Starting phenix.real_space_refine on Wed Mar 4 03:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyw_26196/03_2026/7tyw_26196.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyw_26196/03_2026/7tyw_26196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyw_26196/03_2026/7tyw_26196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyw_26196/03_2026/7tyw_26196.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyw_26196/03_2026/7tyw_26196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyw_26196/03_2026/7tyw_26196.cif" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 427 atoms to isotropic. 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 70 5.16 5 C 6238 2.51 5 N 1683 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9779 Number of models: 1 Model: "" Number of chains: 11 Chain: "E" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 650 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 2, 'ARG:plan': 7, 'PHE:plan': 4, 'ASP:plan': 4, 'TRP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 168 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2898 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 16, 'TRANS': 353} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 5, 'TYR:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1879 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {'NAG': 2, 'PLM': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.01, per 1000 atoms: 0.31 Number of scatterers: 9779 At special positions: 0 Unit cell: (92.448, 101.864, 160.928, 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 70 16.00 O 1788 8.00 N 1683 7.00 C 6238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.04 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 557.5 milliseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 42.8% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.985A pdb=" N GLY E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 38 No H-bonds generated for 'chain 'E' and resid 36 through 38' Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.720A pdb=" N GLU E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.904A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 removed outlier: 4.282A pdb=" N THR E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 98 removed outlier: 3.677A pdb=" N ASP E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS E 97 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 143 removed outlier: 3.615A pdb=" N ILE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 22 Processing helix chain 'R' and resid 39 through 62 removed outlier: 4.048A pdb=" N ARG R 45 " --> pdb=" O TYR R 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.528A pdb=" N ALA R 145 " --> pdb=" O LYS R 141 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.680A pdb=" N TYR R 191 " --> pdb=" O MET R 187 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL R 203 " --> pdb=" O ILE R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.539A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 249 removed outlier: 3.739A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 328 Proline residue: R 304 - end of helix removed outlier: 3.761A pdb=" N VAL R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN R 312 " --> pdb=" O ALA R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 347 removed outlier: 3.731A pdb=" N TYR R 338 " --> pdb=" O GLU R 334 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 341 " --> pdb=" O MET R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 353 Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 removed outlier: 3.619A pdb=" N ALA R 388 " --> pdb=" O GLY R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 404 removed outlier: 4.048A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS R 403 " --> pdb=" O GLN R 399 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG R 404 " --> pdb=" O THR R 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.748A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.966A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.990A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.510A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.617A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.593A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.509A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 3.597A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.536A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.778A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.953A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 92 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.250A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.659A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.614A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.254A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.720A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.775A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.691A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.765A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.718A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1641 1.32 - 1.45: 2734 1.45 - 1.57: 5526 1.57 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9997 Sorted by residual: bond pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 1.522 1.453 0.070 1.20e-02 6.94e+03 3.37e+01 bond pdb=" N ARG N 98 " pdb=" CA ARG N 98 " ideal model delta sigma weight residual 1.454 1.399 0.055 1.23e-02 6.61e+03 1.99e+01 bond pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.20e-02 6.94e+03 1.52e+01 bond pdb=" CA ALA N 97 " pdb=" C ALA N 97 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.21e-02 6.83e+03 1.43e+01 bond pdb=" CA ASN N 31 " pdb=" C ASN N 31 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.31e-02 5.83e+03 1.23e+01 ... (remaining 9992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 13551 4.68 - 9.36: 25 9.36 - 14.04: 3 14.04 - 18.72: 0 18.72 - 23.40: 2 Bond angle restraints: 13581 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 90.32 21.68 1.40e+00 5.10e-01 2.40e+02 angle pdb=" N ARG N 98 " pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 109.72 99.59 10.13 1.60e+00 3.91e-01 4.01e+01 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 112.01 122.57 -10.56 1.84e+00 2.95e-01 3.29e+01 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 148.40 -23.40 4.10e+00 5.95e-02 3.26e+01 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 113.23 119.81 -6.58 1.22e+00 6.72e-01 2.91e+01 ... (remaining 13576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 5715 22.90 - 45.79: 281 45.79 - 68.69: 47 68.69 - 91.58: 14 91.58 - 114.48: 2 Dihedral angle restraints: 6059 sinusoidal: 2403 harmonic: 3656 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 169.62 -76.62 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual 93.00 22.37 70.63 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual -86.00 -145.94 59.94 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 6056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1428 0.078 - 0.157: 94 0.157 - 0.235: 11 0.235 - 0.313: 1 0.313 - 0.392: 2 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C1 NAG R 502 " pdb=" ND2 ASN R 73 " pdb=" C2 NAG R 502 " pdb=" O5 NAG R 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1533 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR N 113 " -0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C THR N 113 " 0.055 2.00e-02 2.50e+03 pdb=" O THR N 113 " -0.020 2.00e-02 2.50e+03 pdb=" N THR N 114 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " 0.037 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO P 32 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 302 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C HIS R 302 " 0.031 2.00e-02 2.50e+03 pdb=" O HIS R 302 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY R 303 " -0.011 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 661 2.74 - 3.28: 9603 3.28 - 3.82: 15631 3.82 - 4.36: 19571 4.36 - 4.90: 33176 Nonbonded interactions: 78642 Sorted by model distance: nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.199 3.040 nonbonded pdb=" O THR R 162 " pdb=" OG SER R 166 " model vdw 2.213 3.040 nonbonded pdb=" O SER R 105 " pdb=" OG SER R 105 " model vdw 2.249 3.040 nonbonded pdb=" NH2 ARG N 38 " pdb=" O GLU N 89 " model vdw 2.260 3.120 nonbonded pdb=" O LEU R 271 " pdb=" OG1 THR R 275 " model vdw 2.265 3.040 ... (remaining 78637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.100 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: 0.010 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 10010 Z= 0.279 Angle : 0.683 23.397 13607 Z= 0.411 Chirality : 0.045 0.392 1536 Planarity : 0.003 0.048 1720 Dihedral : 13.381 114.481 3665 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.41 % Allowed : 14.62 % Favored : 83.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.38 % 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: -4.19 (0.18), residues: 1236 helix: -3.38 (0.14), residues: 479 sheet: -2.07 (0.30), residues: 231 loop : -2.31 (0.22), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.022 0.001 TYR N 32 PHE 0.023 0.001 PHE N 108 TRP 0.014 0.001 TRP N 36 HIS 0.003 0.000 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9997) covalent geometry : angle 0.67676 (13581) SS BOND : bond 0.00622 ( 10) SS BOND : angle 1.13161 ( 20) hydrogen bonds : bond 0.28393 ( 418) hydrogen bonds : angle 9.58194 ( 1203) Misc. bond : bond 0.10912 ( 1) link_NAG-ASN : bond 0.00727 ( 2) link_NAG-ASN : angle 4.22340 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.300 Fit side-chains REVERT: R 99 PHE cc_start: 0.5445 (m-80) cc_final: 0.5128 (m-80) REVERT: R 337 MET cc_start: 0.5881 (ttm) cc_final: 0.5609 (ttp) REVERT: R 405 GLN cc_start: 0.5504 (OUTLIER) cc_final: 0.5089 (tm-30) REVERT: A 15 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6139 (mm-30) REVERT: A 372 ILE cc_start: 0.7951 (pt) cc_final: 0.7633 (pp) REVERT: A 389 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7079 (ttp-110) REVERT: B 22 ARG cc_start: 0.6628 (mtt180) cc_final: 0.6309 (mtt90) REVERT: B 45 MET cc_start: 0.6743 (mtt) cc_final: 0.5611 (mmp) REVERT: G 22 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7068 (mt-10) REVERT: N 43 LYS cc_start: 0.5702 (ptpt) cc_final: 0.5405 (pptt) REVERT: N 46 GLU cc_start: 0.6655 (mm-30) cc_final: 0.5646 (mm-30) REVERT: N 89 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4814 (mm-30) outliers start: 14 outliers final: 5 residues processed: 197 average time/residue: 0.5760 time to fit residues: 120.8487 Evaluate side-chains 147 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 PRO Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0020 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 GLN R 227 GLN R 257 GLN A 14 ASN A 384 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN N 5 GLN N 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.217221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.177685 restraints weight = 10994.817| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.03 r_work: 0.3693 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10010 Z= 0.112 Angle : 0.522 10.200 13607 Z= 0.273 Chirality : 0.041 0.351 1536 Planarity : 0.004 0.050 1720 Dihedral : 7.646 82.049 1582 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.23 % Allowed : 18.65 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.16 (0.21), residues: 1236 helix: -0.88 (0.21), residues: 498 sheet: -1.40 (0.33), residues: 224 loop : -1.88 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 20 TYR 0.017 0.001 TYR N 60 PHE 0.015 0.001 PHE A 376 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9997) covalent geometry : angle 0.51214 (13581) SS BOND : bond 0.00295 ( 10) SS BOND : angle 1.31175 ( 20) hydrogen bonds : bond 0.04694 ( 418) hydrogen bonds : angle 5.01594 ( 1203) Misc. bond : bond 0.00097 ( 1) link_NAG-ASN : bond 0.00846 ( 2) link_NAG-ASN : angle 4.39664 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.366 Fit side-chains REVERT: P 3 ASN cc_start: 0.8349 (m-40) cc_final: 0.8116 (m110) REVERT: P 32 PRO cc_start: 0.5369 (OUTLIER) cc_final: 0.4949 (Cg_endo) REVERT: R 48 MET cc_start: 0.3687 (ttm) cc_final: 0.3271 (mtp) REVERT: R 133 MET cc_start: 0.6403 (mpp) cc_final: 0.6042 (ttm) REVERT: R 140 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.4946 (pt0) REVERT: R 141 LYS cc_start: 0.7174 (mtmm) cc_final: 0.6828 (mtmm) REVERT: R 405 GLN cc_start: 0.5895 (mp10) cc_final: 0.5227 (tm-30) REVERT: A 15 GLU cc_start: 0.5880 (mm-30) cc_final: 0.5503 (mm-30) REVERT: A 35 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7507 (mm110) REVERT: A 38 ARG cc_start: 0.8122 (mmt180) cc_final: 0.7919 (mpt180) REVERT: A 347 ARG cc_start: 0.6140 (tmm160) cc_final: 0.5786 (ttp80) REVERT: A 389 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7157 (ttm110) REVERT: B 22 ARG cc_start: 0.6744 (mtt180) cc_final: 0.6390 (mtt90) REVERT: B 44 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6921 (mt0) REVERT: B 45 MET cc_start: 0.7281 (mtt) cc_final: 0.5630 (mmp) REVERT: B 59 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: B 219 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7865 (mtp180) REVERT: N 5 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.6234 (mp-120) REVERT: N 43 LYS cc_start: 0.6352 (ptpt) cc_final: 0.5684 (pptt) REVERT: N 46 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6339 (mm-30) outliers start: 32 outliers final: 10 residues processed: 179 average time/residue: 0.5369 time to fit residues: 102.9412 Evaluate side-chains 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 PRO Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 392 CYS Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain R residue 402 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 22 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 ASN R 227 GLN R 399 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 75 GLN B 142 HIS B 155 ASN B 293 ASN N 5 GLN N 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.200567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.157747 restraints weight = 11070.390| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.27 r_work: 0.3510 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10010 Z= 0.243 Angle : 0.658 9.671 13607 Z= 0.346 Chirality : 0.047 0.361 1536 Planarity : 0.005 0.056 1720 Dihedral : 7.942 81.638 1573 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.85 % Allowed : 17.94 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.67 (0.22), residues: 1236 helix: -0.17 (0.23), residues: 494 sheet: -1.44 (0.33), residues: 218 loop : -1.80 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 356 TYR 0.021 0.002 TYR N 95 PHE 0.017 0.002 PHE A 312 TRP 0.020 0.002 TRP B 82 HIS 0.009 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 9997) covalent geometry : angle 0.65037 (13581) SS BOND : bond 0.00614 ( 10) SS BOND : angle 1.50340 ( 20) hydrogen bonds : bond 0.04997 ( 418) hydrogen bonds : angle 5.03088 ( 1203) Misc. bond : bond 0.00037 ( 1) link_NAG-ASN : bond 0.00977 ( 2) link_NAG-ASN : angle 4.22205 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 0.275 Fit side-chains REVERT: R 140 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.4882 (pt0) REVERT: R 141 LYS cc_start: 0.7010 (mtmm) cc_final: 0.6806 (mtmm) REVERT: R 264 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7865 (tt) REVERT: A 15 GLU cc_start: 0.6074 (mm-30) cc_final: 0.5657 (mm-30) REVERT: A 35 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7448 (mm110) REVERT: A 58 LYS cc_start: 0.4453 (OUTLIER) cc_final: 0.3354 (mppt) REVERT: A 280 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7984 (pttm) REVERT: A 389 ARG cc_start: 0.8056 (tpp80) cc_final: 0.6953 (ttm110) REVERT: B 13 GLN cc_start: 0.7490 (tt0) cc_final: 0.6880 (mm-40) REVERT: B 44 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6855 (mt0) REVERT: B 45 MET cc_start: 0.7415 (mtt) cc_final: 0.5791 (mmp) REVERT: B 219 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7812 (mtp180) REVERT: B 234 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7481 (t80) REVERT: N 43 LYS cc_start: 0.6897 (ptpt) cc_final: 0.5849 (pptt) REVERT: N 89 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.3630 (tp30) outliers start: 58 outliers final: 23 residues processed: 184 average time/residue: 0.5172 time to fit residues: 102.0600 Evaluate side-chains 163 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 402 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 68 optimal weight: 0.0050 chunk 104 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 257 GLN A 357 HIS B 142 HIS B 155 ASN N 5 GLN N 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.207042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.169062 restraints weight = 11140.032| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.66 r_work: 0.3636 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10010 Z= 0.113 Angle : 0.522 9.696 13607 Z= 0.271 Chirality : 0.041 0.353 1536 Planarity : 0.004 0.036 1720 Dihedral : 7.205 74.982 1570 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.43 % Allowed : 20.46 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1236 helix: 0.50 (0.24), residues: 500 sheet: -1.17 (0.34), residues: 222 loop : -1.63 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.014 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9997) covalent geometry : angle 0.51292 (13581) SS BOND : bond 0.00263 ( 10) SS BOND : angle 1.32368 ( 20) hydrogen bonds : bond 0.03627 ( 418) hydrogen bonds : angle 4.48722 ( 1203) Misc. bond : bond 0.00017 ( 1) link_NAG-ASN : bond 0.00909 ( 2) link_NAG-ASN : angle 4.20206 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.363 Fit side-chains REVERT: R 48 MET cc_start: 0.4073 (ttm) cc_final: 0.3695 (mtp) REVERT: R 141 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6977 (mtmt) REVERT: R 213 ARG cc_start: 0.6475 (mtm-85) cc_final: 0.6129 (mtt90) REVERT: R 397 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: R 405 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5677 (mp10) REVERT: A 15 GLU cc_start: 0.6140 (mm-30) cc_final: 0.5797 (mm-30) REVERT: A 21 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6399 (tt0) REVERT: A 34 LYS cc_start: 0.8819 (tttt) cc_final: 0.8589 (tttp) REVERT: A 35 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7582 (mm110) REVERT: A 389 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7147 (ttm110) REVERT: B 44 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6879 (mt0) REVERT: B 45 MET cc_start: 0.7296 (mtt) cc_final: 0.5802 (mmp) REVERT: G 22 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6581 (tt0) REVERT: N 43 LYS cc_start: 0.6900 (ptpt) cc_final: 0.5946 (pptt) outliers start: 34 outliers final: 17 residues processed: 168 average time/residue: 0.5267 time to fit residues: 94.8525 Evaluate side-chains 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 0.0470 chunk 101 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 142 HIS B 155 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.208018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.170411 restraints weight = 11078.709| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.95 r_work: 0.3600 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10010 Z= 0.128 Angle : 0.529 9.574 13607 Z= 0.273 Chirality : 0.042 0.357 1536 Planarity : 0.004 0.035 1720 Dihedral : 7.025 67.398 1570 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.84 % Allowed : 20.16 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.72 (0.24), residues: 1236 helix: 0.81 (0.24), residues: 499 sheet: -0.97 (0.33), residues: 231 loop : -1.50 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 347 TYR 0.014 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9997) covalent geometry : angle 0.51980 (13581) SS BOND : bond 0.00298 ( 10) SS BOND : angle 1.21265 ( 20) hydrogen bonds : bond 0.03668 ( 418) hydrogen bonds : angle 4.37563 ( 1203) Misc. bond : bond 0.00016 ( 1) link_NAG-ASN : bond 0.00905 ( 2) link_NAG-ASN : angle 4.18411 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.330 Fit side-chains REVERT: R 140 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.4967 (pt0) REVERT: R 141 LYS cc_start: 0.7156 (mtmm) cc_final: 0.6789 (mtpt) REVERT: R 328 ARG cc_start: 0.6117 (mtt-85) cc_final: 0.5792 (mtt-85) REVERT: R 397 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: A 15 GLU cc_start: 0.6098 (mm-30) cc_final: 0.5749 (mm-30) REVERT: A 21 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: A 27 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: A 35 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7565 (mm110) REVERT: A 58 LYS cc_start: 0.4246 (OUTLIER) cc_final: 0.3265 (mppt) REVERT: A 389 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7170 (ttm110) REVERT: B 44 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6859 (mt0) REVERT: B 45 MET cc_start: 0.7248 (mtt) cc_final: 0.5786 (mmp) REVERT: N 5 GLN cc_start: 0.6179 (OUTLIER) cc_final: 0.5851 (mp10) REVERT: N 43 LYS cc_start: 0.6900 (ptpt) cc_final: 0.5904 (pptt) outliers start: 48 outliers final: 24 residues processed: 171 average time/residue: 0.5117 time to fit residues: 93.9508 Evaluate side-chains 159 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 59 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 54 optimal weight: 0.0020 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 257 GLN R 383 GLN A 357 HIS B 142 HIS B 155 ASN N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.207882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.170211 restraints weight = 11099.825| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.77 r_work: 0.3601 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10010 Z= 0.129 Angle : 0.534 9.488 13607 Z= 0.275 Chirality : 0.041 0.353 1536 Planarity : 0.004 0.036 1720 Dihedral : 6.533 58.557 1570 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.04 % Allowed : 20.06 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.54 (0.24), residues: 1236 helix: 0.97 (0.24), residues: 500 sheet: -0.92 (0.34), residues: 227 loop : -1.40 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 347 TYR 0.016 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9997) covalent geometry : angle 0.52642 (13581) SS BOND : bond 0.00269 ( 10) SS BOND : angle 0.97685 ( 20) hydrogen bonds : bond 0.03566 ( 418) hydrogen bonds : angle 4.31380 ( 1203) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00922 ( 2) link_NAG-ASN : angle 4.16375 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.319 Fit side-chains REVERT: R 140 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.4925 (pt0) REVERT: R 141 LYS cc_start: 0.7083 (mtmm) cc_final: 0.6728 (mtpt) REVERT: R 192 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.6692 (tp) REVERT: R 213 ARG cc_start: 0.6347 (mtt180) cc_final: 0.6071 (mtt90) REVERT: R 284 TYR cc_start: 0.6313 (m-10) cc_final: 0.6111 (m-10) REVERT: R 397 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: A 15 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5768 (mm-30) REVERT: A 21 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6466 (tt0) REVERT: A 27 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: A 35 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7494 (mm110) REVERT: A 58 LYS cc_start: 0.4252 (OUTLIER) cc_final: 0.3332 (mppt) REVERT: A 389 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7139 (ttm110) REVERT: B 44 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6835 (mt0) REVERT: B 45 MET cc_start: 0.7275 (mtt) cc_final: 0.5805 (mmp) REVERT: N 5 GLN cc_start: 0.6092 (OUTLIER) cc_final: 0.5803 (mp10) REVERT: N 43 LYS cc_start: 0.6861 (ptpt) cc_final: 0.5852 (pptt) outliers start: 50 outliers final: 24 residues processed: 170 average time/residue: 0.4648 time to fit residues: 85.6072 Evaluate side-chains 162 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 0.0070 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 40.0000 chunk 54 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN A 357 HIS B 142 HIS B 155 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.208692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.168306 restraints weight = 11099.682| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.10 r_work: 0.3602 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10010 Z= 0.095 Angle : 0.489 9.379 13607 Z= 0.252 Chirality : 0.040 0.344 1536 Planarity : 0.003 0.036 1720 Dihedral : 5.643 57.293 1570 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.73 % Allowed : 22.18 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.23 (0.24), residues: 1236 helix: 1.31 (0.24), residues: 501 sheet: -0.87 (0.35), residues: 212 loop : -1.26 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 347 TYR 0.014 0.001 TYR N 95 PHE 0.011 0.001 PHE R 224 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 9997) covalent geometry : angle 0.48029 (13581) SS BOND : bond 0.00207 ( 10) SS BOND : angle 1.04129 ( 20) hydrogen bonds : bond 0.03141 ( 418) hydrogen bonds : angle 4.08271 ( 1203) Misc. bond : bond 0.00008 ( 1) link_NAG-ASN : bond 0.00923 ( 2) link_NAG-ASN : angle 4.08811 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.350 Fit side-chains REVERT: R 48 MET cc_start: 0.3459 (ttm) cc_final: 0.3203 (mtp) REVERT: R 140 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.4820 (pt0) REVERT: R 141 LYS cc_start: 0.7001 (mtmm) cc_final: 0.6639 (mtpt) REVERT: R 174 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7113 (mtt90) REVERT: R 196 MET cc_start: 0.8017 (mtt) cc_final: 0.7719 (mtp) REVERT: R 370 LYS cc_start: 0.6629 (mtpt) cc_final: 0.6136 (mttt) REVERT: R 397 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: A 15 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5582 (mm-30) REVERT: A 27 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: A 35 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7544 (mm110) REVERT: A 58 LYS cc_start: 0.4093 (OUTLIER) cc_final: 0.3182 (mppt) REVERT: A 389 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7120 (ttm110) REVERT: B 44 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6850 (mt0) REVERT: B 45 MET cc_start: 0.7257 (mtt) cc_final: 0.5721 (mmp) REVERT: B 59 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: B 267 ASP cc_start: 0.7923 (m-30) cc_final: 0.7636 (m-30) REVERT: G 22 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6605 (tt0) REVERT: N 5 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.5635 (mp10) REVERT: N 43 LYS cc_start: 0.6807 (ptpt) cc_final: 0.5846 (pptt) outliers start: 37 outliers final: 15 residues processed: 167 average time/residue: 0.4632 time to fit residues: 83.6870 Evaluate side-chains 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 318 ASN Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.0040 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 GLN A 357 HIS B 142 HIS B 155 ASN N 3 GLN N 5 GLN N 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.206924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.168543 restraints weight = 11108.483| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.62 r_work: 0.3627 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10010 Z= 0.111 Angle : 0.515 9.320 13607 Z= 0.266 Chirality : 0.041 0.344 1536 Planarity : 0.003 0.036 1720 Dihedral : 5.552 59.022 1569 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.03 % Allowed : 21.67 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1236 helix: 1.36 (0.24), residues: 502 sheet: -0.73 (0.35), residues: 217 loop : -1.24 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 347 TYR 0.014 0.001 TYR N 95 PHE 0.011 0.001 PHE R 285 TRP 0.015 0.001 TRP R 290 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9997) covalent geometry : angle 0.50617 (13581) SS BOND : bond 0.00253 ( 10) SS BOND : angle 1.07137 ( 20) hydrogen bonds : bond 0.03337 ( 418) hydrogen bonds : angle 4.08908 ( 1203) Misc. bond : bond 0.00008 ( 1) link_NAG-ASN : bond 0.00940 ( 2) link_NAG-ASN : angle 4.07727 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.262 Fit side-chains REVERT: R 48 MET cc_start: 0.3485 (ttm) cc_final: 0.3248 (mtp) REVERT: R 141 LYS cc_start: 0.7010 (mtmm) cc_final: 0.6335 (mmpt) REVERT: R 174 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7351 (mtt90) REVERT: R 196 MET cc_start: 0.7974 (mtt) cc_final: 0.7576 (mtp) REVERT: R 328 ARG cc_start: 0.6024 (mtt-85) cc_final: 0.5250 (mtm110) REVERT: R 370 LYS cc_start: 0.6652 (mtpt) cc_final: 0.6245 (mttt) REVERT: R 396 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7454 (t0) REVERT: R 397 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: A 15 GLU cc_start: 0.5990 (mm-30) cc_final: 0.5679 (mm-30) REVERT: A 21 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: A 27 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: A 35 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7526 (mm110) REVERT: A 58 LYS cc_start: 0.4226 (OUTLIER) cc_final: 0.3218 (mppt) REVERT: A 389 ARG cc_start: 0.8074 (tpp80) cc_final: 0.7093 (ttm110) REVERT: B 44 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6813 (mt0) REVERT: B 45 MET cc_start: 0.7153 (mtt) cc_final: 0.5682 (mmp) REVERT: B 325 MET cc_start: 0.6568 (mtt) cc_final: 0.6333 (mpp) REVERT: N 5 GLN cc_start: 0.5957 (OUTLIER) cc_final: 0.5696 (mt0) REVERT: N 43 LYS cc_start: 0.6768 (ptpt) cc_final: 0.5855 (pptt) outliers start: 40 outliers final: 23 residues processed: 167 average time/residue: 0.5222 time to fit residues: 93.9441 Evaluate side-chains 165 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 392 CYS Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 GLN R 227 GLN R 257 GLN R 399 GLN A 357 HIS A 390 GLN B 142 HIS B 155 ASN N 5 GLN N 120 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.207297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.169056 restraints weight = 11072.952| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.94 r_work: 0.3599 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10010 Z= 0.137 Angle : 0.543 9.232 13607 Z= 0.282 Chirality : 0.042 0.343 1536 Planarity : 0.004 0.038 1720 Dihedral : 5.763 57.739 1569 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.64 % Allowed : 21.27 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.18 (0.24), residues: 1236 helix: 1.31 (0.24), residues: 502 sheet: -0.77 (0.35), residues: 217 loop : -1.23 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 347 TYR 0.017 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9997) covalent geometry : angle 0.53487 (13581) SS BOND : bond 0.00357 ( 10) SS BOND : angle 1.09654 ( 20) hydrogen bonds : bond 0.03558 ( 418) hydrogen bonds : angle 4.18595 ( 1203) Misc. bond : bond 0.00011 ( 1) link_NAG-ASN : bond 0.00955 ( 2) link_NAG-ASN : angle 4.06559 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.362 Fit side-chains REVERT: R 48 MET cc_start: 0.3477 (ttm) cc_final: 0.3256 (mtp) REVERT: R 140 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.4808 (pt0) REVERT: R 141 LYS cc_start: 0.7028 (mtmm) cc_final: 0.6655 (mtpt) REVERT: R 174 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7425 (mtt90) REVERT: R 328 ARG cc_start: 0.6288 (mtt-85) cc_final: 0.5295 (mtm110) REVERT: R 397 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: A 15 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5752 (mm-30) REVERT: A 21 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: A 27 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: A 35 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7564 (mm110) REVERT: A 58 LYS cc_start: 0.4185 (OUTLIER) cc_final: 0.3237 (mppt) REVERT: A 347 ARG cc_start: 0.5981 (ttp80) cc_final: 0.5698 (ttp80) REVERT: A 389 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7079 (ttm110) REVERT: B 44 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6786 (mt0) REVERT: B 45 MET cc_start: 0.7276 (mtt) cc_final: 0.5803 (mmp) REVERT: G 44 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.5998 (t-90) REVERT: N 43 LYS cc_start: 0.6826 (ptpt) cc_final: 0.5856 (pptt) outliers start: 46 outliers final: 24 residues processed: 163 average time/residue: 0.5231 time to fit residues: 91.7155 Evaluate side-chains 157 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 392 CYS Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 105 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 GLN R 257 GLN A 357 HIS A 390 GLN B 142 HIS B 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.211445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.175276 restraints weight = 10976.922| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.41 r_work: 0.3751 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10010 Z= 0.111 Angle : 0.516 9.152 13607 Z= 0.267 Chirality : 0.041 0.336 1536 Planarity : 0.003 0.037 1720 Dihedral : 5.624 59.897 1569 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.73 % Allowed : 22.18 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.02 (0.24), residues: 1236 helix: 1.44 (0.24), residues: 504 sheet: -0.62 (0.35), residues: 215 loop : -1.19 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 347 TYR 0.016 0.001 TYR N 95 PHE 0.020 0.001 PHE R 285 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9997) covalent geometry : angle 0.50825 (13581) SS BOND : bond 0.00250 ( 10) SS BOND : angle 0.95173 ( 20) hydrogen bonds : bond 0.03302 ( 418) hydrogen bonds : angle 4.07909 ( 1203) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00957 ( 2) link_NAG-ASN : angle 4.00377 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.346 Fit side-chains REVERT: R 48 MET cc_start: 0.3445 (ttm) cc_final: 0.3184 (mtp) REVERT: R 140 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.4814 (pt0) REVERT: R 141 LYS cc_start: 0.6916 (mtmm) cc_final: 0.6537 (mtpt) REVERT: R 174 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7241 (mtt90) REVERT: R 192 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.6656 (tp) REVERT: R 196 MET cc_start: 0.7856 (mtt) cc_final: 0.7617 (mtp) REVERT: R 370 LYS cc_start: 0.6631 (mtpt) cc_final: 0.6173 (mttt) REVERT: R 397 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: A 21 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: A 27 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: A 35 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7408 (mm110) REVERT: A 58 LYS cc_start: 0.4229 (OUTLIER) cc_final: 0.3239 (mppt) REVERT: A 389 ARG cc_start: 0.7910 (tpp80) cc_final: 0.6930 (ttm110) REVERT: B 44 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6814 (mt0) REVERT: B 45 MET cc_start: 0.7077 (mtt) cc_final: 0.5644 (mmp) REVERT: G 44 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.5873 (t-90) REVERT: N 43 LYS cc_start: 0.6706 (ptpt) cc_final: 0.5763 (pptt) outliers start: 37 outliers final: 20 residues processed: 158 average time/residue: 0.5014 time to fit residues: 85.3607 Evaluate side-chains 157 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 GLN R 257 GLN A 357 HIS A 390 GLN B 142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.206833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.168074 restraints weight = 11093.763| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.81 r_work: 0.3586 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10010 Z= 0.140 Angle : 0.546 9.024 13607 Z= 0.284 Chirality : 0.042 0.334 1536 Planarity : 0.004 0.038 1720 Dihedral : 5.765 56.827 1569 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.13 % Allowed : 21.77 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.05 (0.24), residues: 1236 helix: 1.43 (0.24), residues: 498 sheet: -0.71 (0.35), residues: 217 loop : -1.15 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 347 TYR 0.019 0.001 TYR N 95 PHE 0.011 0.002 PHE B 199 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9997) covalent geometry : angle 0.53883 (13581) SS BOND : bond 0.00324 ( 10) SS BOND : angle 0.99876 ( 20) hydrogen bonds : bond 0.03596 ( 418) hydrogen bonds : angle 4.20113 ( 1203) Misc. bond : bond 0.00013 ( 1) link_NAG-ASN : bond 0.00977 ( 2) link_NAG-ASN : angle 3.98072 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3548.43 seconds wall clock time: 61 minutes 3.86 seconds (3663.86 seconds total)