Starting phenix.real_space_refine on Thu Jul 2 15:35:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w2z_32268/07_2026/7w2z_32268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w2z_32268/07_2026/7w2z_32268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w2z_32268/07_2026/7w2z_32268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w2z_32268/07_2026/7w2z_32268.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w2z_32268/07_2026/7w2z_32268.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w2z_32268/07_2026/7w2z_32268.cif" model { file = "/net/cci-nas-00/data/ceres_data/7w2z_32268/07_2026/7w2z_32268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w2z_32268/07_2026/7w2z_32268.cif" } resolution = 2.8 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= 0.008 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 61 5.16 5 C 5812 2.51 5 N 1544 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1691 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 2 Chain: "R" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2421 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "L" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 131 Unusual residues: {'K4Q': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11, None: 1} Not linked: pdbres="K4Q L 3 " pdbres="PHE L 4 " Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 9080 At special positions: 0 Unit cell: (109.512, 119.652, 126.75, 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 61 16.00 O 1663 8.00 N 1544 7.00 C 5812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 466.6 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.554A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.320A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.865A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.050A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.524A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 71 removed outlier: 3.947A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL R 56 " --> pdb=" O ALA R 52 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET R 65 " --> pdb=" O ASN R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.586A pdb=" N ARG R 75 " --> pdb=" O ARG R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 76 through 95 removed outlier: 3.937A pdb=" N PHE R 93 " --> pdb=" O ASP R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 105 removed outlier: 3.510A pdb=" N ASP R 99 " --> pdb=" O CYS R 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU R 100 " --> pdb=" O MET R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 147 removed outlier: 3.734A pdb=" N LEU R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 145 " --> pdb=" O ARG R 141 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 175 removed outlier: 3.632A pdb=" N PHE R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 181 Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 208 through 218 removed outlier: 3.673A pdb=" N TRP R 215 " --> pdb=" O THR R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 240 removed outlier: 3.577A pdb=" N LEU R 223 " --> pdb=" O ILE R 219 " (cutoff:3.500A) Proline residue: R 224 - end of helix removed outlier: 3.592A pdb=" N CYS R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL R 230 " --> pdb=" O PHE R 226 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER R 233 " --> pdb=" O THR R 229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG R 237 " --> pdb=" O SER R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 281 removed outlier: 3.596A pdb=" N VAL R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 281 through 289 Processing helix chain 'R' and resid 299 through 304 removed outlier: 3.633A pdb=" N TYR R 303 " --> pdb=" O GLN R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 315 removed outlier: 3.677A pdb=" N VAL R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 323 removed outlier: 3.907A pdb=" N TYR R 323 " --> pdb=" O ASN R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 339 removed outlier: 3.547A pdb=" N ARG R 331 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 332 " --> pdb=" O LYS R 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 22 removed outlier: 4.085A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.542A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.506A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.972A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.725A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.595A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'L' and resid 8 through 14 removed outlier: 3.881A pdb=" N VAL L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 9.069A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 182 through 185 removed outlier: 3.647A pdb=" N ARG R 199 " --> pdb=" O GLY R 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.811A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.298A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.566A pdb=" N VAL S 135 " --> pdb=" O LYS S 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.489A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.841A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.817A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.767A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.945A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.683A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.455A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1104 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: 1.35 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 2 1.21 - 1.37: 3077 1.37 - 1.52: 3750 1.52 - 1.67: 2359 1.67 - 1.82: 86 Bond restraints: 9274 Sorted by residual: bond pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 1.335 1.062 0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C08 K4Q L 3 " pdb=" O09 K4Q L 3 " ideal model delta sigma weight residual 1.204 1.404 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" CB VAL B 71 " pdb=" CG2 VAL B 71 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.24e+01 bond pdb=" C VAL S 12 " pdb=" N GLN S 13 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.60e-02 3.91e+03 1.19e+01 bond pdb=" C MET R 96 " pdb=" N PRO R 97 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.36e-02 5.41e+03 9.51e+00 ... (remaining 9269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.82: 12551 6.82 - 13.64: 15 13.64 - 20.46: 2 20.46 - 27.29: 0 27.29 - 34.11: 2 Bond angle restraints: 12570 Sorted by residual: angle pdb=" C07 K4Q L 3 " pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 118.23 84.12 34.11 3.00e+00 1.11e-01 1.29e+02 angle pdb=" O09 K4Q L 3 " pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 117.69 151.08 -33.39 3.00e+00 1.11e-01 1.24e+02 angle pdb=" N VAL R 212 " pdb=" CA VAL R 212 " pdb=" C VAL R 212 " ideal model delta sigma weight residual 111.00 103.44 7.56 1.09e+00 8.42e-01 4.81e+01 angle pdb=" N LYS R 117 " pdb=" CA LYS R 117 " pdb=" C LYS R 117 " ideal model delta sigma weight residual 111.69 104.40 7.29 1.23e+00 6.61e-01 3.51e+01 angle pdb=" N ASN S 182 " pdb=" CA ASN S 182 " pdb=" C ASN S 182 " ideal model delta sigma weight residual 109.15 117.61 -8.46 1.44e+00 4.82e-01 3.45e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 5332 31.38 - 62.75: 129 62.75 - 94.13: 14 94.13 - 125.51: 2 125.51 - 156.88: 1 Dihedral angle restraints: 5478 sinusoidal: 2141 harmonic: 3337 Sorted by residual: dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N TYR A 354 " pdb=" CA TYR A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" C04 K4Q L 3 " pdb=" C05 K4Q L 3 " pdb=" C06 K4Q L 3 " pdb=" C07 K4Q L 3 " ideal model delta sinusoidal sigma weight residual 182.71 25.83 156.88 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" CA PHE A 260 " pdb=" C PHE A 260 " pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1285 0.097 - 0.194: 130 0.194 - 0.290: 17 0.290 - 0.387: 2 0.387 - 0.484: 1 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA MET S 180 " pdb=" N MET S 180 " pdb=" C MET S 180 " pdb=" CB MET S 180 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CA LYS A 46 " pdb=" N LYS A 46 " pdb=" C LYS A 46 " pdb=" CB LYS A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ARG S 179 " pdb=" N ARG S 179 " pdb=" C ARG S 179 " pdb=" CB ARG S 179 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 1432 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 K4Q L 3 " 0.018 2.00e-02 2.50e+03 1.03e-01 1.07e+02 pdb=" C08 K4Q L 3 " -0.173 2.00e-02 2.50e+03 pdb=" O09 K4Q L 3 " 0.069 2.00e-02 2.50e+03 pdb=" O10 K4Q L 3 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 107 " -0.100 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO R 108 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO R 108 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO R 108 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 277 " 0.050 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO R 278 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO R 278 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 278 " 0.042 5.00e-02 4.00e+02 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 107 2.64 - 3.21: 7511 3.21 - 3.77: 13404 3.77 - 4.34: 19629 4.34 - 4.90: 32621 Nonbonded interactions: 73272 Sorted by model distance: nonbonded pdb=" O ASN A 43 " pdb=" ND2 ASN A 43 " model vdw 2.078 3.120 nonbonded pdb=" OD2 ASP R 99 " pdb=" OH TYR R 313 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU R 197 " pdb=" OG SER L 6 " model vdw 2.258 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.290 3.040 ... (remaining 73267 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: 0.470 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.010 0.273 9279 Z= 0.442 Angle : 1.135 34.107 12576 Z= 0.608 Chirality : 0.064 0.484 1435 Planarity : 0.009 0.150 1577 Dihedral : 14.533 156.882 3313 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 0.82 % Allowed : 6.53 % Favored : 92.65 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % 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: -4.01 (0.20), residues: 1132 helix: -4.36 (0.12), residues: 390 sheet: -0.81 (0.28), residues: 295 loop : -2.09 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 67 TYR 0.048 0.003 TYR B 105 PHE 0.024 0.003 PHE B 234 TRP 0.015 0.003 TRP R 276 HIS 0.008 0.002 HIS R 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.42 ( 9274) covalent geometry : angle 1.13344 / 0.61 (12570) SS BOND : bond 0.01293 / 0.62 ( 3) SS BOND : angle 2.72522 / 1.42 ( 6) hydrogen bonds : bond 0.28360 / 18.65 ( 382) hydrogen bonds : angle 9.72698 / 6.63 ( 1104) Misc. bond : bond 0.10224 / 5.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.272 Fit side-chains REVERT: A 35 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8227 (mtpt) REVERT: A 209 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7636 (tpp80) REVERT: A 252 ASP cc_start: 0.7529 (t0) cc_final: 0.7306 (t0) REVERT: A 271 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7507 (mptp) REVERT: A 309 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7213 (mt-10) REVERT: R 65 MET cc_start: 0.6998 (mtp) cc_final: 0.6746 (mtp) REVERT: R 70 ARG cc_start: 0.6766 (ttt180) cc_final: 0.6444 (ttt90) REVERT: R 326 MET cc_start: 0.6695 (mmm) cc_final: 0.6355 (mmt) REVERT: R 328 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7113 (mptp) REVERT: G 21 MET cc_start: 0.6579 (tpt) cc_final: 0.6049 (pp-130) REVERT: G 38 MET cc_start: 0.8176 (ttp) cc_final: 0.7920 (ttp) REVERT: S 3 GLN cc_start: 0.7676 (pt0) cc_final: 0.7438 (pt0) REVERT: S 147 CYS cc_start: 0.7079 (t) cc_final: 0.6755 (t) REVERT: B 254 ASP cc_start: 0.8484 (p0) cc_final: 0.8156 (p0) REVERT: B 258 ASP cc_start: 0.7730 (t0) cc_final: 0.7195 (t70) outliers start: 8 outliers final: 1 residues processed: 141 average time/residue: 0.5180 time to fit residues: 77.6384 Evaluate side-chains 109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 312 ASN A 330 ASN R 79 ASN R 196 ASN ** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 324 ASN G 11 GLN S 130 GLN B 13 GLN B 32 GLN B 155 ASN B 230 ASN B 239 ASN B 340 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130922 restraints weight = 10447.824| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.01 r_work: 0.3362 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9279 Z= 0.142 Angle : 0.601 7.196 12576 Z= 0.319 Chirality : 0.044 0.247 1435 Planarity : 0.006 0.136 1577 Dihedral : 7.697 108.377 1274 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 3.06 % Allowed : 10.92 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -2.10 (0.23), residues: 1132 helix: -1.87 (0.22), residues: 385 sheet: -0.19 (0.30), residues: 294 loop : -1.61 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 87 TYR 0.021 0.002 TYR A 297 PHE 0.021 0.001 PHE R 119 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9274) covalent geometry : angle 0.59927 / 0.32 (12570) SS BOND : bond 0.00484 / 0.20 ( 3) SS BOND : angle 1.96694 / 1.16 ( 6) hydrogen bonds : bond 0.04817 / 3.10 ( 382) hydrogen bonds : angle 5.05596 / 3.49 ( 1104) Misc. bond : bond 0.00055 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.331 Fit side-chains REVERT: A 21 LYS cc_start: 0.8174 (tttt) cc_final: 0.7880 (ttmm) REVERT: A 35 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8083 (mtpt) REVERT: A 209 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.6389 (ttp-110) REVERT: A 295 ASN cc_start: 0.7525 (t0) cc_final: 0.6813 (m110) REVERT: A 309 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7240 (mt-10) REVERT: R 70 ARG cc_start: 0.6898 (ttt180) cc_final: 0.6354 (ttt90) REVERT: R 308 SER cc_start: 0.7748 (OUTLIER) cc_final: 0.7383 (m) REVERT: R 326 MET cc_start: 0.7561 (mmm) cc_final: 0.7138 (mmt) REVERT: R 328 LYS cc_start: 0.7473 (mmtt) cc_final: 0.7035 (mptp) REVERT: S 83 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7975 (mtp) REVERT: B 219 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7111 (mmt90) REVERT: B 254 ASP cc_start: 0.8800 (p0) cc_final: 0.8593 (p0) REVERT: B 258 ASP cc_start: 0.7955 (t0) cc_final: 0.7209 (t70) REVERT: B 260 GLU cc_start: 0.7975 (pt0) cc_final: 0.7678 (tt0) outliers start: 30 outliers final: 12 residues processed: 140 average time/residue: 0.4845 time to fit residues: 72.5811 Evaluate side-chains 116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 69 optimal weight: 0.0270 chunk 70 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 330 ASN ** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 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 = 0.3838 r_free = 0.3838 target = 0.161588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124740 restraints weight = 9871.630| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.06 r_work: 0.3220 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9279 Z= 0.217 Angle : 0.650 9.205 12576 Z= 0.341 Chirality : 0.046 0.221 1435 Planarity : 0.006 0.132 1577 Dihedral : 7.340 96.455 1272 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 3.67 % Allowed : 13.57 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.36 (0.24), residues: 1132 helix: -0.85 (0.25), residues: 387 sheet: -0.04 (0.30), residues: 295 loop : -1.40 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 87 TYR 0.018 0.002 TYR S 178 PHE 0.030 0.002 PHE R 119 TRP 0.014 0.002 TRP R 109 HIS 0.006 0.002 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 ( 9274) covalent geometry : angle 0.64722 / 0.34 (12570) SS BOND : bond 0.00487 / 0.18 ( 3) SS BOND : angle 2.87834 / 1.67 ( 6) hydrogen bonds : bond 0.04906 / 3.18 ( 382) hydrogen bonds : angle 4.93291 / 3.40 ( 1104) Misc. bond : bond 0.00079 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 35 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8213 (mtpt) REVERT: A 209 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.6395 (ttp-110) REVERT: A 248 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7334 (mt) REVERT: A 309 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7367 (mt-10) REVERT: R 70 ARG cc_start: 0.6867 (ttt180) cc_final: 0.6339 (ttt90) REVERT: R 264 MET cc_start: 0.6680 (mmm) cc_final: 0.6363 (mmm) REVERT: R 308 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7605 (m) REVERT: R 328 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7205 (mptp) REVERT: G 42 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: S 83 MET cc_start: 0.8688 (mtp) cc_final: 0.7914 (mtp) REVERT: B 219 ARG cc_start: 0.7655 (mtm180) cc_final: 0.7163 (mmt90) REVERT: B 254 ASP cc_start: 0.8895 (p0) cc_final: 0.8681 (p0) REVERT: B 258 ASP cc_start: 0.7938 (t0) cc_final: 0.7251 (t70) REVERT: B 260 GLU cc_start: 0.8267 (pt0) cc_final: 0.7997 (tt0) outliers start: 36 outliers final: 17 residues processed: 131 average time/residue: 0.4692 time to fit residues: 65.8755 Evaluate side-chains 122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 173 CYS Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.9990 chunk 78 optimal weight: 0.0000 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 257 ASN ** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 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 = 0.3925 r_free = 0.3925 target = 0.167823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133678 restraints weight = 10498.877| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.20 r_work: 0.3388 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 9279 Z= 0.098 Angle : 0.517 5.616 12576 Z= 0.272 Chirality : 0.041 0.216 1435 Planarity : 0.005 0.127 1577 Dihedral : 6.578 74.619 1272 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 2.65 % Allowed : 15.51 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.61 (0.24), residues: 1132 helix: 0.17 (0.27), residues: 389 sheet: 0.16 (0.30), residues: 288 loop : -1.20 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 87 TYR 0.019 0.001 TYR R 128 PHE 0.014 0.001 PHE R 119 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 9274) covalent geometry : angle 0.51551 / 0.27 (12570) SS BOND : bond 0.00324 / 0.13 ( 3) SS BOND : angle 1.92875 / 1.14 ( 6) hydrogen bonds : bond 0.03414 / 2.21 ( 382) hydrogen bonds : angle 4.29686 / 2.97 ( 1104) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.329 Fit side-chains REVERT: A 25 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.5938 (mp0) REVERT: A 35 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8024 (mtpt) REVERT: A 55 ILE cc_start: 0.7559 (mp) cc_final: 0.7353 (mp) REVERT: A 209 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.6160 (ttp-110) REVERT: A 309 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7219 (mt-10) REVERT: A 323 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8206 (mtm) REVERT: R 70 ARG cc_start: 0.6768 (ttt180) cc_final: 0.6511 (ttt90) REVERT: R 264 MET cc_start: 0.6335 (mmm) cc_final: 0.6025 (mmm) REVERT: R 308 SER cc_start: 0.7471 (OUTLIER) cc_final: 0.6993 (m) REVERT: R 328 LYS cc_start: 0.7337 (mmtt) cc_final: 0.7005 (mptp) REVERT: S 83 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7874 (mtp) REVERT: B 219 ARG cc_start: 0.7537 (mtm180) cc_final: 0.7013 (mmt90) REVERT: B 258 ASP cc_start: 0.7740 (t0) cc_final: 0.6956 (t70) REVERT: B 260 GLU cc_start: 0.8010 (pt0) cc_final: 0.7284 (tt0) outliers start: 26 outliers final: 9 residues processed: 131 average time/residue: 0.5349 time to fit residues: 74.9397 Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 302 GLN ** G 11 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 = 0.3897 r_free = 0.3897 target = 0.165033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130991 restraints weight = 10514.342| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.16 r_work: 0.3353 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9279 Z= 0.140 Angle : 0.556 7.296 12576 Z= 0.291 Chirality : 0.043 0.205 1435 Planarity : 0.005 0.125 1577 Dihedral : 6.602 72.216 1272 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 4.08 % Allowed : 14.69 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.41 (0.25), residues: 1132 helix: 0.38 (0.27), residues: 389 sheet: 0.14 (0.30), residues: 288 loop : -1.02 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 87 TYR 0.015 0.001 TYR S 178 PHE 0.017 0.001 PHE R 119 TRP 0.016 0.001 TRP R 109 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9274) covalent geometry : angle 0.55325 / 0.29 (12570) SS BOND : bond 0.00319 / 0.12 ( 3) SS BOND : angle 2.47163 / 1.47 ( 6) hydrogen bonds : bond 0.03760 / 2.43 ( 382) hydrogen bonds : angle 4.34410 / 2.99 ( 1104) Misc. bond : bond 0.00055 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.226 Fit side-chains REVERT: A 5 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7697 (mm) REVERT: A 17 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7537 (mttt) REVERT: A 25 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: A 35 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8056 (mtpt) REVERT: A 209 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.6216 (ttp-110) REVERT: A 309 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7355 (mt-10) REVERT: R 70 ARG cc_start: 0.6833 (ttt180) cc_final: 0.6478 (ttt90) REVERT: R 264 MET cc_start: 0.6491 (mmm) cc_final: 0.6204 (mmm) REVERT: R 308 SER cc_start: 0.7565 (OUTLIER) cc_final: 0.7082 (m) REVERT: R 328 LYS cc_start: 0.7357 (mmtt) cc_final: 0.7026 (mptp) REVERT: G 42 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6489 (tp30) REVERT: S 83 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: B 219 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7055 (mmt90) REVERT: B 258 ASP cc_start: 0.7692 (t0) cc_final: 0.7110 (t70) REVERT: B 260 GLU cc_start: 0.8114 (pt0) cc_final: 0.7705 (tt0) outliers start: 40 outliers final: 18 residues processed: 124 average time/residue: 0.5665 time to fit residues: 74.6470 Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 173 CYS Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 280 HIS ** G 11 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 = 0.3930 r_free = 0.3930 target = 0.168247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133710 restraints weight = 10448.928| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.99 r_work: 0.3402 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9279 Z= 0.099 Angle : 0.505 6.010 12576 Z= 0.264 Chirality : 0.041 0.201 1435 Planarity : 0.005 0.123 1577 Dihedral : 6.228 62.088 1272 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 3.47 % Allowed : 15.82 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.11 (0.25), residues: 1132 helix: 0.73 (0.27), residues: 395 sheet: 0.21 (0.30), residues: 287 loop : -0.90 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 87 TYR 0.015 0.001 TYR A 297 PHE 0.015 0.001 PHE R 119 TRP 0.014 0.001 TRP R 109 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9274) covalent geometry : angle 0.50278 / 0.26 (12570) SS BOND : bond 0.00315 / 0.14 ( 3) SS BOND : angle 1.99169 / 1.19 ( 6) hydrogen bonds : bond 0.03156 / 2.04 ( 382) hydrogen bonds : angle 4.08106 / 2.81 ( 1104) Misc. bond : bond 0.00031 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.349 Fit side-chains REVERT: A 17 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7433 (mttt) REVERT: A 25 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.5878 (mp0) REVERT: A 35 LYS cc_start: 0.8465 (mtmm) cc_final: 0.7950 (mtpt) REVERT: A 209 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6159 (ttp-110) REVERT: A 244 MET cc_start: 0.7441 (tpp) cc_final: 0.7131 (tpp) REVERT: A 248 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7293 (mt) REVERT: A 296 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7166 (p) REVERT: A 309 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 323 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8218 (mtm) REVERT: R 70 ARG cc_start: 0.6802 (ttt180) cc_final: 0.6523 (ttt90) REVERT: R 240 TRP cc_start: 0.6304 (OUTLIER) cc_final: 0.5805 (t60) REVERT: R 264 MET cc_start: 0.6358 (mmm) cc_final: 0.6092 (mmm) REVERT: R 328 LYS cc_start: 0.7285 (mmtt) cc_final: 0.6926 (mptp) REVERT: G 42 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6440 (tp30) REVERT: S 83 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: B 96 ARG cc_start: 0.7907 (mpt-90) cc_final: 0.7565 (mtt90) REVERT: B 212 ASP cc_start: 0.8242 (t0) cc_final: 0.8028 (t0) REVERT: B 219 ARG cc_start: 0.7514 (mtm180) cc_final: 0.7093 (mmt90) REVERT: B 258 ASP cc_start: 0.7728 (t0) cc_final: 0.7161 (t70) REVERT: B 260 GLU cc_start: 0.7969 (pt0) cc_final: 0.7536 (tt0) outliers start: 34 outliers final: 14 residues processed: 118 average time/residue: 0.5499 time to fit residues: 69.0793 Evaluate side-chains 112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 240 TRP Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 280 HIS ** G 11 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 = 0.3872 r_free = 0.3872 target = 0.164975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127964 restraints weight = 9964.161| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.16 r_work: 0.3262 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9279 Z= 0.143 Angle : 0.550 7.473 12576 Z= 0.287 Chirality : 0.043 0.191 1435 Planarity : 0.005 0.123 1577 Dihedral : 6.325 61.769 1272 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 3.98 % Allowed : 15.41 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1132 helix: 0.72 (0.27), residues: 389 sheet: 0.18 (0.30), residues: 291 loop : -0.82 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 87 TYR 0.016 0.001 TYR S 178 PHE 0.017 0.001 PHE R 119 TRP 0.020 0.001 TRP R 109 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 9274) covalent geometry : angle 0.54763 / 0.29 (12570) SS BOND : bond 0.00302 / 0.12 ( 3) SS BOND : angle 2.48127 / 1.42 ( 6) hydrogen bonds : bond 0.03649 / 2.35 ( 382) hydrogen bonds : angle 4.24129 / 2.91 ( 1104) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 17 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7647 (mttt) REVERT: A 35 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8093 (mtpt) REVERT: A 209 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.6256 (ttp-110) REVERT: A 244 MET cc_start: 0.7361 (tpp) cc_final: 0.7084 (tpp) REVERT: A 248 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7339 (mt) REVERT: A 296 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7124 (p) REVERT: R 70 ARG cc_start: 0.6908 (ttt180) cc_final: 0.6590 (ttt90) REVERT: R 213 MET cc_start: 0.6414 (OUTLIER) cc_final: 0.6007 (tpp) REVERT: R 240 TRP cc_start: 0.6399 (OUTLIER) cc_final: 0.5905 (t60) REVERT: R 264 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6385 (mmm) REVERT: R 308 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7147 (m) REVERT: R 328 LYS cc_start: 0.7428 (mmtt) cc_final: 0.6959 (mptp) REVERT: G 42 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6447 (tp30) REVERT: S 67 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.5660 (ptm-80) REVERT: S 83 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7937 (mtp) REVERT: B 258 ASP cc_start: 0.7751 (t0) cc_final: 0.7172 (t70) REVERT: B 260 GLU cc_start: 0.8147 (pt0) cc_final: 0.7775 (tt0) outliers start: 39 outliers final: 14 residues processed: 114 average time/residue: 0.5337 time to fit residues: 65.0455 Evaluate side-chains 111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 173 CYS Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 240 TRP Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 280 HIS ** G 11 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 = 0.3881 r_free = 0.3881 target = 0.165951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129123 restraints weight = 9907.085| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.17 r_work: 0.3273 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9279 Z= 0.123 Angle : 0.589 24.610 12576 Z= 0.289 Chirality : 0.043 0.278 1435 Planarity : 0.006 0.195 1577 Dihedral : 6.238 59.516 1272 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 3.47 % Allowed : 16.12 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.01 (0.25), residues: 1132 helix: 0.79 (0.27), residues: 395 sheet: 0.26 (0.30), residues: 292 loop : -0.79 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 87 TYR 0.022 0.001 TYR R 284 PHE 0.018 0.001 PHE R 119 TRP 0.015 0.001 TRP R 109 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 9274) covalent geometry : angle 0.58587 / 0.29 (12570) SS BOND : bond 0.00410 / 0.19 ( 3) SS BOND : angle 2.68631 / 1.62 ( 6) hydrogen bonds : bond 0.03418 / 2.20 ( 382) hydrogen bonds : angle 4.20840 / 2.88 ( 1104) Misc. bond : bond 0.00048 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.325 Fit side-chains REVERT: A 5 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7773 (mm) REVERT: A 17 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7637 (mttt) REVERT: A 25 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.5807 (mp0) REVERT: A 35 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8071 (mtpt) REVERT: A 209 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.6224 (ttp-110) REVERT: A 244 MET cc_start: 0.7344 (tpp) cc_final: 0.7113 (tpp) REVERT: A 248 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7350 (mt) REVERT: A 296 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.7055 (p) REVERT: R 70 ARG cc_start: 0.6912 (ttt180) cc_final: 0.6613 (ttt90) REVERT: R 213 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.5981 (tpp) REVERT: R 240 TRP cc_start: 0.6382 (OUTLIER) cc_final: 0.5886 (t60) REVERT: R 264 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6344 (mmm) REVERT: R 328 LYS cc_start: 0.7423 (mmtt) cc_final: 0.6939 (mptp) REVERT: G 42 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6468 (tp30) REVERT: S 67 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.5568 (ptm-80) REVERT: S 83 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8061 (mtp) REVERT: B 258 ASP cc_start: 0.7753 (t0) cc_final: 0.7169 (t70) REVERT: B 260 GLU cc_start: 0.8040 (pt0) cc_final: 0.7646 (tt0) outliers start: 34 outliers final: 19 residues processed: 110 average time/residue: 0.5012 time to fit residues: 59.0541 Evaluate side-chains 116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 173 CYS Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 240 TRP Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.0270 chunk 105 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132258 restraints weight = 9874.938| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.18 r_work: 0.3318 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9279 Z= 0.094 Angle : 0.512 8.691 12576 Z= 0.265 Chirality : 0.041 0.181 1435 Planarity : 0.004 0.084 1577 Dihedral : 6.043 57.559 1272 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.76 % Allowed : 16.63 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.19 (0.25), residues: 1132 helix: 1.02 (0.27), residues: 398 sheet: 0.30 (0.30), residues: 291 loop : -0.73 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 107 TYR 0.019 0.001 TYR R 284 PHE 0.012 0.001 PHE R 119 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 9274) covalent geometry : angle 0.50942 / 0.26 (12570) SS BOND : bond 0.00344 / 0.16 ( 3) SS BOND : angle 2.38501 / 1.44 ( 6) hydrogen bonds : bond 0.02984 / 1.91 ( 382) hydrogen bonds : angle 4.01144 / 2.76 ( 1104) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.231 Fit side-chains REVERT: A 25 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.5816 (mp0) REVERT: A 35 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8030 (mtpt) REVERT: A 209 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.6180 (ttp-110) REVERT: A 296 THR cc_start: 0.7279 (OUTLIER) cc_final: 0.6959 (p) REVERT: A 323 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8151 (mtm) REVERT: R 70 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6717 (ttt90) REVERT: R 180 VAL cc_start: 0.6424 (t) cc_final: 0.6189 (m) REVERT: R 213 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6030 (tpp) REVERT: R 240 TRP cc_start: 0.6308 (OUTLIER) cc_final: 0.5811 (t60) REVERT: R 264 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6315 (mmm) REVERT: R 328 LYS cc_start: 0.7397 (mmtt) cc_final: 0.6920 (mptp) REVERT: G 42 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6449 (tp30) REVERT: S 67 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.5571 (ptm-80) REVERT: S 83 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: B 146 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 258 ASP cc_start: 0.7768 (t0) cc_final: 0.7199 (t70) REVERT: B 260 GLU cc_start: 0.7824 (pt0) cc_final: 0.7384 (tt0) outliers start: 27 outliers final: 11 residues processed: 112 average time/residue: 0.5056 time to fit residues: 60.3199 Evaluate side-chains 113 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 240 TRP Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.168798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132210 restraints weight = 9887.801| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.16 r_work: 0.3316 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9279 Z= 0.099 Angle : 0.524 7.875 12576 Z= 0.270 Chirality : 0.041 0.171 1435 Planarity : 0.004 0.092 1577 Dihedral : 5.944 56.554 1272 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.45 % Allowed : 17.24 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.23 (0.25), residues: 1132 helix: 1.07 (0.27), residues: 398 sheet: 0.29 (0.30), residues: 290 loop : -0.69 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 87 TYR 0.013 0.001 TYR A 297 PHE 0.010 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9274) covalent geometry : angle 0.52253 / 0.27 (12570) SS BOND : bond 0.00391 / 0.19 ( 3) SS BOND : angle 2.01501 / 1.23 ( 6) hydrogen bonds : bond 0.03041 / 1.95 ( 382) hydrogen bonds : angle 4.01152 / 2.75 ( 1104) Misc. bond : bond 0.00031 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.295 Fit side-chains REVERT: A 25 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.5806 (mp0) REVERT: A 35 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8027 (mtpt) REVERT: A 209 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.6164 (ttp-110) REVERT: A 296 THR cc_start: 0.7273 (OUTLIER) cc_final: 0.6947 (p) REVERT: R 42 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5809 (tt) REVERT: R 70 ARG cc_start: 0.6929 (ttt180) cc_final: 0.6713 (ttt90) REVERT: R 109 TRP cc_start: 0.6703 (t-100) cc_final: 0.6467 (t60) REVERT: R 180 VAL cc_start: 0.6408 (t) cc_final: 0.6184 (m) REVERT: R 213 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6010 (tpp) REVERT: R 264 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6294 (mmm) REVERT: R 328 LYS cc_start: 0.7395 (mmtt) cc_final: 0.6923 (mptp) REVERT: G 42 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.6450 (tp30) REVERT: S 67 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.5558 (ptm-80) REVERT: S 83 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8000 (mtp) REVERT: B 146 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8854 (mm) REVERT: B 258 ASP cc_start: 0.7826 (t0) cc_final: 0.7243 (t70) outliers start: 24 outliers final: 11 residues processed: 107 average time/residue: 0.5888 time to fit residues: 67.1797 Evaluate side-chains 109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.167738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131077 restraints weight = 9884.540| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.18 r_work: 0.3296 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9279 Z= 0.110 Angle : 0.532 7.777 12576 Z= 0.275 Chirality : 0.042 0.162 1435 Planarity : 0.004 0.087 1577 Dihedral : 5.942 55.802 1272 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.14 % Allowed : 17.45 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.32 (0.25), residues: 1132 helix: 1.20 (0.28), residues: 385 sheet: 0.28 (0.30), residues: 290 loop : -0.60 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 87 TYR 0.022 0.001 TYR R 128 PHE 0.018 0.001 PHE R 119 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9274) covalent geometry : angle 0.53001 / 0.27 (12570) SS BOND : bond 0.00391 / 0.19 ( 3) SS BOND : angle 2.23950 / 1.36 ( 6) hydrogen bonds : bond 0.03183 / 2.05 ( 382) hydrogen bonds : angle 4.03772 / 2.77 ( 1104) Misc. bond : bond 0.00040 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.30 seconds wall clock time: 56 minutes 5.08 seconds (3365.08 seconds total)