Starting phenix.real_space_refine on Mon Jul 28 13:46:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyw_26196/07_2025/7tyw_26196.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyw_26196/07_2025/7tyw_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_26196/07_2025/7tyw_26196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyw_26196/07_2025/7tyw_26196.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyw_26196/07_2025/7tyw_26196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyw_26196/07_2025/7tyw_26196.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 7} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} 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: 6.28, per 1000 atoms: 0.64 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.09 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: 2.80 Time building geometry restraints manager: 2.87 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: 0.010 Normalize map: mean=0, sd=1: 66.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP N 36 HIS 0.003 0.000 HIS R 302 PHE 0.023 0.001 PHE N 108 TYR 0.022 0.001 TYR N 32 ARG 0.002 0.000 ARG N 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 2) link_NAG-ASN : angle 4.22340 ( 6) hydrogen bonds : bond 0.28393 ( 418) hydrogen bonds : angle 9.58194 ( 1203) SS BOND : bond 0.00622 ( 10) SS BOND : angle 1.13161 ( 20) covalent geometry : bond 0.00382 ( 9997) covalent geometry : angle 0.67676 (13581) Misc. bond : bond 0.10912 ( 1) *********************** 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 : 1.133 Fit side-chains REVERT: R 99 PHE cc_start: 0.5445 (m-80) cc_final: 0.5146 (m-80) REVERT: R 337 MET cc_start: 0.5881 (ttm) cc_final: 0.5608 (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: 0.7950 (pt) cc_final: 0.7632 (pp) REVERT: A 389 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7078 (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: 1.2028 time to fit residues: 254.7423 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 : 0.993 ------------------------------------------------------------------------------- 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 103 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.0670 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 135 ASN R 179 GLN R 227 GLN R 257 GLN ** R 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.214954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.174936 restraints weight = 10948.573| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.01 r_work: 0.3652 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10010 Z= 0.123 Angle : 0.535 10.153 13607 Z= 0.279 Chirality : 0.041 0.358 1536 Planarity : 0.004 0.047 1720 Dihedral : 7.753 82.754 1582 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.63 % Allowed : 18.35 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.21), residues: 1236 helix: -0.91 (0.21), residues: 497 sheet: -1.33 (0.33), residues: 221 loop : -1.91 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.001 PHE B 199 TYR 0.017 0.001 TYR N 60 ARG 0.008 0.001 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00864 ( 2) link_NAG-ASN : angle 4.37975 ( 6) hydrogen bonds : bond 0.04619 ( 418) hydrogen bonds : angle 5.02441 ( 1203) SS BOND : bond 0.00772 ( 10) SS BOND : angle 1.32581 ( 20) covalent geometry : bond 0.00259 ( 9997) covalent geometry : angle 0.52503 (13581) Misc. bond : bond 0.00108 ( 1) *********************** 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 194 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.110 Fit side-chains REVERT: P 3 ASN cc_start: 0.8357 (m-40) cc_final: 0.8111 (m110) REVERT: R 133 MET cc_start: 0.6384 (mpp) cc_final: 0.6053 (ttm) REVERT: R 140 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.4971 (pt0) REVERT: R 141 LYS cc_start: 0.7174 (mtmm) cc_final: 0.6842 (mtmm) REVERT: R 383 GLN cc_start: 0.8442 (tt0) cc_final: 0.8196 (tt0) REVERT: R 405 GLN cc_start: 0.6001 (mp10) cc_final: 0.5297 (tm-30) REVERT: A 15 GLU cc_start: 0.5875 (mm-30) cc_final: 0.5590 (mm-30) REVERT: A 35 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7521 (mm110) REVERT: A 389 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7138 (ttm110) REVERT: B 22 ARG cc_start: 0.6758 (mtt180) cc_final: 0.6378 (mtt90) REVERT: B 44 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6830 (mt0) REVERT: B 45 MET cc_start: 0.7219 (mtt) cc_final: 0.5636 (mmp) REVERT: N 5 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.6190 (mp-120) REVERT: N 43 LYS cc_start: 0.6492 (ptpt) cc_final: 0.5791 (pptt) REVERT: N 46 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6336 (mm-30) outliers start: 36 outliers final: 14 residues processed: 183 average time/residue: 1.7214 time to fit residues: 336.9602 Evaluate side-chains 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 392 CYS Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain R residue 402 VAL Chi-restraints excluded: chain A residue 325 THR 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 7 SER 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 46 optimal weight: 0.9980 chunk 15 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN ** R 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN B 293 ASN N 5 GLN N 123 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.206668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.160793 restraints weight = 11200.733| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.69 r_work: 0.3591 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10010 Z= 0.143 Angle : 0.538 9.477 13607 Z= 0.280 Chirality : 0.042 0.350 1536 Planarity : 0.004 0.038 1720 Dihedral : 6.900 75.275 1571 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.84 % Allowed : 19.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.22), residues: 1236 helix: 0.15 (0.23), residues: 494 sheet: -1.27 (0.33), residues: 217 loop : -1.72 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.015 0.002 PHE R 285 TYR 0.015 0.001 TYR N 95 ARG 0.008 0.001 ARG A 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00922 ( 2) link_NAG-ASN : angle 4.08246 ( 6) hydrogen bonds : bond 0.04240 ( 418) hydrogen bonds : angle 4.65989 ( 1203) SS BOND : bond 0.00490 ( 10) SS BOND : angle 1.21135 ( 20) covalent geometry : bond 0.00321 ( 9997) covalent geometry : angle 0.53001 (13581) Misc. bond : bond 0.00026 ( 1) *********************** 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 192 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.128 Fit side-chains REVERT: P 3 ASN cc_start: 0.8326 (m-40) cc_final: 0.8111 (m110) REVERT: R 99 PHE cc_start: 0.5339 (m-80) cc_final: 0.5067 (m-80) REVERT: R 140 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.4989 (pt0) REVERT: A 15 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5743 (mm-30) REVERT: A 35 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7506 (mm110) REVERT: A 280 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8098 (pttm) REVERT: A 389 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7041 (ttm110) REVERT: B 44 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6853 (mt0) REVERT: B 45 MET cc_start: 0.7446 (mtt) cc_final: 0.5797 (mmp) REVERT: N 28 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8197 (t) REVERT: N 43 LYS cc_start: 0.6717 (ptpt) cc_final: 0.5769 (pptt) REVERT: N 46 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6241 (mm-30) outliers start: 48 outliers final: 17 residues processed: 175 average time/residue: 1.1794 time to fit residues: 222.3078 Evaluate side-chains 151 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 397 GLU Chi-restraints excluded: chain A residue 280 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 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 86 THR Chi-restraints excluded: chain B residue 147 SER 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 99 CYS 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 21 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 120 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 257 GLN ** R 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN B 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.212470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.177148 restraints weight = 11005.690| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.41 r_work: 0.3654 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2622 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= 0.110 Angle : 0.508 9.580 13607 Z= 0.262 Chirality : 0.041 0.353 1536 Planarity : 0.003 0.038 1720 Dihedral : 6.436 61.917 1570 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.93 % Allowed : 19.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1236 helix: 0.73 (0.24), residues: 494 sheet: -0.99 (0.34), residues: 218 loop : -1.52 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.010 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00900 ( 2) link_NAG-ASN : angle 4.13935 ( 6) hydrogen bonds : bond 0.03535 ( 418) hydrogen bonds : angle 4.35411 ( 1203) SS BOND : bond 0.00248 ( 10) SS BOND : angle 1.15648 ( 20) covalent geometry : bond 0.00241 ( 9997) covalent geometry : angle 0.49872 (13581) Misc. bond : bond 0.00007 ( 1) *********************** 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 181 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 1.164 Fit side-chains REVERT: P 3 ASN cc_start: 0.8292 (m-40) cc_final: 0.8072 (m110) REVERT: R 48 MET cc_start: 0.3682 (ttm) cc_final: 0.3475 (ttm) REVERT: A 15 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5502 (mm-30) REVERT: A 34 LYS cc_start: 0.8598 (tttt) cc_final: 0.8327 (tttp) REVERT: A 58 LYS cc_start: 0.4447 (OUTLIER) cc_final: 0.3371 (mppt) REVERT: A 389 ARG cc_start: 0.7998 (tpp80) cc_final: 0.6862 (ttm110) REVERT: B 44 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6810 (mt0) REVERT: B 45 MET cc_start: 0.7113 (mtt) cc_final: 0.5559 (mmp) REVERT: N 28 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7996 (t) REVERT: N 43 LYS cc_start: 0.6706 (ptpt) cc_final: 0.5745 (pptt) REVERT: N 46 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6002 (mm-30) outliers start: 39 outliers final: 19 residues processed: 172 average time/residue: 1.1761 time to fit residues: 218.5140 Evaluate side-chains 159 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 397 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 341 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.0070 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN R 383 GLN A 35 GLN A 357 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN N 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.206403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.164478 restraints weight = 10979.014| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.16 r_work: 0.3577 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2813 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= 0.117 Angle : 0.513 9.531 13607 Z= 0.264 Chirality : 0.041 0.352 1536 Planarity : 0.003 0.038 1720 Dihedral : 5.907 58.034 1570 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.73 % Allowed : 21.07 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.24), residues: 1236 helix: 0.95 (0.24), residues: 499 sheet: -0.92 (0.34), residues: 222 loop : -1.45 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.015 0.001 PHE R 285 TYR 0.020 0.001 TYR N 60 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00903 ( 2) link_NAG-ASN : angle 4.13808 ( 6) hydrogen bonds : bond 0.03500 ( 418) hydrogen bonds : angle 4.29368 ( 1203) SS BOND : bond 0.00237 ( 10) SS BOND : angle 1.08200 ( 20) covalent geometry : bond 0.00261 ( 9997) covalent geometry : angle 0.50424 (13581) Misc. bond : bond 0.00009 ( 1) *********************** 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 176 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.287 Fit side-chains REVERT: P 3 ASN cc_start: 0.8240 (m-40) cc_final: 0.8013 (m110) REVERT: R 99 PHE cc_start: 0.5292 (m-80) cc_final: 0.4876 (m-80) REVERT: R 102 PHE cc_start: 0.5804 (m-80) cc_final: 0.5509 (m-10) REVERT: R 141 LYS cc_start: 0.6943 (mtmm) cc_final: 0.6718 (mtmm) REVERT: R 397 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: A 15 GLU cc_start: 0.5934 (mm-30) cc_final: 0.5595 (mm-30) REVERT: A 21 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6457 (tt0) REVERT: A 58 LYS cc_start: 0.4379 (OUTLIER) cc_final: 0.3352 (mppt) REVERT: A 389 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7042 (ttm110) REVERT: B 44 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6812 (mt0) REVERT: B 45 MET cc_start: 0.7397 (mtt) cc_final: 0.5732 (mmp) REVERT: G 22 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6861 (mt-10) REVERT: N 28 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8124 (t) REVERT: N 43 LYS cc_start: 0.6793 (ptpt) cc_final: 0.5757 (pptt) REVERT: N 89 GLU cc_start: 0.4530 (OUTLIER) cc_final: 0.4172 (mm-30) outliers start: 37 outliers final: 23 residues processed: 169 average time/residue: 1.1431 time to fit residues: 208.1446 Evaluate side-chains 164 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 392 CYS Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 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 386 MET 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 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 7 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 257 GLN ** R 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN A 35 GLN A 357 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN N 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.216357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.181181 restraints weight = 10861.235| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.74 r_work: 0.3724 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10010 Z= 0.097 Angle : 0.483 9.428 13607 Z= 0.249 Chirality : 0.040 0.345 1536 Planarity : 0.003 0.036 1720 Dihedral : 5.470 59.607 1569 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.64 % Allowed : 20.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1236 helix: 1.20 (0.24), residues: 500 sheet: -0.79 (0.35), residues: 210 loop : -1.31 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 362 PHE 0.010 0.001 PHE B 199 TYR 0.016 0.001 TYR N 60 ARG 0.014 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00902 ( 2) link_NAG-ASN : angle 4.12320 ( 6) hydrogen bonds : bond 0.03229 ( 418) hydrogen bonds : angle 4.11145 ( 1203) SS BOND : bond 0.00173 ( 10) SS BOND : angle 0.81018 ( 20) covalent geometry : bond 0.00210 ( 9997) covalent geometry : angle 0.47497 (13581) Misc. bond : bond 0.00010 ( 1) *********************** 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 189 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.014 Fit side-chains REVERT: P 3 ASN cc_start: 0.8296 (m-40) cc_final: 0.8044 (m110) REVERT: R 99 PHE cc_start: 0.5262 (m-80) cc_final: 0.4910 (m-80) REVERT: R 102 PHE cc_start: 0.5764 (m-10) cc_final: 0.5546 (m-10) REVERT: R 141 LYS cc_start: 0.7153 (mtmm) cc_final: 0.6263 (mmpt) REVERT: R 366 LYS cc_start: 0.6393 (ttmt) cc_final: 0.6157 (tmmm) REVERT: R 397 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: A 15 GLU cc_start: 0.6258 (mm-30) cc_final: 0.5929 (mm-30) REVERT: A 21 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6464 (tt0) REVERT: A 27 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: A 58 LYS cc_start: 0.4532 (OUTLIER) cc_final: 0.3477 (mppt) REVERT: A 389 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7227 (ttm110) REVERT: B 44 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6855 (mt0) REVERT: B 45 MET cc_start: 0.7277 (mtt) cc_final: 0.5788 (mmp) REVERT: G 22 GLU cc_start: 0.7224 (mt-10) cc_final: 0.7009 (mt-10) REVERT: N 43 LYS cc_start: 0.6809 (ptpt) cc_final: 0.5993 (pptt) REVERT: N 89 GLU cc_start: 0.4431 (OUTLIER) cc_final: 0.4146 (mm-30) outliers start: 46 outliers final: 21 residues processed: 176 average time/residue: 1.0832 time to fit residues: 205.9098 Evaluate side-chains 160 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 217 VAL 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 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 98 SER 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 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 31 optimal weight: 0.6980 chunk 105 optimal weight: 0.0770 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 110 optimal weight: 0.0000 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 107 optimal weight: 0.0000 overall best weight: 0.1546 ------------------------------------------------------------------------------- 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 357 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.217181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.181455 restraints weight = 11085.179| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.54 r_work: 0.3726 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10010 Z= 0.088 Angle : 0.476 9.351 13607 Z= 0.246 Chirality : 0.040 0.340 1536 Planarity : 0.003 0.035 1720 Dihedral : 5.019 54.571 1569 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.23 % Allowed : 22.28 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1236 helix: 1.47 (0.24), residues: 504 sheet: -0.55 (0.35), residues: 214 loop : -1.17 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.002 0.000 HIS A 362 PHE 0.012 0.001 PHE R 285 TYR 0.015 0.001 TYR N 60 ARG 0.013 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00921 ( 2) link_NAG-ASN : angle 4.03872 ( 6) hydrogen bonds : bond 0.02914 ( 418) hydrogen bonds : angle 3.91139 ( 1203) SS BOND : bond 0.00156 ( 10) SS BOND : angle 0.89576 ( 20) covalent geometry : bond 0.00187 ( 9997) covalent geometry : angle 0.46800 (13581) Misc. bond : bond 0.00002 ( 1) *********************** 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 177 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.991 Fit side-chains REVERT: R 99 PHE cc_start: 0.4990 (m-80) cc_final: 0.4613 (m-80) REVERT: R 141 LYS cc_start: 0.6753 (mtmm) cc_final: 0.5966 (mmpt) REVERT: R 196 MET cc_start: 0.7916 (mtt) cc_final: 0.7645 (mtp) REVERT: R 366 LYS cc_start: 0.6285 (ttmt) cc_final: 0.5876 (tmmm) REVERT: R 370 LYS cc_start: 0.6546 (mtpt) cc_final: 0.6059 (mttt) REVERT: R 397 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: A 15 GLU cc_start: 0.5867 (mm-30) cc_final: 0.5507 (mm-30) REVERT: A 27 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: A 58 LYS cc_start: 0.4380 (OUTLIER) cc_final: 0.3335 (mppt) REVERT: A 345 PHE cc_start: 0.6375 (m-80) cc_final: 0.6146 (m-80) REVERT: A 389 ARG cc_start: 0.7931 (tpp80) cc_final: 0.6828 (ttm110) REVERT: B 22 ARG cc_start: 0.6511 (mtt180) cc_final: 0.6166 (mtt90) REVERT: B 44 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6842 (mt0) REVERT: B 45 MET cc_start: 0.7132 (mtt) cc_final: 0.5520 (mmp) REVERT: B 59 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: N 5 GLN cc_start: 0.5822 (OUTLIER) cc_final: 0.5455 (mp10) REVERT: N 28 THR cc_start: 0.8362 (t) cc_final: 0.7963 (m) REVERT: N 43 LYS cc_start: 0.6646 (ptpt) cc_final: 0.5736 (pptt) REVERT: N 89 GLU cc_start: 0.4237 (OUTLIER) cc_final: 0.4005 (mm-30) outliers start: 32 outliers final: 10 residues processed: 168 average time/residue: 1.1320 time to fit residues: 205.0445 Evaluate side-chains 155 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 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 58 LYS 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 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 5 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 4.9990 chunk 105 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 118 optimal weight: 0.0270 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 102 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN ** R 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 35 GLN A 357 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4302 r_free = 0.4302 target = 0.217265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.182819 restraints weight = 10967.845| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.51 r_work: 0.3750 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10010 Z= 0.095 Angle : 0.486 9.305 13607 Z= 0.252 Chirality : 0.041 0.340 1536 Planarity : 0.003 0.036 1720 Dihedral : 5.035 56.456 1569 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.33 % Allowed : 22.48 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1236 helix: 1.65 (0.24), residues: 501 sheet: -0.50 (0.35), residues: 217 loop : -1.19 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE B 292 TYR 0.019 0.001 TYR N 60 ARG 0.015 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00919 ( 2) link_NAG-ASN : angle 4.06423 ( 6) hydrogen bonds : bond 0.02977 ( 418) hydrogen bonds : angle 3.88685 ( 1203) SS BOND : bond 0.00170 ( 10) SS BOND : angle 0.83566 ( 20) covalent geometry : bond 0.00207 ( 9997) covalent geometry : angle 0.47807 (13581) Misc. bond : bond 0.00008 ( 1) *********************** 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 170 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.003 Fit side-chains REVERT: R 141 LYS cc_start: 0.6959 (mtmm) cc_final: 0.6107 (mmpt) REVERT: R 187 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7446 (tpt) REVERT: R 192 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.6739 (pt) REVERT: R 196 MET cc_start: 0.7966 (mtt) cc_final: 0.7656 (mtp) REVERT: R 337 MET cc_start: 0.5613 (ttm) cc_final: 0.4895 (tmm) REVERT: R 366 LYS cc_start: 0.6357 (ttmt) cc_final: 0.6121 (tmmm) REVERT: R 397 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: A 15 GLU cc_start: 0.5987 (mm-30) cc_final: 0.5630 (mm-30) REVERT: A 27 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: A 58 LYS cc_start: 0.4444 (OUTLIER) cc_final: 0.3345 (mppt) REVERT: A 345 PHE cc_start: 0.6465 (m-80) cc_final: 0.6236 (m-80) REVERT: A 389 ARG cc_start: 0.7939 (tpp80) cc_final: 0.6840 (ttm110) REVERT: B 44 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6801 (mt0) REVERT: B 45 MET cc_start: 0.7241 (mtt) cc_final: 0.5638 (mmp) REVERT: B 59 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: N 28 THR cc_start: 0.8463 (t) cc_final: 0.8116 (m) REVERT: N 43 LYS cc_start: 0.6613 (ptpt) cc_final: 0.5692 (pptt) outliers start: 33 outliers final: 15 residues processed: 162 average time/residue: 1.0809 time to fit residues: 189.2316 Evaluate side-chains 149 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 187 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 335 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 58 LYS 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 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL 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 25 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN R 257 GLN A 35 GLN A 357 HIS A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.208964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.166127 restraints weight = 11056.910| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.43 r_work: 0.3617 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3233 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= 0.151 Angle : 0.550 9.154 13607 Z= 0.287 Chirality : 0.043 0.339 1536 Planarity : 0.004 0.037 1720 Dihedral : 5.523 56.136 1569 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.53 % Allowed : 22.08 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1236 helix: 1.40 (0.24), residues: 502 sheet: -0.55 (0.34), residues: 225 loop : -1.29 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.016 0.002 PHE R 285 TYR 0.019 0.001 TYR N 60 ARG 0.017 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00954 ( 2) link_NAG-ASN : angle 4.00492 ( 6) hydrogen bonds : bond 0.03633 ( 418) hydrogen bonds : angle 4.16645 ( 1203) SS BOND : bond 0.00571 ( 10) SS BOND : angle 1.15870 ( 20) covalent geometry : bond 0.00344 ( 9997) covalent geometry : angle 0.54180 (13581) Misc. bond : bond 0.00014 ( 1) *********************** 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 169 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.124 Fit side-chains REVERT: R 141 LYS cc_start: 0.7073 (mtmm) cc_final: 0.6199 (mmpt) REVERT: R 192 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.6710 (tp) REVERT: R 397 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: R 405 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.5687 (tp40) REVERT: A 15 GLU cc_start: 0.6036 (mm-30) cc_final: 0.5662 (mm-30) REVERT: A 21 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6431 (tt0) REVERT: A 27 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: A 58 LYS cc_start: 0.4313 (OUTLIER) cc_final: 0.3426 (mppt) REVERT: A 389 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7053 (ttm110) REVERT: B 44 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6781 (mt0) REVERT: B 45 MET cc_start: 0.7342 (mtt) cc_final: 0.5834 (mmp) REVERT: B 67 SER cc_start: 0.7653 (t) cc_final: 0.7240 (m) REVERT: N 28 THR cc_start: 0.8537 (t) cc_final: 0.8224 (m) REVERT: N 43 LYS cc_start: 0.6805 (ptpt) cc_final: 0.6407 (ptmm) outliers start: 35 outliers final: 15 residues processed: 157 average time/residue: 1.2158 time to fit residues: 205.1707 Evaluate side-chains 155 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain R residue 335 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 R residue 405 GLN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 LYS 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 307 VAL Chi-restraints excluded: chain B residue 327 VAL 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 77 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 105 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5420 ------------------------------------------------------------------------------- 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 35 GLN A 357 HIS A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4279 r_free = 0.4279 target = 0.214971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.179155 restraints weight = 10971.850| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.03 r_work: 0.3651 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10010 Z= 0.104 Angle : 0.510 9.150 13607 Z= 0.265 Chirality : 0.041 0.333 1536 Planarity : 0.003 0.037 1720 Dihedral : 5.203 55.895 1569 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.42 % Allowed : 23.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1236 helix: 1.54 (0.24), residues: 504 sheet: -0.56 (0.36), residues: 210 loop : -1.25 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.019 0.001 TYR N 60 ARG 0.019 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00956 ( 2) link_NAG-ASN : angle 3.99736 ( 6) hydrogen bonds : bond 0.03170 ( 418) hydrogen bonds : angle 4.00883 ( 1203) SS BOND : bond 0.00232 ( 10) SS BOND : angle 0.93929 ( 20) covalent geometry : bond 0.00229 ( 9997) covalent geometry : angle 0.50189 (13581) Misc. bond : bond 0.00010 ( 1) ********************** 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 155 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.000 Fit side-chains REVERT: R 141 LYS cc_start: 0.7097 (mtmm) cc_final: 0.6249 (mmpt) REVERT: R 192 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.6792 (tp) REVERT: R 370 LYS cc_start: 0.6709 (mtpt) cc_final: 0.6234 (mttt) REVERT: R 397 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: R 405 GLN cc_start: 0.5986 (OUTLIER) cc_final: 0.5659 (tp40) REVERT: A 15 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5703 (mm-30) REVERT: A 21 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6437 (tt0) REVERT: A 27 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: A 58 LYS cc_start: 0.4268 (OUTLIER) cc_final: 0.3394 (mppt) REVERT: A 389 ARG cc_start: 0.8025 (tpp80) cc_final: 0.6984 (ttm110) REVERT: B 44 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6853 (mt0) REVERT: B 45 MET cc_start: 0.7327 (mtt) cc_final: 0.5821 (mmp) REVERT: B 59 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: B 67 SER cc_start: 0.7501 (t) cc_final: 0.7062 (m) REVERT: B 267 ASP cc_start: 0.7993 (m-30) cc_final: 0.7720 (m-30) REVERT: N 28 THR cc_start: 0.8501 (t) cc_final: 0.8180 (m) REVERT: N 43 LYS cc_start: 0.6765 (ptpt) cc_final: 0.5843 (pptt) outliers start: 24 outliers final: 11 residues processed: 149 average time/residue: 1.2866 time to fit residues: 205.8819 Evaluate side-chains 149 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 192 ILE 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 R residue 405 GLN 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 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 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 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 67 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 114 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 257 GLN A 35 GLN A 357 HIS A 390 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.212458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.175328 restraints weight = 10929.228| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.70 r_work: 0.3678 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3357 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= 0.131 Angle : 0.538 9.010 13607 Z= 0.280 Chirality : 0.042 0.331 1536 Planarity : 0.004 0.037 1720 Dihedral : 5.402 56.185 1569 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.92 % Allowed : 23.08 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1236 helix: 1.47 (0.24), residues: 505 sheet: -0.58 (0.35), residues: 215 loop : -1.27 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.022 0.001 PHE R 285 TYR 0.019 0.001 TYR N 60 ARG 0.027 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00966 ( 2) link_NAG-ASN : angle 3.94457 ( 6) hydrogen bonds : bond 0.03432 ( 418) hydrogen bonds : angle 4.10476 ( 1203) SS BOND : bond 0.00337 ( 10) SS BOND : angle 0.97458 ( 20) covalent geometry : bond 0.00296 ( 9997) covalent geometry : angle 0.53119 (13581) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9136.18 seconds wall clock time: 161 minutes 14.19 seconds (9674.19 seconds total)