Starting phenix.real_space_refine on Tue Mar 3 23:03:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v1h_64693/03_2026/9v1h_64693_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v1h_64693/03_2026/9v1h_64693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v1h_64693/03_2026/9v1h_64693_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v1h_64693/03_2026/9v1h_64693_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v1h_64693/03_2026/9v1h_64693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v1h_64693/03_2026/9v1h_64693.map" } resolution = 2.85 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= 0.010 sd= 0.054 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 62 5.16 5 C 5689 2.51 5 N 1533 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8890 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1709 Classifications: {'peptide': 208} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2537 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1698 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 409 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2455 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.01, per 1000 atoms: 0.23 Number of scatterers: 8890 At special positions: 0 Unit cell: (100.74, 116.8, 133.59, 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 62 16.00 O 1606 8.00 N 1533 7.00 C 5689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=1.99 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 206 " distance=2.26 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: 0.64 Conformation dependent library (CDL) restraints added in 232.2 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 36.8% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.609A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.787A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.569A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 250 removed outlier: 3.603A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.824A pdb=" N GLU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.717A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 359 Processing helix chain 'B' and resid 12 through 31 removed outlier: 3.557A pdb=" N ALA B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 removed outlier: 4.050A pdb=" N ASN B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.136A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 Processing helix chain 'G' and resid 29 through 46 removed outlier: 4.567A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 73 removed outlier: 3.504A pdb=" N VAL R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN R 73 " --> pdb=" O ILE R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 78 through 108 removed outlier: 3.845A pdb=" N PHE R 83 " --> pdb=" O VAL R 79 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) Proline residue: R 100 - end of helix removed outlier: 3.625A pdb=" N ASN R 106 " --> pdb=" O THR R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 149 removed outlier: 3.665A pdb=" N ILE R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY R 122 " --> pdb=" O CYS R 118 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL R 129 " --> pdb=" O GLN R 125 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA R 130 " --> pdb=" O GLY R 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR R 135 " --> pdb=" O ALA R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 173 removed outlier: 3.775A pdb=" N ILE R 166 " --> pdb=" O VAL R 162 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP R 168 " --> pdb=" O ILE R 164 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL R 169 " --> pdb=" O MET R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 181 Processing helix chain 'R' and resid 213 through 228 Processing helix chain 'R' and resid 228 through 248 Processing helix chain 'R' and resid 265 through 286 removed outlier: 3.508A pdb=" N LEU R 277 " --> pdb=" O ILE R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 297 removed outlier: 3.591A pdb=" N TRP R 291 " --> pdb=" O TRP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 335 removed outlier: 4.875A pdb=" N TYR R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) Proline residue: R 316 - end of helix removed outlier: 4.333A pdb=" N SER R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER R 327 " --> pdb=" O PHE R 323 " (cutoff:3.500A) Proline residue: R 330 - end of helix Processing helix chain 'R' and resid 337 through 344 removed outlier: 4.060A pdb=" N ARG R 341 " --> pdb=" O ASN R 337 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG R 342 " --> pdb=" O GLU R 338 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.417A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.119A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.516A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.686A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.587A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.902A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 208 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 4.080A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.899A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS B 299 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B 312 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 301 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.509A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.512A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR E 94 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.505A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.816A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 183 through 191 removed outlier: 4.698A pdb=" N VAL R 203 " --> pdb=" O GLU R 187 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1152 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: 1.16 Time building geometry restraints manager: 0.84 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: 2823 1.34 - 1.45: 1344 1.45 - 1.57: 4818 1.57 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9080 Sorted by residual: bond pdb=" N ILE R 227 " pdb=" CA ILE R 227 " ideal model delta sigma weight residual 1.460 1.506 -0.045 8.60e-03 1.35e+04 2.79e+01 bond pdb=" N ILE R 174 " pdb=" CA ILE R 174 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.88e+00 bond pdb=" N VAL R 180 " pdb=" CA VAL R 180 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.41e-02 5.03e+03 8.66e+00 bond pdb=" N PHE R 57 " pdb=" CA PHE R 57 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.58e+00 bond pdb=" N ASP R 298 " pdb=" CA ASP R 298 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.35e-02 5.49e+03 5.67e+00 ... (remaining 9075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 12008 1.45 - 2.91: 227 2.91 - 4.36: 59 4.36 - 5.82: 7 5.82 - 7.27: 4 Bond angle restraints: 12305 Sorted by residual: angle pdb=" N PHE R 57 " pdb=" CA PHE R 57 " pdb=" CB PHE R 57 " ideal model delta sigma weight residual 109.94 117.21 -7.27 1.49e+00 4.50e-01 2.38e+01 angle pdb=" N ASN R 115 " pdb=" CA ASN R 115 " pdb=" C ASN R 115 " ideal model delta sigma weight residual 114.04 108.89 5.15 1.24e+00 6.50e-01 1.72e+01 angle pdb=" C PHE R 56 " pdb=" CA PHE R 56 " pdb=" CB PHE R 56 " ideal model delta sigma weight residual 110.96 117.08 -6.12 1.54e+00 4.22e-01 1.58e+01 angle pdb=" N PHE R 56 " pdb=" CA PHE R 56 " pdb=" C PHE R 56 " ideal model delta sigma weight residual 110.97 106.64 4.33 1.09e+00 8.42e-01 1.58e+01 angle pdb=" C HIS R 77 " pdb=" CA HIS R 77 " pdb=" CB HIS R 77 " ideal model delta sigma weight residual 110.26 116.20 -5.94 1.50e+00 4.44e-01 1.57e+01 ... (remaining 12300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5175 17.65 - 35.29: 143 35.29 - 52.94: 42 52.94 - 70.58: 5 70.58 - 88.23: 1 Dihedral angle restraints: 5366 sinusoidal: 2066 harmonic: 3300 Sorted by residual: dihedral pdb=" CB CYS R 118 " pdb=" SG CYS R 118 " pdb=" SG CYS R 206 " pdb=" CB CYS R 206 " ideal model delta sinusoidal sigma weight residual 93.00 45.27 47.73 1 1.00e+01 1.00e-02 3.14e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 54.25 38.75 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" N ILE R 332 " pdb=" CA ILE R 332 " pdb=" CB ILE R 332 " pdb=" CG1 ILE R 332 " ideal model delta sinusoidal sigma weight residual 60.00 1.66 58.34 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1239 0.065 - 0.130: 149 0.130 - 0.194: 5 0.194 - 0.259: 2 0.259 - 0.324: 2 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA ILE R 47 " pdb=" N ILE R 47 " pdb=" C ILE R 47 " pdb=" CB ILE R 47 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA VAL R 180 " pdb=" N VAL R 180 " pdb=" C VAL R 180 " pdb=" CB VAL R 180 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE R 174 " pdb=" N ILE R 174 " pdb=" C ILE R 174 " pdb=" CB ILE R 174 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1394 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 8 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C GLY L 8 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY L 8 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG L 9 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP R 210 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO R 211 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 176 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO R 177 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 177 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 177 " -0.022 5.00e-02 4.00e+02 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 131 2.65 - 3.21: 8359 3.21 - 3.78: 13199 3.78 - 4.34: 18863 4.34 - 4.90: 31197 Nonbonded interactions: 71749 Sorted by model distance: nonbonded pdb=" OD1 ASN R 86 " pdb=" OG1 THR R 135 " model vdw 2.091 3.040 nonbonded pdb=" OG SER E 52 " pdb=" OG1 THR E 57 " model vdw 2.127 3.040 nonbonded pdb=" OG SER B 152 " pdb=" O MET B 193 " model vdw 2.137 3.040 nonbonded pdb=" OG SER R 90 " pdb=" O SER R 128 " model vdw 2.151 3.040 nonbonded pdb=" OH TYR B 150 " pdb=" OD2 ASP B 191 " model vdw 2.155 3.040 ... (remaining 71744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 0.232 9082 Z= 0.206 Angle : 0.666 39.853 12309 Z= 0.389 Chirality : 0.042 0.324 1397 Planarity : 0.003 0.041 1551 Dihedral : 9.288 88.228 3230 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.70 % Favored : 98.21 % Rotamer: Outliers : 1.05 % Allowed : 5.05 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.27), residues: 1115 helix: 1.62 (0.29), residues: 370 sheet: 1.58 (0.32), residues: 264 loop : 0.14 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 101 TYR 0.007 0.001 TYR R 333 PHE 0.016 0.001 PHE R 344 TRP 0.005 0.001 TRP A 211 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9080) covalent geometry : angle 0.52665 (12305) SS BOND : bond 0.16692 ( 2) SS BOND : angle 22.60166 ( 4) hydrogen bonds : bond 0.19560 ( 410) hydrogen bonds : angle 7.50627 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.7796 (tt0) cc_final: 0.7552 (tm130) REVERT: A 303 ARG cc_start: 0.4630 (mtp180) cc_final: 0.3692 (mmp-170) REVERT: B 176 ILE cc_start: 0.6538 (mm) cc_final: 0.6310 (mp) REVERT: B 193 MET cc_start: 0.7740 (mmm) cc_final: 0.7449 (mmm) REVERT: R 105 ASP cc_start: 0.8060 (t0) cc_final: 0.7756 (t0) REVERT: R 117 MET cc_start: 0.7205 (mtm) cc_final: 0.6878 (tmm) outliers start: 10 outliers final: 5 residues processed: 244 average time/residue: 0.5340 time to fit residues: 138.7619 Evaluate side-chains 162 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 175 MET Chi-restraints excluded: chain R residue 208 GLU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 59 HIS B 80 GLN B 115 ASN B 235 ASN B 264 GLN E 82 GLN R 40 HIS R 41 GLN R 226 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.127926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104388 restraints weight = 16858.107| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.28 r_work: 0.3495 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9082 Z= 0.218 Angle : 0.694 9.528 12309 Z= 0.363 Chirality : 0.047 0.174 1397 Planarity : 0.005 0.061 1551 Dihedral : 5.883 55.920 1248 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 4.32 % Allowed : 14.74 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1115 helix: 1.19 (0.27), residues: 379 sheet: 1.04 (0.31), residues: 267 loop : -0.13 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 87 TYR 0.019 0.002 TYR B 129 PHE 0.024 0.002 PHE B 156 TRP 0.021 0.003 TRP B 87 HIS 0.007 0.002 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 9080) covalent geometry : angle 0.69177 (12305) SS BOND : bond 0.00823 ( 2) SS BOND : angle 2.89377 ( 4) hydrogen bonds : bond 0.04210 ( 410) hydrogen bonds : angle 5.26552 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8205 (mtmm) REVERT: A 190 GLN cc_start: 0.8573 (tt0) cc_final: 0.8117 (tm-30) REVERT: B 101 ARG cc_start: 0.8265 (mmt90) cc_final: 0.7707 (pmt170) REVERT: E 34 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8073 (mtm) REVERT: E 118 THR cc_start: 0.7962 (p) cc_final: 0.7666 (t) REVERT: R 64 THR cc_start: 0.8613 (m) cc_final: 0.8336 (p) REVERT: R 72 ARG cc_start: 0.6999 (tpm170) cc_final: 0.6643 (tpm170) REVERT: R 105 ASP cc_start: 0.8355 (t0) cc_final: 0.7930 (t0) REVERT: R 208 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: R 215 MET cc_start: 0.7295 (mtp) cc_final: 0.6069 (mmp) outliers start: 41 outliers final: 18 residues processed: 190 average time/residue: 0.5218 time to fit residues: 106.0753 Evaluate side-chains 162 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 208 GLU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain R residue 331 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 259 ASN B 80 GLN E 82 GLN E 183 GLN R 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.129257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107046 restraints weight = 16870.407| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.17 r_work: 0.3527 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9082 Z= 0.122 Angle : 0.566 7.025 12309 Z= 0.297 Chirality : 0.042 0.158 1397 Planarity : 0.004 0.060 1551 Dihedral : 5.206 55.951 1241 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.47 % Allowed : 16.95 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1115 helix: 1.43 (0.27), residues: 379 sheet: 1.00 (0.32), residues: 257 loop : -0.11 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 191 TYR 0.013 0.001 TYR A 327 PHE 0.017 0.001 PHE R 97 TRP 0.025 0.002 TRP R 205 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9080) covalent geometry : angle 0.56389 (12305) SS BOND : bond 0.00374 ( 2) SS BOND : angle 3.01072 ( 4) hydrogen bonds : bond 0.03691 ( 410) hydrogen bonds : angle 4.82692 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8510 (tt0) cc_final: 0.7950 (tm130) REVERT: B 101 ARG cc_start: 0.8195 (mmt90) cc_final: 0.7709 (pmt170) REVERT: B 252 ASP cc_start: 0.7166 (t0) cc_final: 0.6962 (t0) REVERT: E 118 THR cc_start: 0.7984 (p) cc_final: 0.7699 (t) REVERT: R 64 THR cc_start: 0.8566 (m) cc_final: 0.8350 (p) REVERT: R 72 ARG cc_start: 0.6576 (tpm170) cc_final: 0.6308 (tpm170) REVERT: R 105 ASP cc_start: 0.8308 (t0) cc_final: 0.7911 (t0) REVERT: R 191 ARG cc_start: 0.7155 (ttm-80) cc_final: 0.6535 (tpp-160) REVERT: R 208 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: R 215 MET cc_start: 0.7343 (mtp) cc_final: 0.6112 (mmp) outliers start: 33 outliers final: 19 residues processed: 172 average time/residue: 0.5275 time to fit residues: 97.0094 Evaluate side-chains 157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 208 GLU Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 24 GLN A 259 ASN B 80 GLN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.127177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.104480 restraints weight = 17191.398| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.33 r_work: 0.3462 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9082 Z= 0.148 Angle : 0.573 6.901 12309 Z= 0.300 Chirality : 0.043 0.148 1397 Planarity : 0.004 0.055 1551 Dihedral : 5.031 58.768 1239 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 4.42 % Allowed : 17.47 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.26), residues: 1115 helix: 1.21 (0.26), residues: 386 sheet: 0.87 (0.32), residues: 257 loop : -0.18 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 191 TYR 0.013 0.001 TYR A 327 PHE 0.017 0.002 PHE R 97 TRP 0.016 0.002 TRP B 87 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9080) covalent geometry : angle 0.57116 (12305) SS BOND : bond 0.00600 ( 2) SS BOND : angle 2.65173 ( 4) hydrogen bonds : bond 0.03706 ( 410) hydrogen bonds : angle 4.84405 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8340 (mt) REVERT: A 190 GLN cc_start: 0.8474 (tt0) cc_final: 0.7990 (tm130) REVERT: B 101 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7609 (pmt170) REVERT: B 252 ASP cc_start: 0.7089 (t0) cc_final: 0.6879 (t0) REVERT: E 34 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7910 (mmm) REVERT: E 118 THR cc_start: 0.8015 (p) cc_final: 0.7769 (t) REVERT: E 140 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.6836 (mmm) REVERT: R 64 THR cc_start: 0.8512 (m) cc_final: 0.8249 (p) REVERT: R 105 ASP cc_start: 0.8275 (t0) cc_final: 0.7881 (t0) REVERT: R 208 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: R 215 MET cc_start: 0.7291 (mtp) cc_final: 0.6081 (mmp) REVERT: R 247 PHE cc_start: 0.5003 (t80) cc_final: 0.4564 (t80) outliers start: 42 outliers final: 21 residues processed: 176 average time/residue: 0.5300 time to fit residues: 99.5091 Evaluate side-chains 171 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 208 GLU Chi-restraints excluded: chain R residue 315 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 259 ASN B 80 GLN E 82 GLN E 194 ASN R 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.128537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104881 restraints weight = 17111.730| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.33 r_work: 0.3498 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9082 Z= 0.110 Angle : 0.536 8.079 12309 Z= 0.281 Chirality : 0.041 0.136 1397 Planarity : 0.004 0.056 1551 Dihedral : 4.831 54.264 1239 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 3.79 % Allowed : 18.84 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1115 helix: 1.41 (0.27), residues: 384 sheet: 0.86 (0.32), residues: 257 loop : -0.24 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 191 TYR 0.012 0.001 TYR E 95 PHE 0.013 0.001 PHE R 344 TRP 0.015 0.001 TRP R 205 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9080) covalent geometry : angle 0.53569 (12305) SS BOND : bond 0.00510 ( 2) SS BOND : angle 1.53009 ( 4) hydrogen bonds : bond 0.03394 ( 410) hydrogen bonds : angle 4.61743 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8588 (tt0) cc_final: 0.8046 (tm130) REVERT: A 250 ARG cc_start: 0.8034 (mmt-90) cc_final: 0.7752 (mtp85) REVERT: B 101 ARG cc_start: 0.8196 (mmt90) cc_final: 0.7694 (pmt170) REVERT: B 252 ASP cc_start: 0.7277 (t0) cc_final: 0.7006 (t0) REVERT: E 34 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8013 (mtm) REVERT: E 118 THR cc_start: 0.8014 (p) cc_final: 0.7760 (t) REVERT: R 64 THR cc_start: 0.8464 (m) cc_final: 0.8213 (p) REVERT: R 72 ARG cc_start: 0.7020 (tpm170) cc_final: 0.6801 (tpm170) REVERT: R 105 ASP cc_start: 0.8260 (t0) cc_final: 0.7858 (t0) REVERT: R 191 ARG cc_start: 0.7187 (ttm-80) cc_final: 0.6563 (tpp-160) REVERT: R 208 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: R 215 MET cc_start: 0.7374 (mtp) cc_final: 0.6136 (mmp) REVERT: R 238 MET cc_start: 0.7267 (mmp) cc_final: 0.6137 (mmt) REVERT: R 247 PHE cc_start: 0.4973 (t80) cc_final: 0.4402 (t80) outliers start: 36 outliers final: 19 residues processed: 174 average time/residue: 0.5018 time to fit residues: 93.5341 Evaluate side-chains 168 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 208 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 80 GLN B 147 HIS E 3 GLN E 82 GLN R 40 HIS R 115 ASN R 226 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.126753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102788 restraints weight = 17143.648| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.34 r_work: 0.3464 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9082 Z= 0.143 Angle : 0.558 7.654 12309 Z= 0.291 Chirality : 0.042 0.145 1397 Planarity : 0.004 0.058 1551 Dihedral : 4.944 55.965 1239 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 4.84 % Allowed : 18.53 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1115 helix: 1.34 (0.26), residues: 383 sheet: 0.79 (0.32), residues: 257 loop : -0.26 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 191 TYR 0.014 0.001 TYR A 327 PHE 0.015 0.001 PHE B 156 TRP 0.015 0.002 TRP B 87 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9080) covalent geometry : angle 0.55700 (12305) SS BOND : bond 0.00587 ( 2) SS BOND : angle 1.72036 ( 4) hydrogen bonds : bond 0.03550 ( 410) hydrogen bonds : angle 4.71012 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8433 (mt) REVERT: A 190 GLN cc_start: 0.8680 (tt0) cc_final: 0.8204 (tm-30) REVERT: A 361 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: B 252 ASP cc_start: 0.7332 (t0) cc_final: 0.7078 (t0) REVERT: E 18 ARG cc_start: 0.8758 (tpp-160) cc_final: 0.8411 (ttt90) REVERT: E 34 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7807 (mmm) REVERT: E 118 THR cc_start: 0.8006 (p) cc_final: 0.7754 (t) REVERT: R 64 THR cc_start: 0.8399 (m) cc_final: 0.8130 (p) REVERT: R 72 ARG cc_start: 0.6644 (tpm170) cc_final: 0.6350 (tpm170) REVERT: R 105 ASP cc_start: 0.8248 (t0) cc_final: 0.7866 (t0) REVERT: R 191 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6531 (tpp-160) REVERT: R 208 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: R 215 MET cc_start: 0.7449 (mtp) cc_final: 0.6103 (mmp) REVERT: R 247 PHE cc_start: 0.4873 (t80) cc_final: 0.4234 (t80) outliers start: 46 outliers final: 27 residues processed: 175 average time/residue: 0.5099 time to fit residues: 95.6082 Evaluate side-chains 177 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 208 GLU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 315 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 24 GLN A 259 ASN B 80 GLN B 147 HIS E 3 GLN E 82 GLN R 40 HIS R 115 ASN R 226 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.125911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.101806 restraints weight = 16956.814| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.35 r_work: 0.3489 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9082 Z= 0.157 Angle : 0.582 7.921 12309 Z= 0.306 Chirality : 0.043 0.162 1397 Planarity : 0.004 0.057 1551 Dihedral : 5.051 58.805 1239 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 4.32 % Allowed : 19.58 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1115 helix: 1.30 (0.26), residues: 383 sheet: 0.76 (0.33), residues: 243 loop : -0.38 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 216 TYR 0.014 0.001 TYR A 327 PHE 0.015 0.002 PHE R 68 TRP 0.015 0.002 TRP B 87 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9080) covalent geometry : angle 0.58130 (12305) SS BOND : bond 0.00545 ( 2) SS BOND : angle 1.71674 ( 4) hydrogen bonds : bond 0.03575 ( 410) hydrogen bonds : angle 4.75953 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 190 GLN cc_start: 0.8702 (tt0) cc_final: 0.8236 (tm-30) REVERT: A 259 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7586 (m-40) REVERT: A 313 LEU cc_start: 0.5235 (mt) cc_final: 0.4557 (tp) REVERT: A 361 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.5941 (m-80) REVERT: B 222 MET cc_start: 0.7198 (pp-130) cc_final: 0.6959 (pp-130) REVERT: B 252 ASP cc_start: 0.7386 (t0) cc_final: 0.7137 (t0) REVERT: E 6 GLU cc_start: 0.7947 (mp0) cc_final: 0.7408 (mp0) REVERT: E 18 ARG cc_start: 0.8790 (tpp-160) cc_final: 0.8503 (ttt90) REVERT: E 34 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: E 118 THR cc_start: 0.8067 (p) cc_final: 0.7837 (t) REVERT: R 64 THR cc_start: 0.8270 (m) cc_final: 0.8017 (p) REVERT: R 72 ARG cc_start: 0.6383 (tpm170) cc_final: 0.6097 (tpm170) REVERT: R 105 ASP cc_start: 0.8271 (t0) cc_final: 0.7889 (t0) REVERT: R 215 MET cc_start: 0.7442 (mtp) cc_final: 0.6065 (mmt) outliers start: 41 outliers final: 31 residues processed: 172 average time/residue: 0.5454 time to fit residues: 100.3994 Evaluate side-chains 179 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 315 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 259 ASN B 21 ASN B 80 GLN B 147 HIS E 3 GLN E 82 GLN R 226 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.126019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103041 restraints weight = 16995.898| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.25 r_work: 0.3450 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9082 Z= 0.142 Angle : 0.564 8.185 12309 Z= 0.296 Chirality : 0.043 0.155 1397 Planarity : 0.004 0.058 1551 Dihedral : 4.664 59.760 1236 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.87 % Favored : 97.04 % Rotamer: Outliers : 4.42 % Allowed : 19.79 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1115 helix: 1.29 (0.26), residues: 383 sheet: 0.79 (0.33), residues: 241 loop : -0.42 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 216 TYR 0.016 0.001 TYR A 325 PHE 0.020 0.002 PHE R 247 TRP 0.015 0.002 TRP B 87 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9080) covalent geometry : angle 0.56298 (12305) SS BOND : bond 0.00590 ( 2) SS BOND : angle 1.50641 ( 4) hydrogen bonds : bond 0.03455 ( 410) hydrogen bonds : angle 4.70383 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8405 (mt) REVERT: A 188 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8162 (mptt) REVERT: A 190 GLN cc_start: 0.8688 (tt0) cc_final: 0.8206 (tm-30) REVERT: A 313 LEU cc_start: 0.5229 (mt) cc_final: 0.4900 (tm) REVERT: A 361 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: B 222 MET cc_start: 0.7235 (pp-130) cc_final: 0.7002 (pp-130) REVERT: B 252 ASP cc_start: 0.7326 (t0) cc_final: 0.7068 (t0) REVERT: E 6 GLU cc_start: 0.7902 (mp0) cc_final: 0.7397 (mp0) REVERT: E 18 ARG cc_start: 0.8775 (tpp-160) cc_final: 0.8516 (ttt90) REVERT: E 34 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7964 (mtm) REVERT: E 118 THR cc_start: 0.7960 (p) cc_final: 0.7707 (t) REVERT: R 64 THR cc_start: 0.8298 (m) cc_final: 0.8013 (p) REVERT: R 72 ARG cc_start: 0.6330 (tpm170) cc_final: 0.6036 (tpm170) REVERT: R 105 ASP cc_start: 0.8272 (t0) cc_final: 0.7883 (t0) REVERT: R 191 ARG cc_start: 0.6887 (ttm-80) cc_final: 0.6504 (ttm170) REVERT: R 215 MET cc_start: 0.7444 (mtp) cc_final: 0.6030 (mmp) REVERT: R 247 PHE cc_start: 0.5035 (t80) cc_final: 0.4746 (t80) outliers start: 42 outliers final: 29 residues processed: 169 average time/residue: 0.5182 time to fit residues: 93.8175 Evaluate side-chains 175 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 221 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.0060 chunk 80 optimal weight: 0.0570 chunk 88 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 259 ASN B 147 HIS E 82 GLN R 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.127241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104798 restraints weight = 17048.559| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.23 r_work: 0.3487 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9082 Z= 0.110 Angle : 0.557 14.894 12309 Z= 0.288 Chirality : 0.042 0.159 1397 Planarity : 0.004 0.058 1551 Dihedral : 4.423 56.218 1236 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.69 % Favored : 97.22 % Rotamer: Outliers : 3.89 % Allowed : 20.84 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1115 helix: 1.52 (0.26), residues: 384 sheet: 0.70 (0.32), residues: 257 loop : -0.31 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 216 TYR 0.016 0.001 TYR A 325 PHE 0.018 0.001 PHE R 344 TRP 0.014 0.001 TRP R 205 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9080) covalent geometry : angle 0.55629 (12305) SS BOND : bond 0.00513 ( 2) SS BOND : angle 1.23512 ( 4) hydrogen bonds : bond 0.03178 ( 410) hydrogen bonds : angle 4.49204 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8481 (mt) REVERT: A 188 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8117 (mptt) REVERT: A 190 GLN cc_start: 0.8666 (tt0) cc_final: 0.8082 (tm130) REVERT: A 313 LEU cc_start: 0.5171 (mt) cc_final: 0.4771 (tm) REVERT: B 80 GLN cc_start: 0.8599 (tp40) cc_final: 0.8344 (mm110) REVERT: B 143 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7156 (mm-30) REVERT: B 210 ASP cc_start: 0.7413 (m-30) cc_final: 0.6986 (p0) REVERT: B 222 MET cc_start: 0.7165 (pp-130) cc_final: 0.6931 (pp-130) REVERT: B 226 THR cc_start: 0.8395 (t) cc_final: 0.7979 (m) REVERT: E 18 ARG cc_start: 0.8775 (tpp-160) cc_final: 0.8520 (ttt90) REVERT: E 34 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7752 (mmm) REVERT: E 59 TYR cc_start: 0.7963 (m-80) cc_final: 0.7632 (m-10) REVERT: E 118 THR cc_start: 0.7998 (p) cc_final: 0.7747 (t) REVERT: R 64 THR cc_start: 0.8214 (m) cc_final: 0.7905 (p) REVERT: R 72 ARG cc_start: 0.6242 (tpm170) cc_final: 0.6030 (tpm170) REVERT: R 105 ASP cc_start: 0.8225 (t0) cc_final: 0.7841 (t0) REVERT: R 215 MET cc_start: 0.7364 (mtp) cc_final: 0.6044 (mmp) REVERT: R 247 PHE cc_start: 0.4855 (t80) cc_final: 0.4546 (t80) outliers start: 37 outliers final: 25 residues processed: 169 average time/residue: 0.4921 time to fit residues: 89.4467 Evaluate side-chains 167 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 315 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 23 optimal weight: 0.0370 chunk 24 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 147 HIS E 82 GLN R 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.126484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.102530 restraints weight = 17066.275| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.35 r_work: 0.3458 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9082 Z= 0.134 Angle : 0.564 8.773 12309 Z= 0.295 Chirality : 0.043 0.150 1397 Planarity : 0.004 0.058 1551 Dihedral : 4.486 52.008 1236 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 3.37 % Allowed : 21.37 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1115 helix: 1.50 (0.26), residues: 384 sheet: 0.63 (0.32), residues: 257 loop : -0.34 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 216 TYR 0.014 0.001 TYR A 327 PHE 0.017 0.002 PHE R 247 TRP 0.014 0.001 TRP B 87 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9080) covalent geometry : angle 0.56385 (12305) SS BOND : bond 0.00525 ( 2) SS BOND : angle 1.36935 ( 4) hydrogen bonds : bond 0.03319 ( 410) hydrogen bonds : angle 4.56896 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8420 (mt) REVERT: A 188 LYS cc_start: 0.8474 (mtmm) cc_final: 0.7809 (mptt) REVERT: A 190 GLN cc_start: 0.8705 (tt0) cc_final: 0.8237 (tm-30) REVERT: A 197 HIS cc_start: 0.8221 (m170) cc_final: 0.7995 (m-70) REVERT: A 313 LEU cc_start: 0.5217 (mt) cc_final: 0.4891 (tm) REVERT: B 80 GLN cc_start: 0.8625 (tp40) cc_final: 0.8401 (mm110) REVERT: B 210 ASP cc_start: 0.7468 (m-30) cc_final: 0.6974 (p0) REVERT: B 222 MET cc_start: 0.7184 (pp-130) cc_final: 0.6977 (pp-130) REVERT: E 18 ARG cc_start: 0.8790 (tpp-160) cc_final: 0.8545 (ttt90) REVERT: E 34 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7823 (mmm) REVERT: E 59 TYR cc_start: 0.8024 (m-80) cc_final: 0.7718 (m-10) REVERT: E 118 THR cc_start: 0.7981 (p) cc_final: 0.7727 (t) REVERT: R 64 THR cc_start: 0.8188 (m) cc_final: 0.7888 (p) REVERT: R 72 ARG cc_start: 0.6158 (tpm170) cc_final: 0.5940 (tpm170) REVERT: R 105 ASP cc_start: 0.8221 (t0) cc_final: 0.7864 (t0) REVERT: R 215 MET cc_start: 0.7371 (mtp) cc_final: 0.6063 (mmp) REVERT: R 247 PHE cc_start: 0.4922 (t80) cc_final: 0.4635 (t80) outliers start: 32 outliers final: 25 residues processed: 163 average time/residue: 0.5010 time to fit residues: 87.4930 Evaluate side-chains 162 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 147 HIS E 82 GLN R 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102454 restraints weight = 16954.465| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.32 r_work: 0.3453 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9082 Z= 0.136 Angle : 0.563 9.451 12309 Z= 0.294 Chirality : 0.043 0.156 1397 Planarity : 0.004 0.057 1551 Dihedral : 4.486 50.077 1236 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.05 % Favored : 96.86 % Rotamer: Outliers : 3.79 % Allowed : 21.37 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1115 helix: 1.55 (0.26), residues: 382 sheet: 0.64 (0.32), residues: 264 loop : -0.39 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 216 TYR 0.015 0.001 TYR A 325 PHE 0.019 0.002 PHE R 68 TRP 0.014 0.001 TRP B 87 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9080) covalent geometry : angle 0.56223 (12305) SS BOND : bond 0.00537 ( 2) SS BOND : angle 1.35697 ( 4) hydrogen bonds : bond 0.03307 ( 410) hydrogen bonds : angle 4.56498 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3804.34 seconds wall clock time: 65 minutes 21.98 seconds (3921.98 seconds total)