Starting phenix.real_space_refine on Fri Aug 22 21:29:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smv_40603/08_2025/8smv_40603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smv_40603/08_2025/8smv_40603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8smv_40603/08_2025/8smv_40603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smv_40603/08_2025/8smv_40603.map" model { file = "/net/cci-nas-00/data/ceres_data/8smv_40603/08_2025/8smv_40603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smv_40603/08_2025/8smv_40603.cif" } resolution = 2.74 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= -0.008 sd= 0.817 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 55 5.16 5 C 5217 2.51 5 N 1404 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 8169 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2152 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1989 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2592 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.95, per 1000 atoms: 0.24 Number of scatterers: 8169 At special positions: 0 Unit cell: (76.54, 104.06, 131.58, 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 55 16.00 O 1493 8.00 N 1404 7.00 C 5217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 178 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 0.50 Conformation dependent library (CDL) restraints added in 284.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 42.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 30 through 55 removed outlier: 3.788A pdb=" N ILE R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 59 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.081A pdb=" N VAL R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 91 Processing helix chain 'R' and resid 96 through 131 removed outlier: 3.654A pdb=" N CYS R 100 " --> pdb=" O GLY R 96 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN R 101 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE R 102 " --> pdb=" O VAL R 98 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY R 119 " --> pdb=" O MET R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 140 through 164 removed outlier: 3.654A pdb=" N TRP R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 182 through 185 Processing helix chain 'R' and resid 187 through 197 removed outlier: 3.666A pdb=" N GLN R 193 " --> pdb=" O THR R 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA R 197 " --> pdb=" O GLN R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 220 removed outlier: 3.669A pdb=" N ARG R 213 " --> pdb=" O GLY R 209 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL R 214 " --> pdb=" O PHE R 210 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG R 220 " --> pdb=" O ARG R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 297 removed outlier: 3.940A pdb=" N PHE R 279 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 298 through 301 removed outlier: 3.843A pdb=" N VAL R 301 " --> pdb=" O LYS R 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 298 through 301' Processing helix chain 'R' and resid 302 through 315 removed outlier: 3.635A pdb=" N SER R 313 " --> pdb=" O ALA R 309 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 315 " --> pdb=" O TRP R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 325 removed outlier: 3.652A pdb=" N CYS R 319 " --> pdb=" O ALA R 315 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 340 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.764A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.682A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.804A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.970A pdb=" N ASN A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.698A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.540A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.716A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.596A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.711A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.606A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.986A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing sheet with id=AA1, first strand: chain 'R' and resid 169 through 172 removed outlier: 3.983A pdb=" N MET R 177 " --> pdb=" O ASP R 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.548A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.344A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.526A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.737A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.991A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.573A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.799A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.954A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.678A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.168A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1113 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: 1.26 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2634 1.34 - 1.46: 2053 1.46 - 1.58: 3586 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8351 Sorted by residual: bond pdb=" C6 CLR R 601 " pdb=" C7 CLR R 601 " ideal model delta sigma weight residual 1.492 1.399 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C10 CLR R 601 " pdb=" C5 CLR R 601 " ideal model delta sigma weight residual 1.519 1.428 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C4 CLR R 601 " pdb=" C5 CLR R 601 " ideal model delta sigma weight residual 1.506 1.416 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C5 CLR R 601 " pdb=" C6 CLR R 601 " ideal model delta sigma weight residual 1.332 1.412 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" N THR A 9 " pdb=" CA THR A 9 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.22e+00 ... (remaining 8346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 10637 1.19 - 2.37: 555 2.37 - 3.56: 96 3.56 - 4.75: 35 4.75 - 5.93: 8 Bond angle restraints: 11331 Sorted by residual: angle pdb=" N THR B 181 " pdb=" CA THR B 181 " pdb=" C THR B 181 " ideal model delta sigma weight residual 110.44 113.70 -3.26 1.20e+00 6.94e-01 7.39e+00 angle pdb=" CA LYS A 338 " pdb=" CB LYS A 338 " pdb=" CG LYS A 338 " ideal model delta sigma weight residual 114.10 118.98 -4.88 2.00e+00 2.50e-01 5.95e+00 angle pdb=" C ASN B 313 " pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 121.56 125.17 -3.61 1.56e+00 4.11e-01 5.36e+00 angle pdb=" N MET R 137 " pdb=" CA MET R 137 " pdb=" C MET R 137 " ideal model delta sigma weight residual 113.88 111.12 2.76 1.23e+00 6.61e-01 5.04e+00 angle pdb=" CA THR B 181 " pdb=" C THR B 181 " pdb=" O THR B 181 " ideal model delta sigma weight residual 121.89 119.03 2.86 1.29e+00 6.01e-01 4.90e+00 ... (remaining 11326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4638 17.73 - 35.47: 284 35.47 - 53.20: 44 53.20 - 70.93: 13 70.93 - 88.67: 9 Dihedral angle restraints: 4988 sinusoidal: 1985 harmonic: 3003 Sorted by residual: dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -149.30 -30.70 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1121 0.064 - 0.128: 139 0.128 - 0.192: 15 0.192 - 0.256: 2 0.256 - 0.320: 1 Chirality restraints: 1278 Sorted by residual: chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C10 CLR R 601 " pdb=" C1 CLR R 601 " pdb=" C5 CLR R 601 " pdb=" C9 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.61 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C20 CLR R 601 " pdb=" C17 CLR R 601 " pdb=" C21 CLR R 601 " pdb=" C22 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.59 2.80 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1275 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 13 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C ARG G 13 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG G 13 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS G 14 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO B 236 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 311 " -0.014 2.00e-02 2.50e+03 1.17e-02 3.41e+00 pdb=" CG TRP R 311 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP R 311 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP R 311 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 311 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 311 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 311 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 311 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 311 " -0.002 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 206 2.71 - 3.26: 7905 3.26 - 3.80: 11827 3.80 - 4.35: 15594 4.35 - 4.90: 27219 Nonbonded interactions: 62751 Sorted by model distance: nonbonded pdb=" O ASN B 313 " pdb=" OG SER B 331 " model vdw 2.162 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASN B 16 " pdb=" NH2 ARG B 19 " model vdw 2.199 3.120 nonbonded pdb=" OD1 ASN B 110 " pdb=" NZ LYS B 127 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLU R 170 " pdb=" NH2 ARG R 184 " model vdw 2.252 3.120 ... (remaining 62746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.004 0.093 8354 Z= 0.185 Angle : 0.648 5.932 11337 Z= 0.359 Chirality : 0.045 0.320 1278 Planarity : 0.004 0.046 1426 Dihedral : 12.716 88.667 3039 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.53 (0.27), residues: 1020 helix: 1.64 (0.28), residues: 374 sheet: 0.68 (0.35), residues: 214 loop : -0.99 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 214 TYR 0.009 0.001 TYR R 324 PHE 0.009 0.001 PHE B 151 TRP 0.031 0.001 TRP R 311 HIS 0.006 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8351) covalent geometry : angle 0.64782 (11331) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.15019 ( 6) hydrogen bonds : bond 0.21192 ( 392) hydrogen bonds : angle 6.67055 ( 1113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.323 Fit side-chains REVERT: A 214 VAL cc_start: 0.8988 (p) cc_final: 0.8734 (t) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.6218 time to fit residues: 101.1987 Evaluate side-chains 115 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 3 GLN N 120 GLN A 220 HIS B 75 GLN B 175 GLN B 176 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121623 restraints weight = 10799.868| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.80 r_work: 0.3344 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8354 Z= 0.117 Angle : 0.550 5.908 11337 Z= 0.299 Chirality : 0.044 0.166 1278 Planarity : 0.004 0.046 1426 Dihedral : 4.682 28.190 1189 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.05 % Allowed : 9.57 % Favored : 88.38 % 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: 0.73 (0.26), residues: 1020 helix: 1.65 (0.27), residues: 398 sheet: 0.87 (0.35), residues: 215 loop : -0.91 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.011 0.001 TYR R 135 PHE 0.013 0.001 PHE A 212 TRP 0.021 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8351) covalent geometry : angle 0.54916 (11331) SS BOND : bond 0.00355 ( 3) SS BOND : angle 1.43060 ( 6) hydrogen bonds : bond 0.04921 ( 392) hydrogen bonds : angle 4.76128 ( 1113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.249 Fit side-chains REVERT: G 47 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 17 LYS cc_start: 0.7854 (mptt) cc_final: 0.7468 (pttt) REVERT: A 19 GLN cc_start: 0.7632 (tt0) cc_final: 0.7322 (pt0) REVERT: B 76 ASP cc_start: 0.8295 (p0) cc_final: 0.8034 (p0) REVERT: B 134 ARG cc_start: 0.7440 (mtm180) cc_final: 0.7113 (mtm-85) REVERT: B 186 ASP cc_start: 0.8181 (m-30) cc_final: 0.7916 (m-30) outliers start: 18 outliers final: 3 residues processed: 146 average time/residue: 0.5986 time to fit residues: 91.8924 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 35 ASN N 120 GLN A 220 HIS B 175 GLN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118908 restraints weight = 10655.019| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.79 r_work: 0.3287 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8354 Z= 0.145 Angle : 0.590 6.880 11337 Z= 0.318 Chirality : 0.046 0.155 1278 Planarity : 0.004 0.046 1426 Dihedral : 4.806 30.016 1189 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.96 % Allowed : 11.16 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.69 (0.26), residues: 1020 helix: 1.66 (0.27), residues: 397 sheet: 0.94 (0.34), residues: 215 loop : -1.04 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.014 0.001 TYR R 135 PHE 0.012 0.001 PHE A 212 TRP 0.021 0.002 TRP R 311 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8351) covalent geometry : angle 0.58917 (11331) SS BOND : bond 0.00445 ( 3) SS BOND : angle 1.45536 ( 6) hydrogen bonds : bond 0.05554 ( 392) hydrogen bonds : angle 4.64029 ( 1113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.324 Fit side-chains REVERT: R 185 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: G 47 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: N 19 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7788 (ptm160) REVERT: A 19 GLN cc_start: 0.7683 (tt0) cc_final: 0.7368 (pt0) REVERT: B 23 LYS cc_start: 0.7983 (tptt) cc_final: 0.7361 (tppt) REVERT: B 134 ARG cc_start: 0.7495 (mtm180) cc_final: 0.7172 (mtm-85) REVERT: B 292 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7599 (p90) outliers start: 26 outliers final: 8 residues processed: 132 average time/residue: 0.6932 time to fit residues: 96.2684 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 35 ASN N 120 GLN A 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112635 restraints weight = 10977.607| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.82 r_work: 0.3175 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8354 Z= 0.250 Angle : 0.734 8.953 11337 Z= 0.392 Chirality : 0.051 0.205 1278 Planarity : 0.005 0.049 1426 Dihedral : 5.412 33.541 1189 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.53 % Allowed : 12.19 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.33 (0.26), residues: 1020 helix: 1.25 (0.26), residues: 398 sheet: 0.95 (0.36), residues: 203 loop : -1.18 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 219 TYR 0.020 0.002 TYR R 150 PHE 0.016 0.002 PHE A 363 TRP 0.030 0.003 TRP R 311 HIS 0.007 0.002 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 8351) covalent geometry : angle 0.73291 (11331) SS BOND : bond 0.00706 ( 3) SS BOND : angle 1.76735 ( 6) hydrogen bonds : bond 0.07381 ( 392) hydrogen bonds : angle 4.88732 ( 1113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.300 Fit side-chains REVERT: R 39 ILE cc_start: 0.9020 (mm) cc_final: 0.8697 (mp) REVERT: R 195 TRP cc_start: 0.8570 (OUTLIER) cc_final: 0.6897 (t60) REVERT: N 19 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8042 (ptm160) REVERT: N 43 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7830 (mtmt) REVERT: A 19 GLN cc_start: 0.7753 (tt0) cc_final: 0.7442 (pt0) REVERT: B 23 LYS cc_start: 0.8152 (tptt) cc_final: 0.7546 (tppt) REVERT: B 127 LYS cc_start: 0.8569 (mttp) cc_final: 0.8367 (mttm) REVERT: B 188 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7511 (mtm) REVERT: B 217 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7705 (ppp) REVERT: B 270 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8361 (mp) REVERT: B 292 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7520 (p90) outliers start: 31 outliers final: 11 residues processed: 131 average time/residue: 0.6885 time to fit residues: 94.7062 Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 75 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119457 restraints weight = 10856.133| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.79 r_work: 0.3275 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8354 Z= 0.115 Angle : 0.537 6.262 11337 Z= 0.293 Chirality : 0.043 0.161 1278 Planarity : 0.004 0.049 1426 Dihedral : 4.577 29.797 1189 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.30 % Allowed : 14.12 % Favored : 82.57 % 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: 0.55 (0.26), residues: 1020 helix: 1.56 (0.26), residues: 399 sheet: 0.98 (0.34), residues: 215 loop : -1.23 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 91 TYR 0.009 0.001 TYR R 135 PHE 0.012 0.001 PHE A 212 TRP 0.024 0.001 TRP N 47 HIS 0.004 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8351) covalent geometry : angle 0.53602 (11331) SS BOND : bond 0.00346 ( 3) SS BOND : angle 1.32943 ( 6) hydrogen bonds : bond 0.04690 ( 392) hydrogen bonds : angle 4.47898 ( 1113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.313 Fit side-chains REVERT: N 5 GLN cc_start: 0.8310 (tt0) cc_final: 0.8099 (tp40) REVERT: N 19 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7732 (ptm160) REVERT: A 17 LYS cc_start: 0.7861 (mptt) cc_final: 0.7461 (pttt) REVERT: A 19 GLN cc_start: 0.7712 (tt0) cc_final: 0.7405 (pt0) REVERT: B 23 LYS cc_start: 0.8040 (tptt) cc_final: 0.7422 (tppt) REVERT: B 188 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7336 (mtm) REVERT: B 217 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7604 (ppp) REVERT: B 292 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7324 (p90) outliers start: 29 outliers final: 10 residues processed: 135 average time/residue: 0.6288 time to fit residues: 89.4648 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118667 restraints weight = 10823.394| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.83 r_work: 0.3286 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8354 Z= 0.120 Angle : 0.547 6.970 11337 Z= 0.297 Chirality : 0.044 0.169 1278 Planarity : 0.004 0.049 1426 Dihedral : 4.497 29.337 1189 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.08 % Allowed : 14.81 % Favored : 82.12 % 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: 0.65 (0.26), residues: 1020 helix: 1.64 (0.27), residues: 399 sheet: 1.08 (0.34), residues: 215 loop : -1.20 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 91 TYR 0.011 0.001 TYR R 135 PHE 0.012 0.001 PHE A 212 TRP 0.023 0.001 TRP N 47 HIS 0.004 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8351) covalent geometry : angle 0.54634 (11331) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.29825 ( 6) hydrogen bonds : bond 0.04828 ( 392) hydrogen bonds : angle 4.40573 ( 1113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.348 Fit side-chains REVERT: R 61 LEU cc_start: 0.9154 (tt) cc_final: 0.8892 (tt) REVERT: N 19 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7744 (ptm160) REVERT: A 17 LYS cc_start: 0.7893 (mptt) cc_final: 0.7493 (pttt) REVERT: A 19 GLN cc_start: 0.7744 (tt0) cc_final: 0.7453 (pt0) REVERT: B 17 GLN cc_start: 0.6755 (tm-30) cc_final: 0.6551 (tm-30) REVERT: B 23 LYS cc_start: 0.8075 (tptt) cc_final: 0.7867 (tptt) REVERT: B 188 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7331 (mtm) REVERT: B 292 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7370 (p90) outliers start: 27 outliers final: 13 residues processed: 129 average time/residue: 0.6270 time to fit residues: 85.3958 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119598 restraints weight = 11032.381| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.85 r_work: 0.3381 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8354 Z= 0.098 Angle : 0.498 6.416 11337 Z= 0.271 Chirality : 0.042 0.172 1278 Planarity : 0.004 0.048 1426 Dihedral : 4.207 27.457 1189 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.51 % Allowed : 15.83 % Favored : 81.66 % 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: 0.76 (0.26), residues: 1020 helix: 1.70 (0.26), residues: 406 sheet: 1.13 (0.34), residues: 217 loop : -1.15 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 91 TYR 0.007 0.001 TYR R 324 PHE 0.012 0.001 PHE A 212 TRP 0.025 0.001 TRP N 47 HIS 0.003 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8351) covalent geometry : angle 0.49780 (11331) SS BOND : bond 0.00293 ( 3) SS BOND : angle 1.10977 ( 6) hydrogen bonds : bond 0.03985 ( 392) hydrogen bonds : angle 4.23248 ( 1113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.321 Fit side-chains REVERT: R 61 LEU cc_start: 0.9075 (tt) cc_final: 0.8781 (tt) REVERT: R 195 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.6712 (t60) REVERT: G 17 GLU cc_start: 0.7073 (mp0) cc_final: 0.6748 (pm20) REVERT: A 17 LYS cc_start: 0.7901 (mptt) cc_final: 0.7569 (pttt) REVERT: A 19 GLN cc_start: 0.7781 (tt0) cc_final: 0.7502 (pt0) REVERT: A 204 THR cc_start: 0.2394 (OUTLIER) cc_final: 0.2038 (p) REVERT: B 46 ARG cc_start: 0.8619 (mtm180) cc_final: 0.7828 (ptp90) REVERT: B 188 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7282 (mtm) REVERT: B 292 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7223 (p90) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.6246 time to fit residues: 87.4764 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116954 restraints weight = 11046.860| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.05 r_work: 0.3414 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8354 Z= 0.132 Angle : 0.564 7.225 11337 Z= 0.304 Chirality : 0.045 0.159 1278 Planarity : 0.004 0.047 1426 Dihedral : 4.462 29.276 1189 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.73 % Allowed : 15.60 % Favored : 81.66 % 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: 0.74 (0.26), residues: 1020 helix: 1.65 (0.26), residues: 405 sheet: 1.18 (0.34), residues: 216 loop : -1.16 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 91 TYR 0.013 0.001 TYR R 135 PHE 0.012 0.001 PHE A 212 TRP 0.022 0.001 TRP N 47 HIS 0.005 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8351) covalent geometry : angle 0.56350 (11331) SS BOND : bond 0.00440 ( 3) SS BOND : angle 1.28886 ( 6) hydrogen bonds : bond 0.05051 ( 392) hydrogen bonds : angle 4.33486 ( 1113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.222 Fit side-chains REVERT: R 61 LEU cc_start: 0.9161 (tt) cc_final: 0.8871 (tt) REVERT: R 185 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: R 195 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.6539 (t60) REVERT: G 17 GLU cc_start: 0.6850 (mp0) cc_final: 0.6584 (pm20) REVERT: N 43 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7652 (mtmt) REVERT: A 17 LYS cc_start: 0.7897 (mptt) cc_final: 0.7492 (pttt) REVERT: A 19 GLN cc_start: 0.7783 (tt0) cc_final: 0.7484 (pt0) REVERT: A 204 THR cc_start: 0.2722 (OUTLIER) cc_final: 0.2412 (p) REVERT: B 17 GLN cc_start: 0.6540 (tm-30) cc_final: 0.6289 (tm-30) REVERT: B 23 LYS cc_start: 0.7773 (tptt) cc_final: 0.7315 (tppt) REVERT: B 46 ARG cc_start: 0.8663 (mtm180) cc_final: 0.7763 (ptp90) REVERT: B 188 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7351 (mtm) REVERT: B 292 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7348 (p90) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.5778 time to fit residues: 82.2346 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 43 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 70 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 123 GLN A 220 HIS B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.149949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124859 restraints weight = 11007.087| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.90 r_work: 0.3498 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8354 Z= 0.093 Angle : 0.487 8.223 11337 Z= 0.264 Chirality : 0.042 0.152 1278 Planarity : 0.004 0.047 1426 Dihedral : 4.032 26.038 1189 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.39 % Allowed : 16.17 % Favored : 81.44 % 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: 0.84 (0.26), residues: 1020 helix: 1.77 (0.26), residues: 406 sheet: 1.08 (0.34), residues: 220 loop : -1.08 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 91 TYR 0.007 0.001 TYR R 324 PHE 0.012 0.001 PHE A 212 TRP 0.023 0.001 TRP N 47 HIS 0.003 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 8351) covalent geometry : angle 0.48657 (11331) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.99794 ( 6) hydrogen bonds : bond 0.03586 ( 392) hydrogen bonds : angle 4.12500 ( 1113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.336 Fit side-chains REVERT: R 61 LEU cc_start: 0.9083 (tt) cc_final: 0.8767 (tt) REVERT: R 195 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.6797 (t60) REVERT: N 19 ARG cc_start: 0.8072 (ptm-80) cc_final: 0.7783 (ttm-80) REVERT: A 17 LYS cc_start: 0.7905 (mptt) cc_final: 0.7578 (pttt) REVERT: A 19 GLN cc_start: 0.7803 (tt0) cc_final: 0.7523 (pt0) REVERT: A 204 THR cc_start: 0.2728 (OUTLIER) cc_final: 0.2401 (p) REVERT: B 17 GLN cc_start: 0.6717 (tm-30) cc_final: 0.6492 (tm-30) REVERT: B 23 LYS cc_start: 0.7905 (tptt) cc_final: 0.7312 (tppt) REVERT: B 46 ARG cc_start: 0.8681 (mtm180) cc_final: 0.7810 (ptp90) REVERT: B 134 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7346 (mtm-85) REVERT: B 186 ASP cc_start: 0.8316 (m-30) cc_final: 0.8067 (m-30) REVERT: B 188 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7188 (mtm) REVERT: B 217 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7426 (ppp) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 0.6673 time to fit residues: 92.8747 Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET 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 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS B 156 GLN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120256 restraints weight = 10930.596| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.03 r_work: 0.3461 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8354 Z= 0.111 Angle : 0.531 8.649 11337 Z= 0.286 Chirality : 0.043 0.177 1278 Planarity : 0.004 0.047 1426 Dihedral : 4.192 27.796 1189 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.71 % Allowed : 16.97 % Favored : 81.32 % 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: 0.80 (0.26), residues: 1020 helix: 1.71 (0.26), residues: 406 sheet: 1.12 (0.34), residues: 220 loop : -1.11 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 91 TYR 0.010 0.001 TYR R 135 PHE 0.012 0.001 PHE A 212 TRP 0.018 0.001 TRP N 47 HIS 0.004 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8351) covalent geometry : angle 0.53018 (11331) SS BOND : bond 0.00354 ( 3) SS BOND : angle 1.15249 ( 6) hydrogen bonds : bond 0.04318 ( 392) hydrogen bonds : angle 4.24350 ( 1113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.326 Fit side-chains REVERT: R 61 LEU cc_start: 0.9118 (tt) cc_final: 0.8816 (tt) REVERT: R 195 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.6504 (t60) REVERT: N 19 ARG cc_start: 0.8128 (ptm-80) cc_final: 0.7852 (ttm-80) REVERT: A 17 LYS cc_start: 0.7827 (mptt) cc_final: 0.7454 (pttt) REVERT: A 19 GLN cc_start: 0.7732 (tt0) cc_final: 0.7463 (pt0) REVERT: A 204 THR cc_start: 0.2599 (OUTLIER) cc_final: 0.2278 (p) REVERT: B 17 GLN cc_start: 0.6492 (tm-30) cc_final: 0.6283 (tm-30) REVERT: B 23 LYS cc_start: 0.7812 (tptt) cc_final: 0.7224 (tppt) REVERT: B 46 ARG cc_start: 0.8673 (mtm180) cc_final: 0.7750 (ptp90) REVERT: B 186 ASP cc_start: 0.8352 (m-30) cc_final: 0.8100 (m-30) REVERT: B 188 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7326 (mtm) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.6915 time to fit residues: 90.4437 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114378 restraints weight = 10774.147| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.82 r_work: 0.3318 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8354 Z= 0.098 Angle : 0.501 8.576 11337 Z= 0.271 Chirality : 0.042 0.194 1278 Planarity : 0.004 0.048 1426 Dihedral : 4.080 26.821 1189 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.05 % Allowed : 17.08 % Favored : 80.87 % 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: 0.87 (0.26), residues: 1020 helix: 1.70 (0.26), residues: 411 sheet: 1.15 (0.33), residues: 225 loop : -1.04 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 91 TYR 0.007 0.001 TYR R 324 PHE 0.011 0.001 PHE A 212 TRP 0.021 0.001 TRP N 47 HIS 0.003 0.001 HIS R 154 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8351) covalent geometry : angle 0.50105 (11331) SS BOND : bond 0.00293 ( 3) SS BOND : angle 1.04353 ( 6) hydrogen bonds : bond 0.03842 ( 392) hydrogen bonds : angle 4.17980 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3099.10 seconds wall clock time: 53 minutes 25.42 seconds (3205.42 seconds total)