Starting phenix.real_space_refine on Sat Dec 28 11:36:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gag_29898/12_2024/8gag_29898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gag_29898/12_2024/8gag_29898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gag_29898/12_2024/8gag_29898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gag_29898/12_2024/8gag_29898.map" model { file = "/net/cci-nas-00/data/ceres_data/8gag_29898/12_2024/8gag_29898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gag_29898/12_2024/8gag_29898.cif" } resolution = 3.3 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= -0.003 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 61 5.16 5 C 5416 2.51 5 N 1454 2.21 5 O 1535 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8469 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1659 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2018 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "S" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YVF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.65 Number of scatterers: 8469 At special positions: 0 Unit cell: (87.7663, 122.702, 126.111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 F 3 9.00 O 1535 8.00 N 1454 7.00 C 5416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.0% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.916A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 31 Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.777A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.602A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.841A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.639A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 301 through 309 removed outlier: 4.285A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.108A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 4.406A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.230A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.911A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.724A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 112 through 139 removed outlier: 4.154A pdb=" N ALA R 120 " --> pdb=" O GLN R 116 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 179 removed outlier: 4.044A pdb=" N ILE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE R 170 " --> pdb=" O GLY R 166 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE R 175 " --> pdb=" O VAL R 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP R 176 " --> pdb=" O TYR R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 220 removed outlier: 4.313A pdb=" N SER R 199 " --> pdb=" O GLY R 195 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE R 200 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL R 204 " --> pdb=" O PHE R 200 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP R 213 " --> pdb=" O LEU R 209 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 removed outlier: 3.507A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 246 removed outlier: 3.693A pdb=" N VAL R 234 " --> pdb=" O ARG R 230 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 253 removed outlier: 3.967A pdb=" N LEU R 252 " --> pdb=" O ALA R 248 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU R 253 " --> pdb=" O VAL R 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 248 through 253' Processing helix chain 'R' and resid 274 through 312 removed outlier: 4.246A pdb=" N ILE R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY R 281 " --> pdb=" O MET R 277 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL R 282 " --> pdb=" O PHE R 278 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET R 295 " --> pdb=" O VAL R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 356 removed outlier: 4.442A pdb=" N THR R 344 " --> pdb=" O ARG R 340 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL R 346 " --> pdb=" O ALA R 342 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE R 353 " --> pdb=" O LEU R 349 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS R 355 " --> pdb=" O VAL R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 369 removed outlier: 3.706A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL R 367 " --> pdb=" O MET R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 383 removed outlier: 3.555A pdb=" N LYS R 376 " --> pdb=" O ASN R 372 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE R 381 " --> pdb=" O THR R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 397 removed outlier: 3.780A pdb=" N VAL R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN R 393 " --> pdb=" O ASN R 389 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 401 through 411 removed outlier: 3.659A pdb=" N ARG R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS R 406 " --> pdb=" O LYS R 402 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG R 409 " --> pdb=" O ARG R 405 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.798A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.758A pdb=" N SER S 55 " --> pdb=" O SER S 52 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.578A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.616A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 removed outlier: 3.959A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.502A pdb=" N ILE A 265 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 266 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.988A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.055A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.077A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.796A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.819A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.863A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 8 removed outlier: 4.017A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.954A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.509A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR S 203 " --> pdb=" O SER S 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER S 192 " --> pdb=" O THR S 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.596A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.596A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 987 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: 2.59 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1337 1.31 - 1.44: 2420 1.44 - 1.57: 4799 1.57 - 1.70: 2 1.70 - 1.83: 87 Bond restraints: 8645 Sorted by residual: bond pdb=" C06 YVF R 501 " pdb=" C07 YVF R 501 " ideal model delta sigma weight residual 1.420 1.527 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C05 YVF R 501 " pdb=" S09 YVF R 501 " ideal model delta sigma weight residual 1.722 1.616 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C12 YVF R 501 " pdb=" N11 YVF R 501 " ideal model delta sigma weight residual 1.345 1.450 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C08 YVF R 501 " pdb=" S09 YVF R 501 " ideal model delta sigma weight residual 1.710 1.616 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C03 YVF R 501 " pdb=" O02 YVF R 501 " ideal model delta sigma weight residual 1.318 1.399 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 8640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 11307 1.86 - 3.71: 349 3.71 - 5.57: 61 5.57 - 7.43: 12 7.43 - 9.28: 6 Bond angle restraints: 11735 Sorted by residual: angle pdb=" C05 YVF R 501 " pdb=" S09 YVF R 501 " pdb=" C08 YVF R 501 " ideal model delta sigma weight residual 92.16 101.44 -9.28 3.00e+00 1.11e-01 9.58e+00 angle pdb=" C SER A 293 " pdb=" N ASN A 294 " pdb=" CA ASN A 294 " ideal model delta sigma weight residual 124.82 130.08 -5.26 1.78e+00 3.16e-01 8.74e+00 angle pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " pdb=" CG TYR S 178 " ideal model delta sigma weight residual 113.90 119.12 -5.22 1.80e+00 3.09e-01 8.42e+00 angle pdb=" CA ASP B 247 " pdb=" CB ASP B 247 " pdb=" CG ASP B 247 " ideal model delta sigma weight residual 112.60 115.47 -2.87 1.00e+00 1.00e+00 8.25e+00 angle pdb=" CA LYS S 43 " pdb=" CB LYS S 43 " pdb=" CG LYS S 43 " ideal model delta sigma weight residual 114.10 119.52 -5.42 2.00e+00 2.50e-01 7.36e+00 ... (remaining 11730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4487 17.93 - 35.86: 496 35.86 - 53.79: 95 53.79 - 71.72: 12 71.72 - 89.65: 10 Dihedral angle restraints: 5100 sinusoidal: 1884 harmonic: 3216 Sorted by residual: dihedral pdb=" CA MET B 325 " pdb=" C MET B 325 " pdb=" N ALA B 326 " pdb=" CA ALA B 326 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLY S 26 " pdb=" C GLY S 26 " pdb=" N PHE S 27 " pdb=" CA PHE S 27 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1051 0.052 - 0.105: 246 0.105 - 0.157: 59 0.157 - 0.209: 3 0.209 - 0.262: 1 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA ASP S 109 " pdb=" N ASP S 109 " pdb=" C ASP S 109 " pdb=" CB ASP S 109 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1357 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 47 " 0.023 2.00e-02 2.50e+03 1.72e-02 7.41e+00 pdb=" CG TRP S 47 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP S 47 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP S 47 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP S 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP S 47 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP S 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 47 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 47 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP S 47 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO C 49 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 180 " 0.013 2.00e-02 2.50e+03 1.60e-02 4.49e+00 pdb=" CG PHE R 180 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE R 180 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 180 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE R 180 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 180 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 180 " 0.001 2.00e-02 2.50e+03 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 194 2.69 - 3.24: 8182 3.24 - 3.79: 12256 3.79 - 4.35: 16124 4.35 - 4.90: 27132 Nonbonded interactions: 63888 Sorted by model distance: nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.132 3.040 nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.137 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.168 3.040 nonbonded pdb=" ND1 HIS R 302 " pdb=" OD2 ASP R 338 " model vdw 2.178 3.120 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.183 3.040 ... (remaining 63883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.410 Find NCS groups from input model: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 8645 Z= 0.341 Angle : 0.811 9.284 11735 Z= 0.432 Chirality : 0.048 0.262 1360 Planarity : 0.005 0.058 1471 Dihedral : 15.819 89.648 3019 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.24), residues: 1088 helix: -0.95 (0.26), residues: 355 sheet: -1.28 (0.32), residues: 253 loop : -1.14 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP S 47 HIS 0.012 0.002 HIS B 311 PHE 0.037 0.003 PHE R 180 TYR 0.026 0.003 TYR S 223 ARG 0.007 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.947 Fit side-chains REVERT: R 343 LYS cc_start: 0.7367 (ttpt) cc_final: 0.7163 (ttpp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2274 time to fit residues: 32.7135 Evaluate side-chains 96 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8645 Z= 0.199 Angle : 0.655 6.974 11735 Z= 0.344 Chirality : 0.044 0.177 1360 Planarity : 0.004 0.035 1471 Dihedral : 6.283 70.745 1226 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.68 % Allowed : 12.33 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.25), residues: 1088 helix: -0.19 (0.28), residues: 361 sheet: -0.81 (0.32), residues: 251 loop : -0.89 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.002 PHE R 237 TYR 0.021 0.002 TYR S 223 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.894 Fit side-chains REVERT: S 225 LEU cc_start: 0.5005 (mt) cc_final: 0.4782 (mt) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.2048 time to fit residues: 30.0702 Evaluate side-chains 93 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain R residue 354 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 32 GLN R 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8645 Z= 0.235 Angle : 0.630 6.449 11735 Z= 0.334 Chirality : 0.044 0.173 1360 Planarity : 0.004 0.038 1471 Dihedral : 6.078 63.926 1226 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.26 % Allowed : 16.21 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.25), residues: 1088 helix: 0.01 (0.28), residues: 361 sheet: -0.76 (0.32), residues: 247 loop : -0.80 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP S 47 HIS 0.007 0.001 HIS B 311 PHE 0.018 0.002 PHE R 237 TYR 0.022 0.002 TYR S 50 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.070 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.2289 time to fit residues: 30.9190 Evaluate side-chains 96 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 44 GLN R 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8645 Z= 0.351 Angle : 0.705 8.427 11735 Z= 0.375 Chirality : 0.046 0.173 1360 Planarity : 0.004 0.038 1471 Dihedral : 6.334 54.996 1226 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.28 % Allowed : 21.00 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.25), residues: 1088 helix: -0.27 (0.28), residues: 363 sheet: -1.18 (0.31), residues: 268 loop : -0.90 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP S 47 HIS 0.008 0.001 HIS B 311 PHE 0.023 0.002 PHE R 237 TYR 0.033 0.003 TYR S 50 ARG 0.003 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.897 Fit side-chains REVERT: A 223 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: B 49 ARG cc_start: 0.7062 (tpp-160) cc_final: 0.6847 (tpp-160) outliers start: 20 outliers final: 15 residues processed: 112 average time/residue: 0.2105 time to fit residues: 32.7459 Evaluate side-chains 106 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 44 GLN R 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8645 Z= 0.183 Angle : 0.586 7.666 11735 Z= 0.310 Chirality : 0.042 0.172 1360 Planarity : 0.004 0.035 1471 Dihedral : 5.815 58.436 1226 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.83 % Allowed : 22.95 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.26), residues: 1088 helix: 0.06 (0.28), residues: 364 sheet: -0.89 (0.31), residues: 257 loop : -0.76 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 47 HIS 0.003 0.001 HIS B 311 PHE 0.016 0.001 PHE R 237 TYR 0.016 0.001 TYR S 223 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.983 Fit side-chains REVERT: A 52 GLN cc_start: 0.5190 (OUTLIER) cc_final: 0.4782 (pm20) outliers start: 16 outliers final: 11 residues processed: 107 average time/residue: 0.2084 time to fit residues: 31.1526 Evaluate side-chains 103 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.0020 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 181 HIS S 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8645 Z= 0.340 Angle : 0.695 10.147 11735 Z= 0.366 Chirality : 0.046 0.178 1360 Planarity : 0.004 0.037 1471 Dihedral : 6.182 51.439 1226 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.54 % Allowed : 22.37 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.25), residues: 1088 helix: -0.05 (0.28), residues: 356 sheet: -1.21 (0.31), residues: 267 loop : -0.87 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP S 47 HIS 0.007 0.001 HIS B 311 PHE 0.023 0.002 PHE B 199 TYR 0.030 0.002 TYR S 50 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.983 Fit side-chains REVERT: A 52 GLN cc_start: 0.5278 (OUTLIER) cc_final: 0.4404 (pm20) REVERT: A 223 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: B 49 ARG cc_start: 0.7045 (tpp-160) cc_final: 0.6762 (tpp-160) REVERT: B 70 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6666 (pt) outliers start: 31 outliers final: 23 residues processed: 121 average time/residue: 0.2074 time to fit residues: 35.0541 Evaluate side-chains 121 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 76 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 44 GLN R 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8645 Z= 0.177 Angle : 0.577 6.812 11735 Z= 0.304 Chirality : 0.042 0.169 1360 Planarity : 0.004 0.034 1471 Dihedral : 5.669 56.055 1226 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.08 % Allowed : 23.40 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.26), residues: 1088 helix: 0.31 (0.29), residues: 356 sheet: -0.92 (0.32), residues: 258 loop : -0.68 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP S 47 HIS 0.004 0.001 HIS B 311 PHE 0.015 0.001 PHE R 237 TYR 0.012 0.001 TYR S 223 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.896 Fit side-chains REVERT: A 52 GLN cc_start: 0.5141 (OUTLIER) cc_final: 0.4407 (pm20) REVERT: A 223 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: R 109 MET cc_start: 0.5428 (ptm) cc_final: 0.5218 (ptm) REVERT: R 289 PHE cc_start: 0.5416 (m-10) cc_final: 0.5044 (m-80) outliers start: 27 outliers final: 22 residues processed: 121 average time/residue: 0.1871 time to fit residues: 32.3007 Evaluate side-chains 121 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8645 Z= 0.290 Angle : 0.653 6.994 11735 Z= 0.345 Chirality : 0.044 0.172 1360 Planarity : 0.004 0.035 1471 Dihedral : 5.935 50.489 1226 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.22 % Allowed : 23.40 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.26), residues: 1088 helix: 0.16 (0.29), residues: 356 sheet: -1.04 (0.31), residues: 266 loop : -0.77 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP S 47 HIS 0.005 0.001 HIS R 304 PHE 0.029 0.002 PHE B 292 TYR 0.026 0.002 TYR S 50 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.935 Fit side-chains REVERT: A 52 GLN cc_start: 0.5238 (OUTLIER) cc_final: 0.4280 (pm20) REVERT: A 223 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: A 354 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5745 (t80) REVERT: B 49 ARG cc_start: 0.6935 (tpp-160) cc_final: 0.6648 (tpp-160) outliers start: 37 outliers final: 28 residues processed: 122 average time/residue: 0.2137 time to fit residues: 36.3575 Evaluate side-chains 126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain R residue 279 TRP Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8645 Z= 0.174 Angle : 0.585 7.292 11735 Z= 0.308 Chirality : 0.042 0.167 1360 Planarity : 0.004 0.037 1471 Dihedral : 5.623 53.777 1226 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.42 % Allowed : 23.97 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.26), residues: 1088 helix: 0.41 (0.29), residues: 358 sheet: -0.92 (0.32), residues: 255 loop : -0.61 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP S 47 HIS 0.002 0.001 HIS B 142 PHE 0.015 0.001 PHE R 237 TYR 0.014 0.001 TYR S 223 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.891 Fit side-chains REVERT: A 52 GLN cc_start: 0.5194 (OUTLIER) cc_final: 0.4204 (pm20) REVERT: A 223 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.6973 (m-80) REVERT: B 49 ARG cc_start: 0.6811 (tpp-160) cc_final: 0.6558 (tpp-160) REVERT: R 289 PHE cc_start: 0.5384 (m-10) cc_final: 0.5020 (m-80) outliers start: 30 outliers final: 28 residues processed: 114 average time/residue: 0.1935 time to fit residues: 31.3083 Evaluate side-chains 123 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain R residue 279 TRP Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 0.0040 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.0030 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8645 Z= 0.145 Angle : 0.553 9.852 11735 Z= 0.288 Chirality : 0.041 0.163 1360 Planarity : 0.003 0.039 1471 Dihedral : 5.282 54.848 1226 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.63 % Allowed : 24.77 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.27), residues: 1088 helix: 0.58 (0.29), residues: 364 sheet: -0.76 (0.32), residues: 259 loop : -0.41 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP S 47 HIS 0.002 0.000 HIS S 35 PHE 0.013 0.001 PHE R 237 TYR 0.013 0.001 TYR R 296 ARG 0.004 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.004 Fit side-chains REVERT: A 52 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.4189 (pm20) REVERT: A 354 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.5525 (t80) REVERT: S 128 MET cc_start: 0.5487 (mmm) cc_final: 0.5263 (mmp) outliers start: 23 outliers final: 17 residues processed: 119 average time/residue: 0.1911 time to fit residues: 32.5526 Evaluate side-chains 112 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 279 TRP Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 85 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.197034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.158540 restraints weight = 9774.866| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.12 r_work: 0.3713 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8645 Z= 0.155 Angle : 0.563 9.865 11735 Z= 0.293 Chirality : 0.041 0.164 1360 Planarity : 0.004 0.039 1471 Dihedral : 5.275 53.065 1226 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.85 % Allowed : 24.66 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.27), residues: 1088 helix: 0.67 (0.29), residues: 364 sheet: -0.70 (0.32), residues: 255 loop : -0.36 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP S 47 HIS 0.002 0.000 HIS B 142 PHE 0.013 0.001 PHE R 237 TYR 0.022 0.001 TYR S 59 ARG 0.006 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.62 seconds wall clock time: 39 minutes 54.61 seconds (2394.61 seconds total)