Starting phenix.real_space_refine on Tue Mar 3 20:35:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vh0_31982/03_2026/7vh0_31982_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vh0_31982/03_2026/7vh0_31982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vh0_31982/03_2026/7vh0_31982_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vh0_31982/03_2026/7vh0_31982_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vh0_31982/03_2026/7vh0_31982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vh0_31982/03_2026/7vh0_31982.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 58 5.16 5 C 5533 2.51 5 N 1463 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 8656 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2122 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1735 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "C" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "D" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1778 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'JEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.24 Number of scatterers: 8656 At special positions: 0 Unit cell: (90.95, 119.85, 128.35, 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 58 16.00 O 1602 8.00 N 1463 7.00 C 5533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 298.1 milliseconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 36.5% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 38 through 68 removed outlier: 3.562A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.631A pdb=" N ARG A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 73' Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.851A pdb=" N SER A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.656A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 117 removed outlier: 3.604A pdb=" N ALA A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.871A pdb=" N ILE A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 removed outlier: 4.146A pdb=" N TYR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.783A pdb=" N LEU A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N CYS A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.878A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.887A pdb=" N ALA A 196 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 197 " --> pdb=" O GLN A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 193 through 197' Processing helix chain 'A' and resid 198 through 209 removed outlier: 3.623A pdb=" N VAL A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 235 removed outlier: 4.360A pdb=" N VAL A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.564A pdb=" N PHE A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.727A pdb=" N ARG A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.950A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.541A pdb=" N THR B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.716A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 255 removed outlier: 3.553A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.791A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.852A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 352 removed outlier: 4.242A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.914A pdb=" N GLU C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.608A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.506A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.693A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.642A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.522A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.799A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190 removed outlier: 3.600A pdb=" N ASP B 200 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.052A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.853A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.856A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.718A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.054A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 3.567A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.362A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.550A pdb=" N MET E 83 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 51 removed outlier: 5.369A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.615A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.645A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 353 hydrogen bonds defined for protein. 975 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: 1.15 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1405 1.31 - 1.43: 2463 1.43 - 1.56: 4893 1.56 - 1.69: 1 1.69 - 1.81: 82 Bond restraints: 8844 Sorted by residual: bond pdb=" CA ILE A 142 " pdb=" C ILE A 142 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.27e-02 6.20e+03 2.99e+01 bond pdb=" CA THR A 252 " pdb=" C THR A 252 " ideal model delta sigma weight residual 1.521 1.460 0.061 1.14e-02 7.69e+03 2.85e+01 bond pdb=" C3 JEV A 401 " pdb=" N1 JEV A 401 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C15 JEV A 401 " pdb=" O1 JEV A 401 " ideal model delta sigma weight residual 1.439 1.351 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CA TYR A 200 " pdb=" C TYR A 200 " ideal model delta sigma weight residual 1.522 1.466 0.057 1.37e-02 5.33e+03 1.72e+01 ... (remaining 8839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11676 2.23 - 4.45: 254 4.45 - 6.68: 50 6.68 - 8.91: 13 8.91 - 11.14: 6 Bond angle restraints: 11999 Sorted by residual: angle pdb=" N THR A 198 " pdb=" CA THR A 198 " pdb=" C THR A 198 " ideal model delta sigma weight residual 112.90 101.76 11.14 1.31e+00 5.83e-01 7.23e+01 angle pdb=" N THR A 201 " pdb=" CA THR A 201 " pdb=" C THR A 201 " ideal model delta sigma weight residual 111.36 102.13 9.23 1.09e+00 8.42e-01 7.17e+01 angle pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" C VAL B 50 " ideal model delta sigma weight residual 113.43 104.43 9.00 1.09e+00 8.42e-01 6.82e+01 angle pdb=" N THR E 144 " pdb=" CA THR E 144 " pdb=" C THR E 144 " ideal model delta sigma weight residual 112.93 104.71 8.22 1.12e+00 7.97e-01 5.39e+01 angle pdb=" N LEU B 227 " pdb=" CA LEU B 227 " pdb=" C LEU B 227 " ideal model delta sigma weight residual 113.50 105.48 8.02 1.23e+00 6.61e-01 4.25e+01 ... (remaining 11994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4565 16.97 - 33.93: 504 33.93 - 50.90: 122 50.90 - 67.87: 27 67.87 - 84.84: 7 Dihedral angle restraints: 5225 sinusoidal: 2005 harmonic: 3220 Sorted by residual: dihedral pdb=" C TYR A 200 " pdb=" N TYR A 200 " pdb=" CA TYR A 200 " pdb=" CB TYR A 200 " ideal model delta harmonic sigma weight residual -122.60 -133.36 10.76 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" CA LEU E 117 " pdb=" C LEU E 117 " pdb=" N THR E 118 " pdb=" CA THR E 118 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" N TYR A 200 " pdb=" C TYR A 200 " pdb=" CA TYR A 200 " pdb=" CB TYR A 200 " ideal model delta harmonic sigma weight residual 122.80 132.98 -10.18 0 2.50e+00 1.60e-01 1.66e+01 ... (remaining 5222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1305 0.111 - 0.222: 51 0.222 - 0.333: 7 0.333 - 0.444: 2 0.444 - 0.555: 1 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA TYR A 200 " pdb=" N TYR A 200 " pdb=" C TYR A 200 " pdb=" CB TYR A 200 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.70e+00 chirality pdb=" CA SER A 145 " pdb=" N SER A 145 " pdb=" C SER A 145 " pdb=" CB SER A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA GLU B 186 " pdb=" N GLU B 186 " pdb=" C GLU B 186 " pdb=" CB GLU B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1363 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 139 " 0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C TYR A 139 " -0.068 2.00e-02 2.50e+03 pdb=" O TYR A 139 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU A 140 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 285 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A 286 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 152 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C TYR A 152 " -0.047 2.00e-02 2.50e+03 pdb=" O TYR A 152 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG A 153 " 0.016 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2176 2.79 - 3.32: 7792 3.32 - 3.85: 13651 3.85 - 4.37: 15636 4.37 - 4.90: 27478 Nonbonded interactions: 66733 Sorted by model distance: nonbonded pdb=" OG SER C 147 " pdb=" O MET C 188 " model vdw 2.266 3.040 nonbonded pdb=" O ARG C 22 " pdb=" NE2 GLN C 259 " model vdw 2.279 3.120 nonbonded pdb=" NH2 ARG E 67 " pdb=" OD1 ASP E 90 " model vdw 2.281 3.120 nonbonded pdb=" OG1 THR C 321 " pdb=" OD1 ASP C 323 " model vdw 2.299 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.300 3.040 ... (remaining 66728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.005 0.107 8845 Z= 0.366 Angle : 0.815 11.135 12001 Z= 0.508 Chirality : 0.055 0.555 1366 Planarity : 0.005 0.077 1512 Dihedral : 15.484 84.837 3146 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.23 % Favored : 93.49 % Rotamer: Outliers : 3.66 % Allowed : 2.26 % Favored : 94.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % 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: -1.57 (0.25), residues: 1091 helix: -0.47 (0.30), residues: 339 sheet: -0.48 (0.31), residues: 288 loop : -1.77 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 160 TYR 0.026 0.001 TYR A 200 PHE 0.021 0.001 PHE A 91 TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 8844) covalent geometry : angle 0.81516 (11999) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.08229 ( 2) hydrogen bonds : bond 0.22906 ( 347) hydrogen bonds : angle 7.85970 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.304 Fit side-chains REVERT: A 64 SER cc_start: 0.6766 (m) cc_final: 0.6271 (p) REVERT: A 259 ILE cc_start: 0.8667 (tp) cc_final: 0.8438 (tp) REVERT: B 53 MET cc_start: 0.6220 (OUTLIER) cc_final: 0.5978 (mmp) REVERT: B 296 TYR cc_start: 0.7513 (t80) cc_final: 0.7278 (t80) REVERT: C 308 LEU cc_start: 0.8487 (mp) cc_final: 0.8250 (mp) REVERT: E 160 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7040 (ttm-80) outliers start: 34 outliers final: 11 residues processed: 227 average time/residue: 0.0941 time to fit residues: 28.7695 Evaluate side-chains 181 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 300 ASN B 52 GLN B 269 ASN C 75 GLN C 176 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112741 restraints weight = 11577.785| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.13 r_work: 0.3192 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8845 Z= 0.152 Angle : 0.602 7.884 12001 Z= 0.315 Chirality : 0.043 0.211 1366 Planarity : 0.004 0.061 1512 Dihedral : 6.878 56.580 1240 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.94 % Allowed : 10.98 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.16 (0.25), residues: 1091 helix: 0.14 (0.30), residues: 342 sheet: -0.44 (0.30), residues: 284 loop : -1.62 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 160 TYR 0.020 0.001 TYR A 200 PHE 0.016 0.002 PHE C 151 TRP 0.012 0.001 TRP C 211 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8844) covalent geometry : angle 0.60164 (11999) SS BOND : bond 0.00348 ( 1) SS BOND : angle 1.69642 ( 2) hydrogen bonds : bond 0.04357 ( 347) hydrogen bonds : angle 5.06110 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 254 PHE cc_start: 0.8412 (t80) cc_final: 0.7935 (t80) REVERT: A 259 ILE cc_start: 0.8745 (tp) cc_final: 0.8520 (tp) REVERT: B 229 ASP cc_start: 0.8206 (m-30) cc_final: 0.7553 (m-30) REVERT: C 98 SER cc_start: 0.8662 (m) cc_final: 0.8334 (p) REVERT: C 308 LEU cc_start: 0.8805 (mp) cc_final: 0.8568 (mp) outliers start: 18 outliers final: 14 residues processed: 196 average time/residue: 0.0954 time to fit residues: 25.3766 Evaluate side-chains 186 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 300 ASN A 304 ASN C 75 GLN C 176 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.165275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111341 restraints weight = 11620.551| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.12 r_work: 0.3180 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8845 Z= 0.140 Angle : 0.572 7.343 12001 Z= 0.296 Chirality : 0.042 0.165 1366 Planarity : 0.004 0.054 1512 Dihedral : 5.949 58.185 1228 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.48 % Allowed : 13.67 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.07 (0.25), residues: 1091 helix: 0.28 (0.30), residues: 355 sheet: -0.52 (0.30), residues: 287 loop : -1.57 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 160 TYR 0.019 0.001 TYR E 190 PHE 0.015 0.001 PHE C 151 TRP 0.010 0.001 TRP C 211 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8844) covalent geometry : angle 0.57177 (11999) SS BOND : bond 0.00446 ( 1) SS BOND : angle 1.53638 ( 2) hydrogen bonds : bond 0.03834 ( 347) hydrogen bonds : angle 4.68557 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 183 TYR cc_start: 0.7441 (t80) cc_final: 0.7114 (t80) REVERT: B 53 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.6209 (mmm) REVERT: C 98 SER cc_start: 0.8486 (m) cc_final: 0.8224 (p) REVERT: E 76 LYS cc_start: 0.8864 (mmtm) cc_final: 0.8020 (tptm) outliers start: 23 outliers final: 16 residues processed: 183 average time/residue: 0.1000 time to fit residues: 24.5911 Evaluate side-chains 176 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 300 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN D 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.159819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105110 restraints weight = 11874.702| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.13 r_work: 0.3089 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 8845 Z= 0.278 Angle : 0.671 11.430 12001 Z= 0.352 Chirality : 0.046 0.244 1366 Planarity : 0.004 0.050 1512 Dihedral : 6.181 53.586 1225 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.44 % Allowed : 16.79 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.23 (0.25), residues: 1091 helix: 0.25 (0.29), residues: 349 sheet: -0.73 (0.30), residues: 286 loop : -1.65 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 22 TYR 0.022 0.002 TYR A 200 PHE 0.021 0.002 PHE C 151 TRP 0.016 0.002 TRP A 165 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 8844) covalent geometry : angle 0.67034 (11999) SS BOND : bond 0.00496 ( 1) SS BOND : angle 1.71054 ( 2) hydrogen bonds : bond 0.04638 ( 347) hydrogen bonds : angle 4.98822 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.340 Fit side-chains REVERT: A 183 TYR cc_start: 0.7475 (t80) cc_final: 0.7079 (t80) REVERT: A 304 ASN cc_start: 0.7927 (m110) cc_final: 0.7598 (t0) REVERT: B 229 ASP cc_start: 0.8144 (m-30) cc_final: 0.6928 (t70) REVERT: B 230 TYR cc_start: 0.8691 (p90) cc_final: 0.8392 (p90) REVERT: C 292 PHE cc_start: 0.8716 (m-10) cc_final: 0.8290 (m-80) REVERT: D 17 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: E 76 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8721 (mmtm) outliers start: 32 outliers final: 23 residues processed: 181 average time/residue: 0.1019 time to fit residues: 24.9905 Evaluate side-chains 177 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 204 GLN B 269 ASN C 340 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110240 restraints weight = 11732.201| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.15 r_work: 0.3167 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8845 Z= 0.116 Angle : 0.551 8.362 12001 Z= 0.285 Chirality : 0.042 0.232 1366 Planarity : 0.003 0.048 1512 Dihedral : 5.702 56.335 1224 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.58 % Allowed : 19.05 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.02 (0.25), residues: 1091 helix: 0.44 (0.29), residues: 350 sheet: -0.64 (0.30), residues: 285 loop : -1.53 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.019 0.001 TYR E 190 PHE 0.013 0.001 PHE C 199 TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8844) covalent geometry : angle 0.55040 (11999) SS BOND : bond 0.00358 ( 1) SS BOND : angle 1.78365 ( 2) hydrogen bonds : bond 0.03451 ( 347) hydrogen bonds : angle 4.56614 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.6956 (m170) cc_final: 0.6523 (m170) REVERT: A 183 TYR cc_start: 0.7450 (t80) cc_final: 0.7033 (t80) REVERT: B 53 MET cc_start: 0.6044 (mmm) cc_final: 0.5690 (mmp) REVERT: B 229 ASP cc_start: 0.8026 (m-30) cc_final: 0.6240 (t0) REVERT: B 230 TYR cc_start: 0.8696 (p90) cc_final: 0.8274 (p90) REVERT: B 243 MET cc_start: 0.8962 (tpp) cc_final: 0.8498 (tpp) REVERT: C 118 ASP cc_start: 0.8463 (p0) cc_final: 0.8193 (p0) REVERT: C 292 PHE cc_start: 0.8692 (m-10) cc_final: 0.8284 (m-80) REVERT: C 331 SER cc_start: 0.9424 (p) cc_final: 0.9157 (p) REVERT: E 93 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7471 (tpt) outliers start: 24 outliers final: 18 residues processed: 184 average time/residue: 0.0963 time to fit residues: 24.0471 Evaluate side-chains 179 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN C 13 GLN C 75 GLN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.161644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107308 restraints weight = 11672.055| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.11 r_work: 0.3125 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8845 Z= 0.191 Angle : 0.605 10.095 12001 Z= 0.313 Chirality : 0.043 0.204 1366 Planarity : 0.004 0.047 1512 Dihedral : 5.706 55.414 1224 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.66 % Allowed : 18.73 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.05 (0.25), residues: 1091 helix: 0.45 (0.29), residues: 356 sheet: -0.74 (0.30), residues: 285 loop : -1.53 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 214 TYR 0.020 0.002 TYR A 200 PHE 0.019 0.002 PHE E 212 TRP 0.013 0.001 TRP A 165 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8844) covalent geometry : angle 0.60423 (11999) SS BOND : bond 0.00356 ( 1) SS BOND : angle 1.95627 ( 2) hydrogen bonds : bond 0.03816 ( 347) hydrogen bonds : angle 4.66646 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 TYR cc_start: 0.7437 (t80) cc_final: 0.7224 (t80) REVERT: B 53 MET cc_start: 0.6153 (mmm) cc_final: 0.5780 (mmp) REVERT: B 229 ASP cc_start: 0.8015 (m-30) cc_final: 0.6716 (t0) REVERT: B 230 TYR cc_start: 0.8666 (p90) cc_final: 0.8294 (p90) REVERT: C 118 ASP cc_start: 0.8571 (p0) cc_final: 0.8324 (p0) REVERT: C 291 ASP cc_start: 0.7850 (t0) cc_final: 0.7645 (t0) REVERT: C 292 PHE cc_start: 0.8727 (m-10) cc_final: 0.8306 (m-80) REVERT: E 67 ARG cc_start: 0.7775 (mtm110) cc_final: 0.7561 (mtm110) REVERT: E 76 LYS cc_start: 0.8629 (mmtm) cc_final: 0.7916 (tptm) REVERT: E 140 MET cc_start: 0.9004 (mmm) cc_final: 0.8726 (mmm) outliers start: 34 outliers final: 26 residues processed: 184 average time/residue: 0.1069 time to fit residues: 26.2423 Evaluate side-chains 187 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS B 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.164333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110037 restraints weight = 11724.728| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.14 r_work: 0.3162 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8845 Z= 0.121 Angle : 0.566 9.851 12001 Z= 0.289 Chirality : 0.042 0.201 1366 Planarity : 0.003 0.043 1512 Dihedral : 5.500 56.655 1222 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.12 % Allowed : 20.13 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.89 (0.26), residues: 1091 helix: 0.69 (0.30), residues: 350 sheet: -0.69 (0.30), residues: 285 loop : -1.47 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 160 TYR 0.018 0.001 TYR E 190 PHE 0.017 0.001 PHE E 212 TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8844) covalent geometry : angle 0.56516 (11999) SS BOND : bond 0.00367 ( 1) SS BOND : angle 1.66667 ( 2) hydrogen bonds : bond 0.03345 ( 347) hydrogen bonds : angle 4.50154 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 MET cc_start: 0.6067 (mmm) cc_final: 0.5594 (mmp) REVERT: C 118 ASP cc_start: 0.8473 (p0) cc_final: 0.8251 (p0) REVERT: C 192 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8450 (pp) REVERT: C 292 PHE cc_start: 0.8714 (m-10) cc_final: 0.8316 (m-80) REVERT: D 47 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: E 76 LYS cc_start: 0.8644 (mmtm) cc_final: 0.7918 (tptm) REVERT: E 93 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7519 (tpt) REVERT: E 140 MET cc_start: 0.8983 (mmm) cc_final: 0.8709 (mmm) outliers start: 29 outliers final: 23 residues processed: 192 average time/residue: 0.0979 time to fit residues: 25.2476 Evaluate side-chains 185 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 0.5980 chunk 98 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN C 75 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112028 restraints weight = 11498.673| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.11 r_work: 0.3188 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8845 Z= 0.108 Angle : 0.568 11.051 12001 Z= 0.287 Chirality : 0.042 0.275 1366 Planarity : 0.003 0.041 1512 Dihedral : 5.361 58.248 1222 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.12 % Allowed : 20.78 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1091 helix: 0.83 (0.30), residues: 349 sheet: -0.65 (0.30), residues: 285 loop : -1.42 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.018 0.001 TYR E 190 PHE 0.014 0.001 PHE E 212 TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8844) covalent geometry : angle 0.56761 (11999) SS BOND : bond 0.00352 ( 1) SS BOND : angle 1.55307 ( 2) hydrogen bonds : bond 0.03148 ( 347) hydrogen bonds : angle 4.40398 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 HIS cc_start: 0.7059 (m90) cc_final: 0.6423 (m170) REVERT: A 183 TYR cc_start: 0.7266 (t80) cc_final: 0.6874 (t80) REVERT: B 53 MET cc_start: 0.6154 (mmm) cc_final: 0.5650 (mmp) REVERT: C 118 ASP cc_start: 0.8412 (p0) cc_final: 0.8207 (p0) REVERT: C 292 PHE cc_start: 0.8713 (m-10) cc_final: 0.8370 (m-80) REVERT: D 47 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: E 82 GLN cc_start: 0.7360 (mm110) cc_final: 0.7113 (mm-40) REVERT: E 93 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7566 (tpt) REVERT: E 140 MET cc_start: 0.8990 (mmm) cc_final: 0.8744 (mmm) outliers start: 29 outliers final: 22 residues processed: 190 average time/residue: 0.1036 time to fit residues: 26.2616 Evaluate side-chains 187 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.165016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110750 restraints weight = 11473.305| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.11 r_work: 0.3172 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8845 Z= 0.125 Angle : 0.584 11.318 12001 Z= 0.294 Chirality : 0.042 0.273 1366 Planarity : 0.003 0.040 1512 Dihedral : 5.327 59.693 1222 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.55 % Allowed : 20.67 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.26), residues: 1091 helix: 0.91 (0.30), residues: 348 sheet: -0.64 (0.30), residues: 285 loop : -1.42 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 160 TYR 0.018 0.001 TYR E 190 PHE 0.014 0.001 PHE E 68 TRP 0.013 0.001 TRP A 165 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8844) covalent geometry : angle 0.58364 (11999) SS BOND : bond 0.00424 ( 1) SS BOND : angle 1.75576 ( 2) hydrogen bonds : bond 0.03240 ( 347) hydrogen bonds : angle 4.38271 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 CYS cc_start: 0.8176 (t) cc_final: 0.7734 (t) REVERT: A 156 HIS cc_start: 0.7056 (m90) cc_final: 0.6650 (m170) REVERT: A 183 TYR cc_start: 0.7256 (t80) cc_final: 0.6857 (t80) REVERT: B 24 ARG cc_start: 0.7482 (ttp-170) cc_final: 0.7055 (ttp-170) REVERT: B 52 GLN cc_start: 0.6236 (OUTLIER) cc_final: 0.5526 (pt0) REVERT: B 53 MET cc_start: 0.6218 (mmm) cc_final: 0.5858 (mmp) REVERT: B 229 ASP cc_start: 0.7863 (m-30) cc_final: 0.6701 (t0) REVERT: C 118 ASP cc_start: 0.8430 (p0) cc_final: 0.8217 (p0) REVERT: C 292 PHE cc_start: 0.8699 (m-10) cc_final: 0.8307 (m-80) REVERT: D 47 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: E 76 LYS cc_start: 0.8593 (mmtm) cc_final: 0.7904 (tptm) REVERT: E 93 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7534 (tpt) REVERT: E 140 MET cc_start: 0.8965 (mmm) cc_final: 0.8693 (mmm) outliers start: 33 outliers final: 27 residues processed: 187 average time/residue: 0.1024 time to fit residues: 25.9108 Evaluate side-chains 189 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 102 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109379 restraints weight = 11387.811| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.21 r_work: 0.3138 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8845 Z= 0.108 Angle : 0.580 10.968 12001 Z= 0.293 Chirality : 0.042 0.270 1366 Planarity : 0.003 0.040 1512 Dihedral : 5.265 58.270 1222 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.12 % Allowed : 21.64 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.65 (0.26), residues: 1091 helix: 0.98 (0.30), residues: 349 sheet: -0.62 (0.30), residues: 287 loop : -1.37 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 205 TYR 0.018 0.001 TYR E 190 PHE 0.015 0.001 PHE E 68 TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8844) covalent geometry : angle 0.57959 (11999) SS BOND : bond 0.00383 ( 1) SS BOND : angle 2.26578 ( 2) hydrogen bonds : bond 0.03126 ( 347) hydrogen bonds : angle 4.33570 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 CYS cc_start: 0.8101 (t) cc_final: 0.7606 (t) REVERT: A 156 HIS cc_start: 0.6928 (m90) cc_final: 0.6422 (m170) REVERT: A 177 PHE cc_start: 0.6951 (m-80) cc_final: 0.6688 (m-80) REVERT: A 183 TYR cc_start: 0.7263 (t80) cc_final: 0.6869 (t80) REVERT: A 299 PHE cc_start: 0.9012 (t80) cc_final: 0.8783 (t80) REVERT: B 52 GLN cc_start: 0.6151 (OUTLIER) cc_final: 0.5500 (pt0) REVERT: B 53 MET cc_start: 0.6015 (mmm) cc_final: 0.5722 (mmp) REVERT: B 229 ASP cc_start: 0.7744 (m-30) cc_final: 0.6591 (t0) REVERT: B 304 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 118 ASP cc_start: 0.8390 (p0) cc_final: 0.8181 (p0) REVERT: C 291 ASP cc_start: 0.7569 (t0) cc_final: 0.7259 (p0) REVERT: D 47 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: E 76 LYS cc_start: 0.8501 (mmtm) cc_final: 0.7725 (tptm) REVERT: E 93 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7369 (tpt) REVERT: E 140 MET cc_start: 0.8878 (mmm) cc_final: 0.8551 (mmm) outliers start: 29 outliers final: 24 residues processed: 189 average time/residue: 0.1011 time to fit residues: 25.9101 Evaluate side-chains 189 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.0020 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110772 restraints weight = 11400.293| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.23 r_work: 0.3158 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8845 Z= 0.101 Angle : 0.580 10.650 12001 Z= 0.290 Chirality : 0.042 0.269 1366 Planarity : 0.003 0.040 1512 Dihedral : 5.114 56.450 1222 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.05 % Allowed : 23.25 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.55 (0.26), residues: 1091 helix: 1.09 (0.31), residues: 348 sheet: -0.56 (0.30), residues: 287 loop : -1.33 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 67 TYR 0.018 0.001 TYR E 190 PHE 0.024 0.001 PHE E 212 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8844) covalent geometry : angle 0.57978 (11999) SS BOND : bond 0.00295 ( 1) SS BOND : angle 2.24499 ( 2) hydrogen bonds : bond 0.03013 ( 347) hydrogen bonds : angle 4.20961 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.25 seconds wall clock time: 37 minutes 43.37 seconds (2263.37 seconds total)