 0.7524 (ttp) REVERT: E 230 MET cc_start: 0.8471 (ttp) cc_final: 0.8259 (ttt) outliers start: 6 outliers final: 2 residues processed: 321 average time/residue: 0.5193 time to fit residues: 177.9004 Evaluate side-chains 172 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN B 161 GLN B 225 GLN B 273 ASN B 298 ASN E 12 GLN E 34 HIS ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN R 297 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.172111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.136317 restraints weight = 10243.171| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.23 r_work: 0.3564 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9196 Z= 0.130 Angle : 0.560 7.115 12437 Z= 0.292 Chirality : 0.042 0.149 1411 Planarity : 0.005 0.074 1572 Dihedral : 6.264 103.596 1277 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.15 % Allowed : 14.34 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.47 (0.25), residues: 1129 helix: 1.69 (0.26), residues: 409 sheet: 0.12 (0.30), residues: 269 loop : -0.82 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 300 TYR 0.015 0.002 TYR R 92 PHE 0.021 0.002 PHE R 207 TRP 0.015 0.002 TRP B 174 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9195) covalent geometry : angle 0.56004 (12435) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.97468 ( 2) hydrogen bonds : bond 0.03720 ( 453) hydrogen bonds : angle 4.57645 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7334 (mt) cc_final: 0.7057 (mp) REVERT: A 182 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7657 (p) REVERT: A 310 LYS cc_start: 0.7925 (tptt) cc_final: 0.7633 (tppt) REVERT: A 314 ASP cc_start: 0.7746 (m-30) cc_final: 0.7300 (m-30) REVERT: B 64 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: B 233 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: E 58 TYR cc_start: 0.8298 (m-10) cc_final: 0.7941 (m-10) REVERT: E 89 ASP cc_start: 0.6677 (m-30) cc_final: 0.6416 (m-30) REVERT: E 92 MET cc_start: 0.8412 (ttm) cc_final: 0.8150 (ttp) REVERT: E 219 LEU cc_start: 0.8435 (tt) cc_final: 0.8191 (tm) REVERT: E 245 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7353 (mp) REVERT: R 53 LYS cc_start: 0.7427 (ttpt) cc_final: 0.6958 (tptp) REVERT: R 148 THR cc_start: 0.7750 (m) cc_final: 0.7503 (p) outliers start: 31 outliers final: 12 residues processed: 202 average time/residue: 0.4625 time to fit residues: 100.3392 Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 271 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 57 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 235 ASN B 273 ASN E 171 ASN R 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115255 restraints weight = 10557.573| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.28 r_work: 0.3284 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9196 Z= 0.199 Angle : 0.616 7.483 12437 Z= 0.324 Chirality : 0.044 0.174 1411 Planarity : 0.005 0.077 1572 Dihedral : 6.485 120.462 1276 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.87 % Allowed : 16.68 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.72 (0.25), residues: 1129 helix: 1.89 (0.26), residues: 406 sheet: 0.14 (0.31), residues: 273 loop : -0.57 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 139 TYR 0.018 0.002 TYR E 190 PHE 0.024 0.002 PHE R 200 TRP 0.013 0.002 TRP E 35 HIS 0.009 0.002 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9195) covalent geometry : angle 0.61580 (12435) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.82651 ( 2) hydrogen bonds : bond 0.04410 ( 453) hydrogen bonds : angle 4.56554 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8507 (tttm) cc_final: 0.7846 (tptm) REVERT: A 235 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 247 ARG cc_start: 0.8260 (ptm160) cc_final: 0.7714 (ttt180) REVERT: A 250 ARG cc_start: 0.8291 (ptp-110) cc_final: 0.7891 (ptp-170) REVERT: A 276 GLU cc_start: 0.7733 (tp30) cc_final: 0.7450 (tp30) REVERT: B 27 ARG cc_start: 0.5670 (ttm170) cc_final: 0.5461 (mtt180) REVERT: E 160 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7328 (mtm110) REVERT: E 183 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7310 (mm-40) REVERT: R 53 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7284 (tptp) REVERT: R 148 THR cc_start: 0.7918 (m) cc_final: 0.7618 (p) outliers start: 38 outliers final: 18 residues processed: 185 average time/residue: 0.5959 time to fit residues: 117.3373 Evaluate side-chains 159 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 235 ASN B 264 GLN B 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117616 restraints weight = 10580.643| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.27 r_work: 0.3321 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9196 Z= 0.129 Angle : 0.530 7.569 12437 Z= 0.278 Chirality : 0.041 0.141 1411 Planarity : 0.004 0.067 1572 Dihedral : 6.115 117.023 1274 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.36 % Allowed : 18.11 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.00 (0.25), residues: 1129 helix: 2.04 (0.26), residues: 416 sheet: 0.30 (0.31), residues: 271 loop : -0.39 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 139 TYR 0.011 0.001 TYR E 190 PHE 0.022 0.002 PHE R 207 TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9195) covalent geometry : angle 0.52986 (12435) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.57425 ( 2) hydrogen bonds : bond 0.03604 ( 453) hydrogen bonds : angle 4.27337 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.360 Fit side-chains REVERT: A 182 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7621 (p) REVERT: A 235 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7458 (mt-10) REVERT: A 250 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.7997 (ptp-170) REVERT: A 276 GLU cc_start: 0.7665 (tp30) cc_final: 0.7428 (tp30) REVERT: B 219 ARG cc_start: 0.7780 (mmt-90) cc_final: 0.7470 (mtp85) REVERT: E 160 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7353 (mtm110) REVERT: E 183 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7242 (mm-40) REVERT: E 219 LEU cc_start: 0.8717 (tt) cc_final: 0.8426 (tm) REVERT: E 234 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: R 52 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.5871 (mtm) REVERT: R 53 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7194 (tptp) REVERT: R 139 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7837 (mtpp) REVERT: R 148 THR cc_start: 0.7801 (m) cc_final: 0.7511 (p) outliers start: 33 outliers final: 17 residues processed: 169 average time/residue: 0.6273 time to fit residues: 112.4773 Evaluate side-chains 156 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS B 181 GLN B 225 GLN B 264 GLN B 273 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115303 restraints weight = 10603.334| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.23 r_work: 0.3291 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9196 Z= 0.176 Angle : 0.580 7.063 12437 Z= 0.307 Chirality : 0.043 0.169 1411 Planarity : 0.004 0.060 1572 Dihedral : 6.203 118.225 1274 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.07 % Allowed : 18.01 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.91 (0.25), residues: 1129 helix: 1.97 (0.26), residues: 412 sheet: 0.18 (0.31), residues: 272 loop : -0.36 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 139 TYR 0.016 0.002 TYR E 190 PHE 0.025 0.002 PHE R 207 TRP 0.011 0.001 TRP B 216 HIS 0.008 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9195) covalent geometry : angle 0.58036 (12435) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.66054 ( 2) hydrogen bonds : bond 0.04088 ( 453) hydrogen bonds : angle 4.41650 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.355 Fit side-chains REVERT: A 182 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7605 (p) REVERT: A 235 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7523 (mt-10) REVERT: A 250 ARG cc_start: 0.8424 (ptp-110) cc_final: 0.8217 (ptp-170) REVERT: B 43 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7609 (t70) REVERT: B 219 ARG cc_start: 0.7844 (mmt-90) cc_final: 0.7516 (mtp85) REVERT: E 160 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7432 (mtm110) REVERT: E 183 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7459 (mm-40) REVERT: E 234 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: G 41 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7866 (mm-30) REVERT: R 53 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7283 (tptp) REVERT: R 148 THR cc_start: 0.7909 (m) cc_final: 0.7644 (p) outliers start: 40 outliers final: 21 residues processed: 171 average time/residue: 0.6170 time to fit residues: 112.1221 Evaluate side-chains 155 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 264 GLN B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113163 restraints weight = 10595.039| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.20 r_work: 0.3259 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9196 Z= 0.205 Angle : 0.614 8.618 12437 Z= 0.322 Chirality : 0.045 0.182 1411 Planarity : 0.004 0.055 1572 Dihedral : 6.310 118.574 1274 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.78 % Allowed : 18.31 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1129 helix: 1.84 (0.26), residues: 414 sheet: 0.14 (0.31), residues: 263 loop : -0.37 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 139 TYR 0.016 0.002 TYR E 190 PHE 0.025 0.002 PHE R 207 TRP 0.011 0.002 TRP E 35 HIS 0.007 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9195) covalent geometry : angle 0.61440 (12435) SS BOND : bond 0.00354 ( 1) SS BOND : angle 0.71525 ( 2) hydrogen bonds : bond 0.04325 ( 453) hydrogen bonds : angle 4.53587 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.377 Fit side-chains REVERT: A 182 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7536 (p) REVERT: A 247 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7820 (ptm160) REVERT: B 43 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7603 (t70) REVERT: B 222 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8304 (ppp) REVERT: E 160 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7407 (mtm110) REVERT: E 183 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7508 (mm-40) REVERT: E 234 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: R 53 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7290 (tptp) REVERT: R 148 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7672 (p) REVERT: R 313 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8106 (ptpp) outliers start: 47 outliers final: 25 residues processed: 165 average time/residue: 0.6372 time to fit residues: 111.6469 Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 292 MET Chi-restraints excluded: chain R residue 313 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.155024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117209 restraints weight = 10503.105| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.19 r_work: 0.3314 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.127 Angle : 0.555 8.494 12437 Z= 0.291 Chirality : 0.042 0.178 1411 Planarity : 0.004 0.054 1572 Dihedral : 6.081 114.579 1274 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.36 % Allowed : 20.35 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.08 (0.25), residues: 1129 helix: 2.17 (0.26), residues: 411 sheet: 0.27 (0.31), residues: 269 loop : -0.32 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 139 TYR 0.011 0.001 TYR E 190 PHE 0.020 0.001 PHE A 189 TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9195) covalent geometry : angle 0.55472 (12435) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.48491 ( 2) hydrogen bonds : bond 0.03622 ( 453) hydrogen bonds : angle 4.32747 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.381 Fit side-chains REVERT: A 182 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7496 (p) REVERT: B 27 ARG cc_start: 0.5480 (mtt180) cc_final: 0.5218 (mtt180) REVERT: B 49 GLN cc_start: 0.8270 (mm-40) cc_final: 0.8025 (mp10) REVERT: B 222 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8255 (ppp) REVERT: E 160 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7351 (mtm110) REVERT: E 183 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7468 (mm-40) REVERT: E 234 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: G 20 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6908 (mtt) REVERT: G 45 LYS cc_start: 0.8840 (mptt) cc_final: 0.8266 (pttt) REVERT: G 57 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7235 (mp0) REVERT: R 53 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7201 (tptp) REVERT: R 100 ARG cc_start: 0.6172 (tmm-80) cc_final: 0.5790 (ttt90) REVERT: R 148 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7584 (p) outliers start: 33 outliers final: 22 residues processed: 157 average time/residue: 0.6667 time to fit residues: 111.5009 Evaluate side-chains 156 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.0040 chunk 68 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 225 GLN B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.155073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117211 restraints weight = 10517.928| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.20 r_work: 0.3320 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.129 Angle : 0.557 8.444 12437 Z= 0.291 Chirality : 0.042 0.156 1411 Planarity : 0.004 0.057 1572 Dihedral : 5.988 110.745 1274 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.56 % Allowed : 19.94 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.14 (0.25), residues: 1129 helix: 2.22 (0.26), residues: 412 sheet: 0.29 (0.31), residues: 270 loop : -0.28 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 139 TYR 0.012 0.001 TYR E 190 PHE 0.021 0.001 PHE A 189 TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9195) covalent geometry : angle 0.55697 (12435) SS BOND : bond 0.00165 ( 1) SS BOND : angle 0.46851 ( 2) hydrogen bonds : bond 0.03595 ( 453) hydrogen bonds : angle 4.27653 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.355 Fit side-chains REVERT: A 182 SER cc_start: 0.7966 (OUTLIER) cc_final: 0.7451 (p) REVERT: A 247 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7600 (ttt180) REVERT: B 222 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8261 (ppp) REVERT: E 160 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7280 (mtm110) REVERT: E 183 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7374 (mt0) REVERT: E 234 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: G 20 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: G 45 LYS cc_start: 0.8852 (mptt) cc_final: 0.8268 (pttt) REVERT: G 57 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7240 (mp0) REVERT: R 53 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7196 (tptp) REVERT: R 100 ARG cc_start: 0.6232 (tmm-80) cc_final: 0.5862 (ttt90) REVERT: R 148 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7562 (p) outliers start: 35 outliers final: 23 residues processed: 152 average time/residue: 0.6337 time to fit residues: 102.1637 Evaluate side-chains 155 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 76 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.157878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120921 restraints weight = 10356.004| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.17 r_work: 0.3365 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9196 Z= 0.110 Angle : 0.537 8.881 12437 Z= 0.279 Chirality : 0.041 0.156 1411 Planarity : 0.004 0.047 1572 Dihedral : 5.821 104.886 1274 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.85 % Allowed : 20.75 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.28 (0.26), residues: 1129 helix: 2.35 (0.26), residues: 416 sheet: 0.37 (0.31), residues: 270 loop : -0.23 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 139 TYR 0.011 0.001 TYR R 177 PHE 0.021 0.001 PHE A 189 TRP 0.009 0.001 TRP B 216 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9195) covalent geometry : angle 0.53679 (12435) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.38840 ( 2) hydrogen bonds : bond 0.03265 ( 453) hydrogen bonds : angle 4.17759 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.322 Fit side-chains REVERT: A 247 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7569 (ttt180) REVERT: B 143 GLU cc_start: 0.8270 (tt0) cc_final: 0.7979 (tt0) REVERT: E 82 MET cc_start: 0.8768 (mtm) cc_final: 0.8555 (mtt) REVERT: E 160 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7264 (mtm110) REVERT: E 219 LEU cc_start: 0.8627 (tt) cc_final: 0.8367 (tm) REVERT: G 45 LYS cc_start: 0.8821 (mptt) cc_final: 0.8260 (pttt) REVERT: G 57 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7247 (mp0) REVERT: R 53 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7134 (tptp) REVERT: R 100 ARG cc_start: 0.6215 (tmm-80) cc_final: 0.5869 (ttt90) outliers start: 28 outliers final: 19 residues processed: 152 average time/residue: 0.6760 time to fit residues: 108.9984 Evaluate side-chains 150 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 0.0060 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 115 ASN B 225 GLN B 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126274 restraints weight = 10311.858| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.11 r_work: 0.3422 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9196 Z= 0.111 Angle : 0.538 8.631 12437 Z= 0.280 Chirality : 0.041 0.157 1411 Planarity : 0.004 0.047 1572 Dihedral : 5.780 100.320 1274 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.83 % Allowed : 22.28 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.35 (0.26), residues: 1129 helix: 2.41 (0.26), residues: 416 sheet: 0.42 (0.31), residues: 270 loop : -0.21 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 17 TYR 0.015 0.001 TYR R 177 PHE 0.020 0.001 PHE A 189 TRP 0.009 0.001 TRP A 211 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9195) covalent geometry : angle 0.53831 (12435) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.35085 ( 2) hydrogen bonds : bond 0.03285 ( 453) hydrogen bonds : angle 4.15342 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.353 Fit side-chains REVERT: A 188 LYS cc_start: 0.8416 (mmtm) cc_final: 0.8157 (mmmt) REVERT: A 247 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7588 (ttt180) REVERT: B 22 GLN cc_start: 0.7533 (tt0) cc_final: 0.7316 (tm-30) REVERT: B 143 GLU cc_start: 0.8262 (tt0) cc_final: 0.8037 (tt0) REVERT: B 219 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7536 (mtp85) REVERT: E 160 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7316 (mtm110) REVERT: E 219 LEU cc_start: 0.8599 (tt) cc_final: 0.8357 (tm) REVERT: G 45 LYS cc_start: 0.8840 (mptt) cc_final: 0.8319 (pttt) REVERT: G 57 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7303 (mp0) REVERT: R 53 LYS cc_start: 0.7725 (ttpt) cc_final: 0.7227 (tptp) REVERT: R 100 ARG cc_start: 0.6148 (tmm-80) cc_final: 0.5839 (ttt90) outliers start: 18 outliers final: 18 residues processed: 146 average time/residue: 0.6763 time to fit residues: 104.8858 Evaluate side-chains 150 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123584 restraints weight = 10240.477| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.14 r_work: 0.3391 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9196 Z= 0.125 Angle : 0.561 11.614 12437 Z= 0.289 Chirality : 0.042 0.162 1411 Planarity : 0.004 0.061 1572 Dihedral : 5.826 99.004 1274 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.14 % Allowed : 22.38 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.36 (0.26), residues: 1129 helix: 2.38 (0.26), residues: 414 sheet: 0.51 (0.31), residues: 268 loop : -0.22 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 139 TYR 0.019 0.001 TYR R 177 PHE 0.021 0.001 PHE A 189 TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9195) covalent geometry : angle 0.56136 (12435) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.48799 ( 2) hydrogen bonds : bond 0.03452 ( 453) hydrogen bonds : angle 4.20287 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4082.64 seconds wall clock time: 70 minutes 16.43 seconds (4216.43 seconds total)