Starting phenix.real_space_refine on Wed Aug 5 05:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh5_39281/08_2026/8yh5_39281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh5_39281/08_2026/8yh5_39281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yh5_39281/08_2026/8yh5_39281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh5_39281/08_2026/8yh5_39281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yh5_39281/08_2026/8yh5_39281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh5_39281/08_2026/8yh5_39281.map" } resolution = 3.66 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= 0.002 sd= 1.084 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 66 5.16 5 C 5564 2.51 5 N 1462 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8695 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 2 Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'ZIR%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.20 Number of scatterers: 8695 At special positions: 0 Unit cell: (89.91, 122.1, 124.32, 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 66 16.00 O 1603 8.00 N 1462 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " 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: 0.53 Conformation dependent library (CDL) restraints added in 321.6 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 37.8% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.863A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 33 through 44 removed outlier: 3.506A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.706A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.576A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.501A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.541A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.665A pdb=" N LYS A 279 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.682A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.544A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 40 removed outlier: 3.659A pdb=" N LYS R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 64 removed outlier: 3.637A pdb=" N PHE R 50 " --> pdb=" O THR R 46 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 removed outlier: 3.613A pdb=" N PHE R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR R 94 " --> pdb=" O MET R 90 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 removed outlier: 3.786A pdb=" N GLY R 148 " --> pdb=" O PRO R 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 145 through 148' Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.684A pdb=" N MET R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 removed outlier: 4.020A pdb=" N MET R 176 " --> pdb=" O ARG R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 removed outlier: 3.591A pdb=" N CYS R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) Proline residue: R 244 - end of helix removed outlier: 3.561A pdb=" N TYR R 253 " --> pdb=" O ASN R 249 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE R 254 " --> pdb=" O CYS R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.517A pdb=" N ILE R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.728A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.840A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.974A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.512A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.541A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.303A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.458A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.780A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.123A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 129 through 130 removed outlier: 3.591A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.049A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE S 165 " --> pdb=" O TYR S 216 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.500A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1107 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: 1.24 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2733 1.34 - 1.46: 1661 1.46 - 1.58: 4386 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 8878 Sorted by residual: bond pdb=" N ILE R 248 " pdb=" CA ILE R 248 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.16e+00 bond pdb=" N ARG S 18 " pdb=" CA ARG S 18 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.16e-02 7.43e+03 8.96e+00 bond pdb=" N LYS S 19 " pdb=" CA LYS S 19 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.42e+00 bond pdb=" N GLN B 259 " pdb=" CA GLN B 259 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.39e+00 bond pdb=" N ARG S 98 " pdb=" CA ARG S 98 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.68e+00 ... (remaining 8873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 11314 1.37 - 2.73: 551 2.73 - 4.10: 130 4.10 - 5.47: 23 5.47 - 6.84: 5 Bond angle restraints: 12023 Sorted by residual: angle pdb=" N ASN R 249 " pdb=" CA ASN R 249 " pdb=" C ASN R 249 " ideal model delta sigma weight residual 113.28 107.60 5.68 1.22e+00 6.72e-01 2.17e+01 angle pdb=" CA ILE S 100 " pdb=" C ILE S 100 " pdb=" O ILE S 100 " ideal model delta sigma weight residual 120.36 115.52 4.84 1.06e+00 8.90e-01 2.08e+01 angle pdb=" N ILE R 185 " pdb=" CA ILE R 185 " pdb=" C ILE R 185 " ideal model delta sigma weight residual 112.12 108.39 3.73 8.40e-01 1.42e+00 1.97e+01 angle pdb=" N GLU G 22 " pdb=" CA GLU G 22 " pdb=" C GLU G 22 " ideal model delta sigma weight residual 112.54 107.53 5.01 1.22e+00 6.72e-01 1.69e+01 angle pdb=" CA ARG S 18 " pdb=" C ARG S 18 " pdb=" O ARG S 18 " ideal model delta sigma weight residual 121.89 116.71 5.18 1.27e+00 6.20e-01 1.67e+01 ... (remaining 12018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 5044 25.20 - 50.40: 213 50.40 - 75.60: 17 75.60 - 100.80: 1 100.80 - 126.00: 1 Dihedral angle restraints: 5276 sinusoidal: 2074 harmonic: 3202 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 136.18 -43.18 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CD ARG S 18 " pdb=" NE ARG S 18 " pdb=" CZ ARG S 18 " pdb=" NH1 ARG S 18 " ideal model delta sinusoidal sigma weight residual 0.00 -41.92 41.92 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 5273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1004 0.040 - 0.080: 258 0.080 - 0.121: 82 0.121 - 0.161: 24 0.161 - 0.201: 8 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C3' ZIR R 801 " pdb=" C2' ZIR R 801 " pdb=" C4' ZIR R 801 " pdb=" O3' ZIR R 801 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE R 248 " pdb=" N ILE R 248 " pdb=" C ILE R 248 " pdb=" CB ILE R 248 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA ILE S 100 " pdb=" N ILE S 100 " pdb=" C ILE S 100 " pdb=" CB ILE S 100 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1373 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 18 " 0.713 9.50e-02 1.11e+02 3.20e-01 6.24e+01 pdb=" NE ARG S 18 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG S 18 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG S 18 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG S 18 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 219 " -0.671 9.50e-02 1.11e+02 3.01e-01 5.51e+01 pdb=" NE ARG B 219 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG B 219 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 219 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 219 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 52 " -0.586 9.50e-02 1.11e+02 2.63e-01 4.23e+01 pdb=" NE ARG B 52 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG B 52 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 52 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 52 " -0.017 2.00e-02 2.50e+03 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 191 2.66 - 3.22: 8904 3.22 - 3.78: 13512 3.78 - 4.34: 18835 4.34 - 4.90: 30019 Nonbonded interactions: 71461 Sorted by model distance: nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.102 3.040 nonbonded pdb=" OG SER B 160 " pdb=" O VAL B 187 " model vdw 2.108 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.113 3.040 nonbonded pdb=" OE1 GLN R 260 " pdb=" OH TYR R 264 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.150 3.040 ... (remaining 71456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 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 0.051 8882 Z= 0.263 Angle : 0.719 6.835 12031 Z= 0.454 Chirality : 0.045 0.201 1376 Planarity : 0.017 0.320 1499 Dihedral : 13.334 125.995 3198 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.10 % Allowed : 0.42 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.26), residues: 1085 helix: 0.28 (0.27), residues: 375 sheet: -1.68 (0.30), residues: 290 loop : -1.51 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 172 TYR 0.012 0.001 TYR B 289 PHE 0.021 0.001 PHE A 267 TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.26 ( 8878) covalent geometry : angle 0.71549 / 0.45 (12023) SS BOND : bond 0.00548 / 0.29 ( 4) SS BOND : angle 2.79689 / 1.56 ( 8) hydrogen bonds : bond 0.23728 / 16.10 ( 392) hydrogen bonds : angle 8.63096 / 5.99 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 GLU cc_start: 0.8491 (mp0) cc_final: 0.8262 (mp0) REVERT: B 260 GLU cc_start: 0.5471 (tt0) cc_final: 0.4674 (tm-30) REVERT: G 58 GLU cc_start: 0.8754 (mp0) cc_final: 0.8537 (mp0) REVERT: S 46 GLU cc_start: 0.6451 (tp30) cc_final: 0.6006 (tt0) REVERT: S 93 MET cc_start: 0.6921 (tpt) cc_final: 0.6669 (tpt) REVERT: S 190 ARG cc_start: 0.4456 (mtp-110) cc_final: 0.4223 (mtp180) REVERT: S 219 GLN cc_start: 0.3092 (pp30) cc_final: 0.2330 (pp30) REVERT: A 276 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7803 (mp0) REVERT: A 322 HIS cc_start: 0.6592 (t70) cc_final: 0.6254 (t-90) REVERT: A 333 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8132 (mm-40) REVERT: A 345 LYS cc_start: 0.7926 (mptt) cc_final: 0.7539 (tptp) REVERT: R 173 MET cc_start: 0.8499 (mmt) cc_final: 0.8139 (mmt) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.0831 time to fit residues: 25.9915 Evaluate side-chains 170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN B 230 ASN S 82 GLN S 219 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 306 GLN R 30 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.166549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.137837 restraints weight = 19811.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.141593 restraints weight = 10923.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.144380 restraints weight = 7498.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.146021 restraints weight = 5814.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.146904 restraints weight = 4929.786| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8882 Z= 0.142 Angle : 0.680 11.208 12031 Z= 0.351 Chirality : 0.045 0.196 1376 Planarity : 0.004 0.035 1499 Dihedral : 6.138 114.500 1216 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.52 % Allowed : 11.75 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.26), residues: 1085 helix: 0.61 (0.26), residues: 386 sheet: -1.17 (0.32), residues: 276 loop : -1.40 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 172 TYR 0.023 0.002 TYR S 178 PHE 0.020 0.002 PHE R 288 TRP 0.020 0.002 TRP R 35 HIS 0.004 0.001 HIS S 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8878) covalent geometry : angle 0.67839 / 0.35 (12023) SS BOND : bond 0.00576 / 0.30 ( 4) SS BOND : angle 2.09106 / 1.11 ( 8) hydrogen bonds : bond 0.04258 / 2.97 ( 392) hydrogen bonds : angle 5.60198 / 3.90 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7189 (tmm) cc_final: 0.6984 (tmm) REVERT: G 22 GLU cc_start: 0.2775 (tp30) cc_final: 0.2167 (tp30) REVERT: S 34 MET cc_start: 0.5935 (mmm) cc_final: 0.5670 (mmm) REVERT: S 210 GLU cc_start: 0.6050 (mp0) cc_final: 0.5552 (mp0) REVERT: A 20 ASP cc_start: 0.6515 (t0) cc_final: 0.6300 (m-30) REVERT: A 275 GLU cc_start: 0.8156 (pp20) cc_final: 0.7751 (pm20) REVERT: A 289 GLU cc_start: 0.8654 (tp30) cc_final: 0.7829 (mp0) REVERT: A 313 ARG cc_start: 0.6691 (mtt180) cc_final: 0.6163 (mmt90) REVERT: A 333 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8329 (mm-40) REVERT: A 345 LYS cc_start: 0.7921 (mptt) cc_final: 0.7622 (tptp) REVERT: R 19 GLU cc_start: 0.6475 (tp30) cc_final: 0.6207 (mm-30) outliers start: 24 outliers final: 10 residues processed: 212 average time/residue: 0.0723 time to fit residues: 21.3646 Evaluate side-chains 180 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN S 219 GLN A 213 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS R 273 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.163147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.134646 restraints weight = 19783.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.138269 restraints weight = 11125.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.140841 restraints weight = 7713.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.142561 restraints weight = 6069.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143438 restraints weight = 5164.609| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8882 Z= 0.155 Angle : 0.662 10.191 12031 Z= 0.346 Chirality : 0.044 0.206 1376 Planarity : 0.004 0.046 1499 Dihedral : 6.186 118.957 1216 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.52 % Allowed : 15.53 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.26), residues: 1085 helix: 0.87 (0.26), residues: 377 sheet: -1.25 (0.31), residues: 275 loop : -1.05 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 190 TYR 0.021 0.002 TYR S 178 PHE 0.018 0.002 PHE S 108 TRP 0.015 0.002 TRP B 297 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 8878) covalent geometry : angle 0.65903 / 0.34 (12023) SS BOND : bond 0.00255 / 0.13 ( 4) SS BOND : angle 2.62504 / 1.42 ( 8) hydrogen bonds : bond 0.04163 / 2.88 ( 392) hydrogen bonds : angle 5.26056 / 3.69 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.7810 (m100) cc_final: 0.7336 (m100) REVERT: B 217 MET cc_start: 0.7515 (tmm) cc_final: 0.7155 (tmm) REVERT: B 256 ARG cc_start: 0.7605 (mmp-170) cc_final: 0.7121 (mmp80) REVERT: B 266 HIS cc_start: 0.7144 (t-90) cc_final: 0.6926 (t70) REVERT: G 22 GLU cc_start: 0.2861 (tp30) cc_final: 0.2412 (tp30) REVERT: S 180 MET cc_start: 0.6375 (tpt) cc_final: 0.6106 (tpt) REVERT: S 190 ARG cc_start: 0.5210 (mtp-110) cc_final: 0.4860 (mtp-110) REVERT: A 256 ASN cc_start: 0.7599 (m110) cc_final: 0.7088 (m110) REVERT: A 313 ARG cc_start: 0.6612 (mtt180) cc_final: 0.6237 (mmt90) REVERT: A 333 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8386 (mm-40) REVERT: A 345 LYS cc_start: 0.7807 (mptt) cc_final: 0.7453 (tptp) REVERT: R 140 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7628 (tp) REVERT: R 173 MET cc_start: 0.8027 (mmt) cc_final: 0.7767 (mmt) outliers start: 24 outliers final: 14 residues processed: 196 average time/residue: 0.0787 time to fit residues: 21.7305 Evaluate side-chains 173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN S 219 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 347 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.162876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.133836 restraints weight = 20058.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.137454 restraints weight = 11456.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.140140 restraints weight = 8030.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.141647 restraints weight = 6310.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.143093 restraints weight = 5424.963| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8882 Z= 0.133 Angle : 0.645 9.413 12031 Z= 0.334 Chirality : 0.043 0.217 1376 Planarity : 0.004 0.038 1499 Dihedral : 5.928 112.459 1216 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.04 % Allowed : 16.79 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.26), residues: 1085 helix: 0.97 (0.26), residues: 378 sheet: -0.96 (0.31), residues: 277 loop : -1.02 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 148 TYR 0.022 0.002 TYR S 178 PHE 0.015 0.001 PHE S 200 TRP 0.019 0.002 TRP R 184 HIS 0.003 0.001 HIS S 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8878) covalent geometry : angle 0.64041 / 0.33 (12023) SS BOND : bond 0.00795 / 0.42 ( 4) SS BOND : angle 3.06764 / 1.64 ( 8) hydrogen bonds : bond 0.03700 / 2.59 ( 392) hydrogen bonds : angle 4.98209 / 3.50 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.7851 (m100) cc_final: 0.7477 (m100) REVERT: B 256 ARG cc_start: 0.7542 (mmp-170) cc_final: 0.7126 (mmp80) REVERT: G 21 MET cc_start: 0.7519 (ppp) cc_final: 0.6888 (ppp) REVERT: G 22 GLU cc_start: 0.3188 (tp30) cc_final: 0.2514 (tp30) REVERT: S 171 GLN cc_start: 0.8316 (mp-120) cc_final: 0.7592 (mp10) REVERT: S 208 GLU cc_start: 0.7934 (mp0) cc_final: 0.7101 (mp0) REVERT: A 216 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 275 GLU cc_start: 0.8081 (pp20) cc_final: 0.7682 (pm20) REVERT: A 287 TYR cc_start: 0.7409 (m-80) cc_final: 0.7081 (m-80) REVERT: A 313 ARG cc_start: 0.6562 (mtt180) cc_final: 0.6086 (mmt90) REVERT: A 318 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6595 (mm-30) REVERT: A 333 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8397 (mm-40) outliers start: 29 outliers final: 19 residues processed: 196 average time/residue: 0.0816 time to fit residues: 21.9221 Evaluate side-chains 182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN B 75 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN S 219 GLN S 220 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.161120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132325 restraints weight = 20206.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.135865 restraints weight = 11612.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.138500 restraints weight = 8228.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139978 restraints weight = 6509.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.141376 restraints weight = 5591.713| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8882 Z= 0.142 Angle : 0.680 10.674 12031 Z= 0.346 Chirality : 0.044 0.227 1376 Planarity : 0.004 0.038 1499 Dihedral : 6.176 114.609 1216 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.30 % Allowed : 18.89 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.26), residues: 1085 helix: 1.11 (0.26), residues: 377 sheet: -0.79 (0.31), residues: 268 loop : -1.02 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 168 TYR 0.021 0.002 TYR S 178 PHE 0.015 0.002 PHE S 200 TRP 0.022 0.001 TRP R 184 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8878) covalent geometry : angle 0.67213 / 0.34 (12023) SS BOND : bond 0.00504 / 0.26 ( 4) SS BOND : angle 4.08288 / 2.26 ( 8) hydrogen bonds : bond 0.03743 / 2.62 ( 392) hydrogen bonds : angle 4.86115 / 3.43 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.7901 (m100) cc_final: 0.7578 (m100) REVERT: B 256 ARG cc_start: 0.7679 (mmp-170) cc_final: 0.7112 (mmp80) REVERT: G 21 MET cc_start: 0.7672 (ppp) cc_final: 0.7113 (ppp) REVERT: G 22 GLU cc_start: 0.3523 (tp30) cc_final: 0.2910 (tp30) REVERT: G 48 ASP cc_start: 0.7151 (m-30) cc_final: 0.6913 (m-30) REVERT: A 275 GLU cc_start: 0.8091 (pp20) cc_final: 0.7661 (pm20) REVERT: A 313 ARG cc_start: 0.6541 (mtt180) cc_final: 0.6314 (mmt90) REVERT: A 315 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7637 (p0) REVERT: R 117 ARG cc_start: 0.5486 (mtm-85) cc_final: 0.5136 (mtm-85) REVERT: R 140 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7606 (tp) REVERT: R 173 MET cc_start: 0.7896 (mmt) cc_final: 0.7532 (mmt) outliers start: 41 outliers final: 25 residues processed: 198 average time/residue: 0.0769 time to fit residues: 21.0773 Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN S 219 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.159838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131640 restraints weight = 20032.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.134764 restraints weight = 11594.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.136989 restraints weight = 8199.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.138668 restraints weight = 6575.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.139499 restraints weight = 5655.435| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8882 Z= 0.148 Angle : 0.718 10.404 12031 Z= 0.363 Chirality : 0.044 0.244 1376 Planarity : 0.004 0.036 1499 Dihedral : 6.246 113.385 1216 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.09 % Allowed : 21.20 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.26), residues: 1085 helix: 1.15 (0.26), residues: 376 sheet: -0.71 (0.32), residues: 264 loop : -0.92 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 168 TYR 0.021 0.002 TYR S 178 PHE 0.017 0.002 PHE S 200 TRP 0.014 0.001 TRP R 184 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8878) covalent geometry : angle 0.71033 / 0.36 (12023) SS BOND : bond 0.00276 / 0.14 ( 4) SS BOND : angle 4.06585 / 2.25 ( 8) hydrogen bonds : bond 0.03808 / 2.66 ( 392) hydrogen bonds : angle 4.87227 / 3.45 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.8041 (m100) cc_final: 0.7746 (m100) REVERT: B 234 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.6191 (m-80) REVERT: B 256 ARG cc_start: 0.7823 (mmp-170) cc_final: 0.7239 (mmp80) REVERT: G 21 MET cc_start: 0.7654 (ppp) cc_final: 0.7089 (ppp) REVERT: G 22 GLU cc_start: 0.3874 (tp30) cc_final: 0.3079 (tp30) REVERT: G 48 ASP cc_start: 0.7240 (m-30) cc_final: 0.6901 (m-30) REVERT: S 168 ARG cc_start: 0.8625 (tpm170) cc_final: 0.8262 (tpm170) REVERT: S 206 ARG cc_start: 0.8794 (mpp80) cc_final: 0.8326 (mpp80) REVERT: S 219 GLN cc_start: 0.3892 (OUTLIER) cc_final: 0.3691 (pp30) REVERT: A 306 GLN cc_start: 0.7815 (tp40) cc_final: 0.7594 (tp-100) REVERT: A 313 ARG cc_start: 0.6592 (mtt180) cc_final: 0.6352 (mmt90) REVERT: A 315 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7855 (p0) REVERT: R 117 ARG cc_start: 0.5535 (mtm-85) cc_final: 0.5160 (mtm-85) REVERT: R 140 LEU cc_start: 0.7868 (tt) cc_final: 0.7570 (tp) REVERT: R 171 MET cc_start: 0.8599 (tpp) cc_final: 0.8238 (tpp) REVERT: R 173 MET cc_start: 0.7659 (mmt) cc_final: 0.7355 (mmt) outliers start: 39 outliers final: 29 residues processed: 198 average time/residue: 0.0768 time to fit residues: 20.8920 Evaluate side-chains 195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 98 optimal weight: 6.9990 chunk 85 optimal weight: 0.0270 chunk 105 optimal weight: 5.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN S 219 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.162052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.132734 restraints weight = 20132.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.136359 restraints weight = 11668.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.139053 restraints weight = 8216.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.140682 restraints weight = 6477.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.141556 restraints weight = 5544.952| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8882 Z= 0.122 Angle : 0.699 9.303 12031 Z= 0.350 Chirality : 0.044 0.253 1376 Planarity : 0.004 0.039 1499 Dihedral : 6.036 113.446 1216 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 4.41 % Allowed : 22.56 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 1085 helix: 1.11 (0.26), residues: 384 sheet: -0.70 (0.32), residues: 272 loop : -0.86 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 168 TYR 0.021 0.001 TYR S 178 PHE 0.013 0.001 PHE S 200 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8878) covalent geometry : angle 0.69312 / 0.35 (12023) SS BOND : bond 0.00280 / 0.14 ( 4) SS BOND : angle 3.43451 / 1.90 ( 8) hydrogen bonds : bond 0.03531 / 2.47 ( 392) hydrogen bonds : angle 4.76563 / 3.37 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.7952 (m100) cc_final: 0.7716 (m100) REVERT: B 101 MET cc_start: 0.6771 (mpp) cc_final: 0.6370 (mpp) REVERT: B 234 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.6238 (m-80) REVERT: B 256 ARG cc_start: 0.7777 (mmp-170) cc_final: 0.7255 (mmp80) REVERT: G 21 MET cc_start: 0.7693 (ppp) cc_final: 0.7169 (ppp) REVERT: G 22 GLU cc_start: 0.3842 (tp30) cc_final: 0.3094 (tp30) REVERT: G 48 ASP cc_start: 0.7015 (m-30) cc_final: 0.6729 (m-30) REVERT: S 206 ARG cc_start: 0.8727 (mpp80) cc_final: 0.8241 (mpp80) REVERT: A 315 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7841 (p0) REVERT: R 40 ASN cc_start: 0.7731 (t0) cc_final: 0.7131 (m-40) REVERT: R 99 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6851 (mmm) REVERT: R 117 ARG cc_start: 0.5498 (mtm-85) cc_final: 0.5108 (mtm-85) REVERT: R 140 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7697 (tp) REVERT: R 152 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7834 (mptt) REVERT: R 171 MET cc_start: 0.8548 (tpp) cc_final: 0.8203 (tpp) REVERT: R 173 MET cc_start: 0.7597 (mmt) cc_final: 0.7364 (mmt) outliers start: 42 outliers final: 28 residues processed: 203 average time/residue: 0.0744 time to fit residues: 20.8544 Evaluate side-chains 200 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.161493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.132641 restraints weight = 19973.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.136230 restraints weight = 11489.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.138954 restraints weight = 8117.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.140473 restraints weight = 6384.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.141689 restraints weight = 5474.227| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8882 Z= 0.137 Angle : 0.755 10.227 12031 Z= 0.373 Chirality : 0.045 0.264 1376 Planarity : 0.004 0.045 1499 Dihedral : 5.775 112.576 1216 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 3.78 % Allowed : 22.98 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1085 helix: 1.21 (0.26), residues: 376 sheet: -0.58 (0.32), residues: 264 loop : -0.83 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 190 TYR 0.021 0.001 TYR B 105 PHE 0.019 0.001 PHE S 200 TRP 0.015 0.001 TRP B 82 HIS 0.009 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8878) covalent geometry : angle 0.75018 / 0.37 (12023) SS BOND : bond 0.00172 / 0.09 ( 4) SS BOND : angle 3.30167 / 1.82 ( 8) hydrogen bonds : bond 0.03654 / 2.55 ( 392) hydrogen bonds : angle 4.78475 / 3.39 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7242 (t0) cc_final: 0.6739 (t0) REVERT: B 82 TRP cc_start: 0.7991 (m100) cc_final: 0.7707 (m100) REVERT: B 101 MET cc_start: 0.6682 (mpp) cc_final: 0.6321 (mpp) REVERT: B 234 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.6333 (m-80) REVERT: G 21 MET cc_start: 0.7736 (ppp) cc_final: 0.7251 (ppp) REVERT: G 22 GLU cc_start: 0.3838 (tp30) cc_final: 0.3085 (tp30) REVERT: G 48 ASP cc_start: 0.6928 (m-30) cc_final: 0.6628 (m-30) REVERT: S 168 ARG cc_start: 0.8516 (tpm170) cc_final: 0.8171 (tpm170) REVERT: A 315 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7883 (p0) REVERT: R 40 ASN cc_start: 0.7665 (t0) cc_final: 0.7272 (m-40) REVERT: R 117 ARG cc_start: 0.5721 (mtm-85) cc_final: 0.5278 (mtm-85) REVERT: R 140 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7660 (tp) outliers start: 36 outliers final: 28 residues processed: 199 average time/residue: 0.0798 time to fit residues: 22.2655 Evaluate side-chains 200 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 285 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 0.0000 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.163517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.134889 restraints weight = 19913.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.138409 restraints weight = 11447.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.140993 restraints weight = 8041.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.142757 restraints weight = 6347.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.143752 restraints weight = 5417.021| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8882 Z= 0.133 Angle : 0.779 14.445 12031 Z= 0.380 Chirality : 0.045 0.321 1376 Planarity : 0.004 0.043 1499 Dihedral : 5.656 110.146 1216 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 3.57 % Allowed : 22.88 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.26), residues: 1085 helix: 1.10 (0.26), residues: 385 sheet: -0.53 (0.33), residues: 257 loop : -0.83 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 148 TYR 0.020 0.001 TYR S 178 PHE 0.018 0.001 PHE S 200 TRP 0.012 0.001 TRP R 35 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8878) covalent geometry : angle 0.77485 / 0.38 (12023) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 3.16439 / 1.75 ( 8) hydrogen bonds : bond 0.03601 / 2.52 ( 392) hydrogen bonds : angle 4.77377 / 3.38 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7424 (t0) cc_final: 0.6968 (t0) REVERT: B 82 TRP cc_start: 0.7922 (m100) cc_final: 0.7708 (m100) REVERT: B 101 MET cc_start: 0.6525 (mpp) cc_final: 0.6202 (mpp) REVERT: B 188 MET cc_start: 0.6655 (ppp) cc_final: 0.6424 (ppp) REVERT: B 234 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.6316 (m-80) REVERT: B 256 ARG cc_start: 0.7712 (mmp-170) cc_final: 0.7417 (mmp-170) REVERT: G 21 MET cc_start: 0.7802 (ppp) cc_final: 0.7329 (ppp) REVERT: G 22 GLU cc_start: 0.4074 (tp30) cc_final: 0.3321 (tp30) REVERT: G 48 ASP cc_start: 0.6928 (m-30) cc_final: 0.6625 (m-30) REVERT: S 168 ARG cc_start: 0.8519 (tpm170) cc_final: 0.8225 (tpm170) REVERT: A 276 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8542 (mm-30) REVERT: A 315 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7944 (p0) REVERT: R 40 ASN cc_start: 0.7303 (t0) cc_final: 0.6955 (m-40) REVERT: R 117 ARG cc_start: 0.5679 (mtm-85) cc_final: 0.5315 (mtm-85) REVERT: R 140 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7721 (tp) REVERT: R 152 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7597 (mmtt) outliers start: 34 outliers final: 29 residues processed: 203 average time/residue: 0.0710 time to fit residues: 19.8512 Evaluate side-chains 206 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain R residue 44 GLN Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 285 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 68 optimal weight: 0.0020 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 269 ASN A 322 HIS R 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.164031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.136310 restraints weight = 19591.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.139858 restraints weight = 11271.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.142425 restraints weight = 7876.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.144100 restraints weight = 6181.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.145170 restraints weight = 5251.427| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8882 Z= 0.128 Angle : 0.773 13.609 12031 Z= 0.376 Chirality : 0.045 0.284 1376 Planarity : 0.004 0.043 1499 Dihedral : 5.614 109.268 1216 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 3.04 % Allowed : 23.29 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1085 helix: 1.11 (0.26), residues: 387 sheet: -0.53 (0.32), residues: 262 loop : -0.72 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 179 TYR 0.020 0.001 TYR S 178 PHE 0.016 0.001 PHE S 200 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8878) covalent geometry : angle 0.76907 / 0.37 (12023) SS BOND : bond 0.00236 / 0.12 ( 4) SS BOND : angle 3.03571 / 1.68 ( 8) hydrogen bonds : bond 0.03560 / 2.50 ( 392) hydrogen bonds : angle 4.76670 / 3.39 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7335 (t0) cc_final: 0.6903 (t0) REVERT: B 82 TRP cc_start: 0.7827 (m100) cc_final: 0.7626 (m100) REVERT: B 101 MET cc_start: 0.6285 (mpp) cc_final: 0.5979 (mpp) REVERT: B 188 MET cc_start: 0.6839 (ppp) cc_final: 0.6618 (ppp) REVERT: B 234 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.6335 (m-80) REVERT: B 256 ARG cc_start: 0.7732 (mmp-170) cc_final: 0.7306 (mmp-170) REVERT: G 21 MET cc_start: 0.7697 (ppp) cc_final: 0.7254 (ppp) REVERT: G 22 GLU cc_start: 0.3819 (tp30) cc_final: 0.3056 (tp30) REVERT: G 48 ASP cc_start: 0.6809 (m-30) cc_final: 0.6536 (m-30) REVERT: A 14 GLU cc_start: 0.6342 (tm-30) cc_final: 0.6128 (tm-30) REVERT: A 276 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8430 (mm-30) REVERT: A 315 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7973 (p0) REVERT: R 40 ASN cc_start: 0.6997 (t0) cc_final: 0.6747 (m-40) REVERT: R 117 ARG cc_start: 0.5615 (mtm-85) cc_final: 0.5253 (mtm-85) REVERT: R 140 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7781 (tp) REVERT: R 151 MET cc_start: 0.8192 (mmm) cc_final: 0.7770 (mmm) REVERT: R 173 MET cc_start: 0.7809 (mmt) cc_final: 0.7324 (mmt) outliers start: 29 outliers final: 21 residues processed: 199 average time/residue: 0.0782 time to fit residues: 21.2755 Evaluate side-chains 196 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 0.0040 chunk 71 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 0.0040 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 269 ASN A 322 HIS R 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.159955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131119 restraints weight = 19774.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.134630 restraints weight = 11449.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.136906 restraints weight = 8095.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.138868 restraints weight = 6464.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139639 restraints weight = 5468.694| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8882 Z= 0.161 Angle : 0.804 12.279 12031 Z= 0.395 Chirality : 0.046 0.278 1376 Planarity : 0.004 0.083 1499 Dihedral : 5.629 108.263 1216 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 2.73 % Allowed : 24.03 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1085 helix: 1.05 (0.26), residues: 390 sheet: -0.58 (0.33), residues: 256 loop : -0.71 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 148 TYR 0.023 0.002 TYR B 105 PHE 0.014 0.001 PHE S 200 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8878) covalent geometry : angle 0.80053 / 0.39 (12023) SS BOND : bond 0.00121 / 0.06 ( 4) SS BOND : angle 3.18561 / 1.76 ( 8) hydrogen bonds : bond 0.03953 / 2.77 ( 392) hydrogen bonds : angle 4.83753 / 3.45 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1535.35 seconds wall clock time: 27 minutes 12.61 seconds (1632.61 seconds total)