Starting phenix.real_space_refine on Wed Mar 12 16:00:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smv_40603/03_2025/8smv_40603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smv_40603/03_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_40603/03_2025/8smv_40603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smv_40603/03_2025/8smv_40603.map" model { file = "/net/cci-nas-00/data/ceres_data/8smv_40603/03_2025/8smv_40603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smv_40603/03_2025/8smv_40603.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 2, 'ARG: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: 5.04, per 1000 atoms: 0.62 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: 1.95 Conformation dependent library (CDL) restraints added in 909.8 milliseconds 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: 0.83 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: 2.45 Time building geometry restraints manager: 2.33 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: 5.450 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.420 ------------------------------------------------------------------------------- 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 8351 Z= 0.232 Angle : 0.648 5.932 11331 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.031 0.001 TRP R 311 HIS 0.006 0.001 HIS R 154 PHE 0.009 0.001 PHE B 151 TYR 0.009 0.001 TYR R 324 ARG 0.004 0.001 ARG B 214 *********************** 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 : 0.896 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: 1.5474 time to fit residues: 252.6345 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 : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.147216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122056 restraints weight = 10780.602| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.80 r_work: 0.3330 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8351 Z= 0.154 Angle : 0.544 5.938 11331 Z= 0.296 Chirality : 0.044 0.163 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.667 28.056 1189 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.28 % Allowed : 9.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1020 helix: 1.64 (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 TRP 0.022 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR R 135 ARG 0.005 0.000 ARG A 347 *********************** 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 159 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.871 Fit side-chains REVERT: G 47 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: A 17 LYS cc_start: 0.7824 (mptt) cc_final: 0.7551 (ttpt) REVERT: A 19 GLN cc_start: 0.7612 (tt0) cc_final: 0.7302 (pt0) REVERT: B 76 ASP cc_start: 0.8312 (p0) cc_final: 0.8095 (p0) REVERT: B 134 ARG cc_start: 0.7447 (mtm180) cc_final: 0.7104 (mtm-85) REVERT: B 188 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7182 (mtm) outliers start: 20 outliers final: 2 residues processed: 147 average time/residue: 1.3689 time to fit residues: 212.1633 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 : 0.864 ------------------------------------------------------------------------------- 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 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 0.0010 overall best weight: 0.5344 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.148502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123456 restraints weight = 10908.528| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.80 r_work: 0.3464 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8351 Z= 0.129 Angle : 0.491 5.985 11331 Z= 0.267 Chirality : 0.042 0.150 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.269 26.431 1189 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.51 % Allowed : 11.28 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1020 helix: 1.86 (0.27), residues: 400 sheet: 0.93 (0.34), residues: 215 loop : -0.98 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 311 HIS 0.003 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR R 135 ARG 0.004 0.000 ARG A 347 *********************** 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 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.877 Fit side-chains REVERT: R 185 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: N 19 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7436 (ptm160) REVERT: A 17 LYS cc_start: 0.7714 (mptt) cc_final: 0.7500 (ttpt) REVERT: A 19 GLN cc_start: 0.7663 (tt0) cc_final: 0.7365 (pt0) REVERT: A 28 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7909 (ptpt) REVERT: B 23 LYS cc_start: 0.7927 (tptt) cc_final: 0.7314 (tppt) REVERT: B 46 ARG cc_start: 0.8639 (mtm180) cc_final: 0.7648 (ptp90) REVERT: B 134 ARG cc_start: 0.7461 (mtm180) cc_final: 0.7158 (mtm-85) REVERT: B 270 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8201 (mp) outliers start: 22 outliers final: 7 residues processed: 138 average time/residue: 1.5976 time to fit residues: 232.3158 Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 91 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.0060 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.3214 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.154359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129816 restraints weight = 10808.641| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.79 r_work: 0.3511 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8351 Z= 0.113 Angle : 0.458 5.915 11331 Z= 0.250 Chirality : 0.041 0.152 1278 Planarity : 0.003 0.044 1426 Dihedral : 3.961 25.813 1189 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.05 % Allowed : 13.44 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1020 helix: 2.06 (0.27), residues: 400 sheet: 0.90 (0.33), residues: 220 loop : -0.95 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 47 HIS 0.003 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.006 0.001 TYR R 324 ARG 0.005 0.000 ARG R 91 *********************** 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 146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.104 Fit side-chains REVERT: A 19 GLN cc_start: 0.7693 (tt0) cc_final: 0.7388 (pt0) REVERT: B 23 LYS cc_start: 0.8014 (tptt) cc_final: 0.7404 (tppt) REVERT: B 46 ARG cc_start: 0.8540 (mtm180) cc_final: 0.7697 (ptp90) REVERT: B 134 ARG cc_start: 0.7430 (mtm180) cc_final: 0.7186 (mtm-85) REVERT: B 270 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8127 (mp) outliers start: 18 outliers final: 4 residues processed: 137 average time/residue: 1.4267 time to fit residues: 205.7391 Evaluate side-chains 117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 0.0270 chunk 56 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.151682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126696 restraints weight = 10842.709| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.83 r_work: 0.3444 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8351 Z= 0.117 Angle : 0.458 5.939 11331 Z= 0.250 Chirality : 0.041 0.157 1278 Planarity : 0.003 0.044 1426 Dihedral : 3.878 24.502 1189 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.51 % Allowed : 14.46 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1020 helix: 2.11 (0.26), residues: 406 sheet: 1.12 (0.33), residues: 215 loop : -0.94 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 311 HIS 0.003 0.001 HIS R 154 PHE 0.016 0.001 PHE R 279 TYR 0.007 0.001 TYR R 135 ARG 0.006 0.000 ARG R 91 *********************** 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 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.878 Fit side-chains REVERT: R 287 MET cc_start: 0.9005 (mmp) cc_final: 0.8605 (mmt) REVERT: A 19 GLN cc_start: 0.7708 (tt0) cc_final: 0.7429 (pt0) REVERT: B 17 GLN cc_start: 0.6680 (tm-30) cc_final: 0.6474 (tm-30) REVERT: B 23 LYS cc_start: 0.7993 (tptt) cc_final: 0.7380 (tppt) REVERT: B 46 ARG cc_start: 0.8556 (mtm180) cc_final: 0.7693 (ptp90) REVERT: B 134 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7186 (mtm-85) REVERT: B 261 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8045 (pp) REVERT: B 270 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8129 (mp) outliers start: 22 outliers final: 10 residues processed: 134 average time/residue: 1.3584 time to fit residues: 191.9033 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS 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 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 72 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.146139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120741 restraints weight = 10866.866| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.81 r_work: 0.3364 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8351 Z= 0.158 Angle : 0.510 5.947 11331 Z= 0.276 Chirality : 0.043 0.162 1278 Planarity : 0.004 0.044 1426 Dihedral : 4.151 27.386 1189 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.96 % Allowed : 14.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1020 helix: 2.05 (0.26), residues: 405 sheet: 1.09 (0.33), residues: 218 loop : -0.99 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 311 HIS 0.003 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR R 135 ARG 0.005 0.000 ARG R 91 *********************** 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: 26 poor density : 117 time to evaluate : 0.925 Fit side-chains REVERT: R 287 MET cc_start: 0.9011 (mmp) cc_final: 0.8597 (mmt) REVERT: G 17 GLU cc_start: 0.7006 (mp0) cc_final: 0.6684 (pm20) REVERT: N 19 ARG cc_start: 0.7981 (ptm-80) cc_final: 0.7700 (ttm-80) REVERT: A 19 GLN cc_start: 0.7743 (tt0) cc_final: 0.7462 (pt0) REVERT: B 14 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7109 (mm) REVERT: B 23 LYS cc_start: 0.8059 (tptt) cc_final: 0.7830 (tptt) REVERT: B 46 ARG cc_start: 0.8571 (mtm180) cc_final: 0.7746 (ptp90) REVERT: B 134 ARG cc_start: 0.7498 (mtm180) cc_final: 0.7234 (mtm-85) REVERT: B 270 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8205 (mp) outliers start: 26 outliers final: 13 residues processed: 132 average time/residue: 1.3101 time to fit residues: 182.8312 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 14 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 270 ILE 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 84 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 76 optimal weight: 0.0270 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.146751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120918 restraints weight = 10948.247| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.97 r_work: 0.3444 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8351 Z= 0.190 Angle : 0.543 6.155 11331 Z= 0.294 Chirality : 0.044 0.150 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.339 28.818 1189 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.96 % Allowed : 15.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1020 helix: 1.99 (0.26), residues: 405 sheet: 1.11 (0.33), residues: 218 loop : -1.06 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.026 0.001 TYR R 150 ARG 0.006 0.000 ARG R 91 *********************** 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 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.865 Fit side-chains REVERT: R 185 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: G 36 ASP cc_start: 0.8335 (m-30) cc_final: 0.8069 (m-30) REVERT: N 19 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7741 (ttm-80) REVERT: A 19 GLN cc_start: 0.7761 (tt0) cc_final: 0.7481 (pt0) REVERT: B 17 GLN cc_start: 0.6674 (tm-30) cc_final: 0.6467 (tm-30) REVERT: B 23 LYS cc_start: 0.8165 (tptt) cc_final: 0.7593 (tppt) REVERT: B 46 ARG cc_start: 0.8668 (mtm180) cc_final: 0.7840 (ptp90) REVERT: B 188 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7321 (mtm) outliers start: 26 outliers final: 11 residues processed: 133 average time/residue: 1.3338 time to fit residues: 187.5333 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 : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS 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 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 90 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114250 restraints weight = 10710.116| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.88 r_work: 0.3315 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8351 Z= 0.145 Angle : 0.512 7.218 11331 Z= 0.275 Chirality : 0.043 0.175 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.143 27.277 1189 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.28 % Allowed : 16.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1020 helix: 2.02 (0.26), residues: 405 sheet: 1.14 (0.33), residues: 218 loop : -1.02 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.010 0.001 TYR R 135 ARG 0.006 0.000 ARG R 91 *********************** 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 137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.858 Fit side-chains REVERT: R 61 LEU cc_start: 0.9111 (tt) cc_final: 0.8880 (tt) REVERT: R 185 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: R 195 TRP cc_start: 0.8432 (OUTLIER) cc_final: 0.6498 (t60) REVERT: R 287 MET cc_start: 0.9015 (mmp) cc_final: 0.8575 (mmt) REVERT: N 19 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7716 (ttm-80) REVERT: A 19 GLN cc_start: 0.7837 (tt0) cc_final: 0.7584 (pt0) REVERT: B 46 ARG cc_start: 0.8613 (mtm180) cc_final: 0.7789 (ptp90) REVERT: B 134 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7355 (mtm-85) REVERT: B 188 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7281 (mtm) outliers start: 20 outliers final: 11 residues processed: 126 average time/residue: 1.3419 time to fit residues: 178.5255 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 : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 306 SER 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 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 33 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114545 restraints weight = 11245.985| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.07 r_work: 0.3386 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8351 Z= 0.315 Angle : 0.661 7.874 11331 Z= 0.352 Chirality : 0.048 0.188 1278 Planarity : 0.004 0.044 1426 Dihedral : 4.839 32.111 1189 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.62 % Allowed : 16.51 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1020 helix: 1.74 (0.26), residues: 399 sheet: 1.13 (0.35), residues: 207 loop : -1.11 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP R 311 HIS 0.006 0.002 HIS R 154 PHE 0.016 0.002 PHE A 363 TYR 0.019 0.002 TYR R 135 ARG 0.006 0.001 ARG R 91 *********************** 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 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.891 Fit side-chains REVERT: R 61 LEU cc_start: 0.9239 (tt) cc_final: 0.8970 (tt) REVERT: G 36 ASP cc_start: 0.8368 (m-30) cc_final: 0.8115 (m-30) REVERT: N 43 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7704 (mtmt) REVERT: A 19 GLN cc_start: 0.7729 (tt0) cc_final: 0.7476 (pt0) REVERT: B 17 GLN cc_start: 0.6576 (tm-30) cc_final: 0.6036 (tm-30) REVERT: B 23 LYS cc_start: 0.7701 (tptt) cc_final: 0.7272 (tppt) REVERT: B 46 ARG cc_start: 0.8705 (mtm180) cc_final: 0.7810 (ptp90) outliers start: 23 outliers final: 8 residues processed: 130 average time/residue: 1.4187 time to fit residues: 194.9558 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU 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 33 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114636 restraints weight = 10537.596| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.82 r_work: 0.3287 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8351 Z= 0.155 Angle : 0.526 7.499 11331 Z= 0.285 Chirality : 0.043 0.149 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.310 28.695 1189 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.48 % Allowed : 17.54 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1020 helix: 1.86 (0.26), residues: 406 sheet: 1.14 (0.33), residues: 215 loop : -1.10 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.008 0.001 TYR R 324 ARG 0.006 0.000 ARG R 91 ********************** 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 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.911 Fit side-chains REVERT: R 61 LEU cc_start: 0.9116 (tt) cc_final: 0.8820 (tt) REVERT: R 195 TRP cc_start: 0.8419 (OUTLIER) cc_final: 0.6687 (t60) REVERT: G 36 ASP cc_start: 0.8343 (m-30) cc_final: 0.8140 (m-30) REVERT: N 19 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7734 (ttm-80) REVERT: A 19 GLN cc_start: 0.7792 (tt0) cc_final: 0.7564 (pt0) REVERT: B 17 GLN cc_start: 0.6728 (tm-30) cc_final: 0.6159 (tm-30) REVERT: B 23 LYS cc_start: 0.7901 (tptt) cc_final: 0.7325 (tppt) REVERT: B 46 ARG cc_start: 0.8607 (mtm180) cc_final: 0.7813 (ptp90) outliers start: 13 outliers final: 7 residues processed: 122 average time/residue: 1.3109 time to fit residues: 169.2651 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 195 TRP 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 198 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 76 optimal weight: 0.0070 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114435 restraints weight = 10880.275| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.88 r_work: 0.3319 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8351 Z= 0.139 Angle : 0.507 7.503 11331 Z= 0.275 Chirality : 0.042 0.132 1278 Planarity : 0.004 0.046 1426 Dihedral : 4.069 26.520 1189 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.25 % Allowed : 17.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1020 helix: 1.98 (0.26), residues: 406 sheet: 1.06 (0.33), residues: 225 loop : -0.98 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.013 0.001 PHE A 212 TYR 0.017 0.001 TYR R 57 ARG 0.006 0.000 ARG R 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6594.05 seconds wall clock time: 113 minutes 42.70 seconds (6822.70 seconds total)