Starting phenix.real_space_refine on Wed Mar 12 14:46:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvn_32145/03_2025/7vvn_32145.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvn_32145/03_2025/7vvn_32145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vvn_32145/03_2025/7vvn_32145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvn_32145/03_2025/7vvn_32145.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvn_32145/03_2025/7vvn_32145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvn_32145/03_2025/7vvn_32145.cif" } resolution = 3.8 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 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 47 5.16 5 C 5147 2.51 5 N 1427 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8130 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1845 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2544 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 410 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 196 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'PHE%COO:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "R" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2169 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain breaks: 9 Unresolved non-hydrogen bonds: 363 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 5, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 252 Time building chain proxies: 5.18, per 1000 atoms: 0.64 Number of scatterers: 8130 At special positions: 0 Unit cell: (123.947, 105.134, 115.094, 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 47 16.00 O 1509 8.00 N 1427 7.00 C 5147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.09 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 11 sheets defined 41.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.864A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.502A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.549A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.875A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.557A pdb=" N GLU A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.135A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.548A pdb=" N ARG A 307 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.572A pdb=" N ALA A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 382 removed outlier: 3.574A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.730A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.013A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.545A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.004A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 16 through 19 removed outlier: 4.105A pdb=" N GLU P 19 " --> pdb=" O ASN P 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 16 through 19' Processing helix chain 'P' and resid 20 through 34 Processing helix chain 'R' and resid 34 through 49 Processing helix chain 'R' and resid 182 through 207 removed outlier: 3.634A pdb=" N GLY R 188 " --> pdb=" O PHE R 184 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET R 189 " --> pdb=" O ASP R 185 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY R 194 " --> pdb=" O ILE R 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 211 Processing helix chain 'R' and resid 219 through 244 removed outlier: 3.596A pdb=" N MET R 224 " --> pdb=" O ASN R 220 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS R 225 " --> pdb=" O TYR R 221 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS R 240 " --> pdb=" O SER R 236 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 312 removed outlier: 3.900A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER R 308 " --> pdb=" O LEU R 304 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET R 312 " --> pdb=" O SER R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 326 Processing helix chain 'R' and resid 329 through 346 removed outlier: 3.758A pdb=" N ALA R 333 " --> pdb=" O TRP R 329 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL R 338 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP R 339 " --> pdb=" O PHE R 335 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER R 341 " --> pdb=" O ALA R 337 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL R 342 " --> pdb=" O VAL R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 379 Processing helix chain 'R' and resid 381 through 391 removed outlier: 3.704A pdb=" N LEU R 385 " --> pdb=" O ILE R 381 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG R 390 " --> pdb=" O ALA R 386 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU R 391 " --> pdb=" O THR R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 401 through 413 removed outlier: 3.656A pdb=" N LEU R 407 " --> pdb=" O TYR R 403 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 412 " --> pdb=" O LYS R 408 " (cutoff:3.500A) Processing helix chain 'R' and resid 418 through 420 No H-bonds generated for 'chain 'R' and resid 418 through 420' Processing helix chain 'R' and resid 421 through 426 removed outlier: 4.589A pdb=" N ALA R 426 " --> pdb=" O ILE R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 451 removed outlier: 3.754A pdb=" N GLU R 444 " --> pdb=" O GLN R 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 452 through 454 No H-bonds generated for 'chain 'R' and resid 452 through 454' Processing helix chain 'R' and resid 455 through 461 Processing helix chain 'R' and resid 463 through 480 removed outlier: 3.710A pdb=" N LYS R 472 " --> pdb=" O ALA R 468 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER R 475 " --> pdb=" O LYS R 471 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA R 480 " --> pdb=" O ARG R 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.712A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 210 removed outlier: 5.903A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 7.242A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.521A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.482A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.610A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.912A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.550A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.514A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.152A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 996 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: 2.14 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1368 1.32 - 1.45: 2255 1.45 - 1.57: 4593 1.57 - 1.70: 0 1.70 - 1.83: 66 Bond restraints: 8282 Sorted by residual: bond pdb=" CA SER B 97 " pdb=" CB SER B 97 " ideal model delta sigma weight residual 1.526 1.461 0.066 1.53e-02 4.27e+03 1.85e+01 bond pdb=" N VAL R 455 " pdb=" CA VAL R 455 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.06e-02 8.90e+03 1.44e+01 bond pdb=" C SER B 72 " pdb=" O SER B 72 " ideal model delta sigma weight residual 1.234 1.188 0.046 1.22e-02 6.72e+03 1.42e+01 bond pdb=" N HIS R 420 " pdb=" CA HIS R 420 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.23e-02 6.61e+03 1.26e+01 bond pdb=" CA SER B 160 " pdb=" CB SER B 160 " ideal model delta sigma weight residual 1.531 1.478 0.052 1.52e-02 4.33e+03 1.19e+01 ... (remaining 8277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 6672 1.51 - 3.01: 3549 3.01 - 4.52: 927 4.52 - 6.02: 97 6.02 - 7.53: 6 Bond angle restraints: 11251 Sorted by residual: angle pdb=" CA PHE R 335 " pdb=" CB PHE R 335 " pdb=" CG PHE R 335 " ideal model delta sigma weight residual 113.80 108.42 5.38 1.00e+00 1.00e+00 2.90e+01 angle pdb=" C GLU B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta sigma weight residual 119.98 125.38 -5.40 1.11e+00 8.12e-01 2.37e+01 angle pdb=" C ASP A 215 " pdb=" CA ASP A 215 " pdb=" CB ASP A 215 " ideal model delta sigma weight residual 111.80 118.72 -6.92 1.46e+00 4.69e-01 2.25e+01 angle pdb=" CA ILE R 381 " pdb=" C ILE R 381 " pdb=" O ILE R 381 " ideal model delta sigma weight residual 119.29 115.44 3.85 8.40e-01 1.42e+00 2.10e+01 angle pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" O ARG A 231 " ideal model delta sigma weight residual 121.34 116.02 5.32 1.18e+00 7.18e-01 2.04e+01 ... (remaining 11246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4351 17.93 - 35.85: 444 35.85 - 53.78: 69 53.78 - 71.71: 15 71.71 - 89.63: 9 Dihedral angle restraints: 4888 sinusoidal: 1738 harmonic: 3150 Sorted by residual: dihedral pdb=" CA PHE R 314 " pdb=" C PHE R 314 " pdb=" N PHE R 315 " pdb=" CA PHE R 315 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU B 190 " pdb=" C LEU B 190 " pdb=" N SER B 191 " pdb=" CA SER B 191 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 4885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 601 0.057 - 0.113: 463 0.113 - 0.170: 189 0.170 - 0.226: 44 0.226 - 0.283: 4 Chirality restraints: 1301 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE B 338 " pdb=" CA ILE B 338 " pdb=" CG1 ILE B 338 " pdb=" CG2 ILE B 338 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE B 229 " pdb=" CA ILE B 229 " pdb=" CG1 ILE B 229 " pdb=" CG2 ILE B 229 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1298 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 335 " -0.046 2.00e-02 2.50e+03 3.20e-02 1.80e+01 pdb=" CG PHE R 335 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE R 335 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 335 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 335 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE R 335 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE R 335 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.034 2.00e-02 2.50e+03 2.42e-02 1.18e+01 pdb=" CG TYR B 59 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 339 " -0.032 2.00e-02 2.50e+03 1.90e-02 9.06e+00 pdb=" CG TRP B 339 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 339 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 339 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP B 339 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 339 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 339 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 339 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 339 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 339 " -0.005 2.00e-02 2.50e+03 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 377 2.73 - 3.27: 8411 3.27 - 3.81: 12432 3.81 - 4.36: 16717 4.36 - 4.90: 26899 Nonbonded interactions: 64836 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.185 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.266 3.040 nonbonded pdb=" O SER N 30 " pdb=" NE2 GLN N 53 " model vdw 2.286 3.120 ... (remaining 64831 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.013 0.066 8282 Z= 0.890 Angle : 1.780 7.525 11251 Z= 1.314 Chirality : 0.084 0.283 1301 Planarity : 0.006 0.032 1446 Dihedral : 15.145 89.634 2828 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.83 % Rotamer: Outliers : 0.37 % Allowed : 7.49 % Favored : 92.13 % 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: -2.22 (0.23), residues: 1054 helix: -0.50 (0.24), residues: 388 sheet: -2.25 (0.31), residues: 176 loop : -1.91 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.007 TRP B 339 HIS 0.023 0.005 HIS R 420 PHE 0.068 0.006 PHE R 335 TYR 0.058 0.007 TYR B 59 ARG 0.015 0.002 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.4218 (mm-40) cc_final: 0.4009 (mm110) REVERT: A 27 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6850 (mm-30) REVERT: A 28 LYS cc_start: 0.8166 (tttm) cc_final: 0.7740 (ttmt) REVERT: A 34 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7383 (tmtt) REVERT: A 38 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8350 (mmm-85) REVERT: A 230 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8275 (mp0) REVERT: A 270 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7900 (ttm110) REVERT: A 284 GLN cc_start: 0.7188 (mm110) cc_final: 0.6983 (mm110) REVERT: A 297 LYS cc_start: 0.8263 (ptpp) cc_final: 0.7584 (ptmt) REVERT: A 360 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6658 (tp30) REVERT: B 23 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7288 (mptt) REVERT: B 35 ASN cc_start: 0.7926 (t0) cc_final: 0.7710 (t0) REVERT: B 42 ARG cc_start: 0.7081 (tpm170) cc_final: 0.6450 (mmt90) REVERT: B 52 ARG cc_start: 0.7708 (mtt90) cc_final: 0.7252 (mmt90) REVERT: B 82 TRP cc_start: 0.8751 (m-90) cc_final: 0.8364 (m-90) REVERT: B 85 TYR cc_start: 0.7751 (m-80) cc_final: 0.7497 (m-80) REVERT: B 124 TYR cc_start: 0.8483 (m-80) cc_final: 0.8081 (m-80) REVERT: B 217 MET cc_start: 0.7585 (ppp) cc_final: 0.7220 (ppp) REVERT: B 219 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7842 (ttp80) REVERT: B 261 LEU cc_start: 0.7442 (mm) cc_final: 0.7094 (mp) REVERT: B 268 ASN cc_start: 0.8492 (m-40) cc_final: 0.8183 (t0) REVERT: B 280 LYS cc_start: 0.7070 (mmtm) cc_final: 0.5984 (ttmt) REVERT: G 38 MET cc_start: 0.8542 (mmm) cc_final: 0.8199 (mmm) REVERT: G 44 HIS cc_start: 0.8279 (m-70) cc_final: 0.8040 (m-70) REVERT: N 5 GLN cc_start: 0.8055 (mt0) cc_final: 0.7835 (pm20) REVERT: N 32 TYR cc_start: 0.8029 (m-80) cc_final: 0.7734 (m-80) REVERT: N 39 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8165 (tp-100) REVERT: N 80 TYR cc_start: 0.8153 (m-80) cc_final: 0.7863 (m-80) REVERT: N 83 MET cc_start: 0.7999 (mmm) cc_final: 0.7789 (mmt) REVERT: N 95 TYR cc_start: 0.7829 (m-80) cc_final: 0.7501 (m-80) REVERT: R 185 ASP cc_start: 0.7416 (m-30) cc_final: 0.7152 (m-30) REVERT: R 220 ASN cc_start: 0.7792 (m110) cc_final: 0.7457 (m-40) REVERT: R 312 MET cc_start: 0.6686 (mmt) cc_final: 0.6147 (mtp) REVERT: R 408 LYS cc_start: 0.7138 (tttp) cc_final: 0.6896 (tmtt) REVERT: R 466 VAL cc_start: 0.8131 (p) cc_final: 0.7549 (m) REVERT: R 470 ILE cc_start: 0.7897 (tt) cc_final: 0.7608 (pt) outliers start: 3 outliers final: 0 residues processed: 206 average time/residue: 0.2317 time to fit residues: 62.4423 Evaluate side-chains 139 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 17 GLN B 340 ASN R 295 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.143375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120533 restraints weight = 13609.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122962 restraints weight = 8612.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124380 restraints weight = 6241.503| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8282 Z= 0.296 Angle : 0.653 7.560 11251 Z= 0.347 Chirality : 0.042 0.146 1301 Planarity : 0.004 0.033 1446 Dihedral : 5.322 38.344 1163 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.50 % Allowed : 14.36 % Favored : 83.15 % 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: -1.10 (0.25), residues: 1054 helix: 0.46 (0.25), residues: 409 sheet: -1.72 (0.32), residues: 215 loop : -1.25 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.008 0.001 HIS A 347 PHE 0.025 0.002 PHE R 454 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.4419 (mm-40) cc_final: 0.4171 (mm110) REVERT: A 28 LYS cc_start: 0.6626 (tttm) cc_final: 0.6353 (ttmt) REVERT: A 360 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7092 (tp30) REVERT: B 23 LYS cc_start: 0.7328 (mmmt) cc_final: 0.6767 (mmtp) REVERT: B 219 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7727 (ttp-170) REVERT: R 231 MET cc_start: 0.7260 (mmt) cc_final: 0.6979 (mmp) REVERT: R 413 LEU cc_start: 0.7138 (tt) cc_final: 0.6885 (tp) REVERT: R 466 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7674 (t) REVERT: R 470 ILE cc_start: 0.8234 (tt) cc_final: 0.7959 (pt) outliers start: 20 outliers final: 14 residues processed: 165 average time/residue: 0.2311 time to fit residues: 50.0602 Evaluate side-chains 137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 466 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN N 53 GLN N 74 ASN P 10 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.146032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123306 restraints weight = 13594.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125914 restraints weight = 8500.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127743 restraints weight = 6063.246| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8282 Z= 0.189 Angle : 0.558 6.197 11251 Z= 0.297 Chirality : 0.040 0.143 1301 Planarity : 0.003 0.027 1446 Dihedral : 4.764 27.749 1159 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.87 % Allowed : 17.48 % Favored : 79.65 % 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: -0.58 (0.26), residues: 1054 helix: 0.89 (0.26), residues: 403 sheet: -1.32 (0.32), residues: 212 loop : -1.01 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 347 PHE 0.019 0.001 PHE R 454 TYR 0.019 0.001 TYR R 191 ARG 0.005 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.4678 (mm-40) cc_final: 0.4444 (mm110) REVERT: A 27 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 28 LYS cc_start: 0.6550 (tttm) cc_final: 0.6282 (ttmm) REVERT: B 6 GLN cc_start: 0.4298 (tm-30) cc_final: 0.3830 (pt0) REVERT: B 23 LYS cc_start: 0.7308 (mmmt) cc_final: 0.6848 (mppt) REVERT: B 82 TRP cc_start: 0.7596 (m-90) cc_final: 0.6935 (m-90) REVERT: B 215 GLU cc_start: 0.6939 (mp0) cc_final: 0.6643 (mt-10) REVERT: B 219 ARG cc_start: 0.8097 (mtp-110) cc_final: 0.7850 (ttt-90) REVERT: B 261 LEU cc_start: 0.6706 (mm) cc_final: 0.6281 (mp) REVERT: R 231 MET cc_start: 0.7361 (mmt) cc_final: 0.7122 (mmp) REVERT: R 466 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7662 (t) outliers start: 23 outliers final: 14 residues processed: 164 average time/residue: 0.2172 time to fit residues: 47.8340 Evaluate side-chains 145 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 466 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 74 ASN P 10 ASN R 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119873 restraints weight = 14289.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119910 restraints weight = 11870.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120283 restraints weight = 10284.866| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8282 Z= 0.280 Angle : 0.596 7.297 11251 Z= 0.318 Chirality : 0.042 0.149 1301 Planarity : 0.004 0.033 1446 Dihedral : 4.849 26.193 1159 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.49 % Allowed : 19.60 % Favored : 75.91 % 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: -0.54 (0.26), residues: 1054 helix: 0.85 (0.26), residues: 391 sheet: -1.38 (0.34), residues: 201 loop : -0.83 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 347 PHE 0.026 0.002 PHE R 454 TYR 0.019 0.002 TYR B 105 ARG 0.005 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6870 (tttp) REVERT: B 52 ARG cc_start: 0.7263 (mmt90) cc_final: 0.6876 (mtt90) REVERT: B 215 GLU cc_start: 0.6856 (mp0) cc_final: 0.6483 (mt-10) REVERT: B 219 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7855 (ttt-90) REVERT: B 261 LEU cc_start: 0.6783 (mm) cc_final: 0.6423 (mp) REVERT: B 284 LEU cc_start: 0.7339 (mp) cc_final: 0.7128 (tp) REVERT: R 231 MET cc_start: 0.7517 (mmt) cc_final: 0.7192 (mmp) REVERT: R 466 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7742 (t) outliers start: 36 outliers final: 25 residues processed: 161 average time/residue: 0.1982 time to fit residues: 43.5390 Evaluate side-chains 142 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 78 optimal weight: 0.0070 chunk 64 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 340 ASN N 74 ASN P 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.141016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121967 restraints weight = 13991.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.122281 restraints weight = 11624.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122501 restraints weight = 9809.440| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8282 Z= 0.210 Angle : 0.559 7.960 11251 Z= 0.295 Chirality : 0.040 0.144 1301 Planarity : 0.003 0.036 1446 Dihedral : 4.670 26.831 1159 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.12 % Allowed : 19.85 % Favored : 75.03 % 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: -0.31 (0.26), residues: 1054 helix: 0.95 (0.27), residues: 393 sheet: -1.10 (0.33), residues: 218 loop : -0.67 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.028 0.002 PHE A 222 TYR 0.013 0.001 TYR R 459 ARG 0.003 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7701 (mmm-85) REVERT: A 369 CYS cc_start: 0.7023 (p) cc_final: 0.6401 (m) REVERT: B 23 LYS cc_start: 0.7225 (mmmt) cc_final: 0.6891 (tttp) REVERT: B 52 ARG cc_start: 0.7294 (mmt90) cc_final: 0.6983 (mtt90) REVERT: B 215 GLU cc_start: 0.6772 (mp0) cc_final: 0.6460 (mt-10) REVERT: B 219 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7783 (ttt-90) REVERT: R 231 MET cc_start: 0.7524 (mmt) cc_final: 0.7227 (mmp) REVERT: R 466 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7738 (t) outliers start: 41 outliers final: 29 residues processed: 165 average time/residue: 0.1900 time to fit residues: 43.3138 Evaluate side-chains 151 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 466 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 0.0040 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN N 53 GLN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124940 restraints weight = 14074.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125314 restraints weight = 11210.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.126969 restraints weight = 9353.272| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8282 Z= 0.158 Angle : 0.536 9.900 11251 Z= 0.281 Chirality : 0.039 0.130 1301 Planarity : 0.003 0.037 1446 Dihedral : 4.426 31.863 1159 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.62 % Allowed : 22.10 % Favored : 73.28 % 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: -0.12 (0.27), residues: 1054 helix: 0.96 (0.26), residues: 401 sheet: -0.87 (0.35), residues: 203 loop : -0.53 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.001 PHE R 454 TYR 0.011 0.001 TYR B 264 ARG 0.003 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 369 CYS cc_start: 0.6831 (p) cc_final: 0.6242 (m) REVERT: B 23 LYS cc_start: 0.7269 (mmmt) cc_final: 0.6904 (tttp) REVERT: B 52 ARG cc_start: 0.7194 (mmt90) cc_final: 0.6968 (mtt90) REVERT: B 215 GLU cc_start: 0.6882 (mp0) cc_final: 0.6675 (mt-10) REVERT: B 219 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7717 (ttt-90) REVERT: B 234 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: B 254 ASP cc_start: 0.6165 (t70) cc_final: 0.5921 (t70) REVERT: B 261 LEU cc_start: 0.6759 (mm) cc_final: 0.6447 (mp) REVERT: P 15 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6333 (tt) REVERT: R 292 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7873 (tp) REVERT: R 466 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7694 (t) outliers start: 37 outliers final: 24 residues processed: 161 average time/residue: 0.1997 time to fit residues: 43.9768 Evaluate side-chains 157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 450 PHE Chi-restraints excluded: chain R residue 466 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 5.9990 chunk 80 optimal weight: 50.0000 chunk 67 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 340 ASN G 18 GLN N 53 GLN N 74 ASN P 10 ASN R 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.138308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120167 restraints weight = 14280.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119609 restraints weight = 11207.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.120848 restraints weight = 10101.555| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8282 Z= 0.310 Angle : 0.631 10.303 11251 Z= 0.330 Chirality : 0.042 0.153 1301 Planarity : 0.004 0.034 1446 Dihedral : 4.871 30.834 1159 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.49 % Allowed : 21.72 % Favored : 72.78 % 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: -0.41 (0.26), residues: 1054 helix: 0.77 (0.26), residues: 395 sheet: -1.13 (0.33), residues: 209 loop : -0.65 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.008 0.001 HIS A 347 PHE 0.027 0.002 PHE A 222 TYR 0.017 0.002 TYR B 105 ARG 0.003 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8262 (tpp80) cc_final: 0.7702 (mmm-85) REVERT: A 369 CYS cc_start: 0.6768 (p) cc_final: 0.6325 (m) REVERT: B 23 LYS cc_start: 0.7179 (mmmt) cc_final: 0.6820 (tttp) REVERT: B 215 GLU cc_start: 0.6941 (mp0) cc_final: 0.6674 (mt-10) REVERT: B 219 ARG cc_start: 0.8242 (mtp-110) cc_final: 0.7749 (ttt-90) REVERT: B 234 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: B 261 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6433 (mp) REVERT: R 192 THR cc_start: 0.7686 (m) cc_final: 0.7296 (p) REVERT: R 327 PHE cc_start: 0.7349 (t80) cc_final: 0.7104 (t80) REVERT: R 466 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7835 (t) outliers start: 44 outliers final: 31 residues processed: 150 average time/residue: 0.1945 time to fit residues: 39.8212 Evaluate side-chains 145 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 450 PHE Chi-restraints excluded: chain R residue 466 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 87 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 340 ASN N 53 GLN N 74 ASN R 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125042 restraints weight = 14112.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125545 restraints weight = 11111.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127973 restraints weight = 8699.253| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8282 Z= 0.151 Angle : 0.551 9.050 11251 Z= 0.285 Chirality : 0.039 0.141 1301 Planarity : 0.003 0.030 1446 Dihedral : 4.462 27.810 1159 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.87 % Allowed : 23.35 % Favored : 72.78 % 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: -0.13 (0.26), residues: 1054 helix: 0.96 (0.26), residues: 398 sheet: -0.90 (0.34), residues: 204 loop : -0.51 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.016 0.001 PHE R 454 TYR 0.012 0.001 TYR B 264 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 38 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7633 (mmm-85) REVERT: A 369 CYS cc_start: 0.6557 (p) cc_final: 0.6274 (m) REVERT: B 23 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6832 (tttp) REVERT: B 45 MET cc_start: 0.7050 (mtp) cc_final: 0.6738 (mtp) REVERT: B 52 ARG cc_start: 0.7208 (mmt90) cc_final: 0.6657 (mmt180) REVERT: B 215 GLU cc_start: 0.7032 (mp0) cc_final: 0.6811 (mt-10) REVERT: B 219 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7701 (ttt-90) REVERT: B 234 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6299 (m-80) REVERT: B 261 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6217 (mp) REVERT: B 317 CYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7498 (p) REVERT: P 15 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6373 (tt) REVERT: R 292 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7869 (tp) outliers start: 31 outliers final: 22 residues processed: 150 average time/residue: 0.1961 time to fit residues: 40.0836 Evaluate side-chains 146 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 450 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 80 optimal weight: 50.0000 chunk 97 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.141436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121171 restraints weight = 14450.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123061 restraints weight = 9840.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124070 restraints weight = 7502.663| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8282 Z= 0.224 Angle : 0.584 9.210 11251 Z= 0.302 Chirality : 0.040 0.192 1301 Planarity : 0.003 0.030 1446 Dihedral : 4.567 35.158 1159 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.62 % Allowed : 22.35 % Favored : 73.03 % 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: -0.21 (0.26), residues: 1054 helix: 0.94 (0.26), residues: 400 sheet: -0.94 (0.34), residues: 198 loop : -0.64 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.020 0.002 PHE R 454 TYR 0.014 0.002 TYR B 264 ARG 0.004 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7649 (mmm-85) REVERT: A 369 CYS cc_start: 0.6584 (p) cc_final: 0.6307 (m) REVERT: B 23 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6832 (tttp) REVERT: B 45 MET cc_start: 0.6991 (mtp) cc_final: 0.6606 (mtp) REVERT: B 52 ARG cc_start: 0.7223 (mmt90) cc_final: 0.6436 (mmt180) REVERT: B 215 GLU cc_start: 0.7008 (mp0) cc_final: 0.6763 (mt-10) REVERT: B 219 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7740 (ttt-90) REVERT: B 234 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: B 261 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6336 (mp) REVERT: B 317 CYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7547 (p) REVERT: R 192 THR cc_start: 0.7626 (m) cc_final: 0.7283 (p) REVERT: R 231 MET cc_start: 0.7572 (mmp) cc_final: 0.7283 (mmp) REVERT: R 292 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7922 (tp) REVERT: R 307 HIS cc_start: 0.6950 (t-90) cc_final: 0.6716 (t-90) REVERT: R 327 PHE cc_start: 0.7470 (t80) cc_final: 0.7247 (t80) REVERT: R 444 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6285 (mt-10) outliers start: 37 outliers final: 30 residues processed: 145 average time/residue: 0.2114 time to fit residues: 42.5056 Evaluate side-chains 151 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 474 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 340 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128084 restraints weight = 13893.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129425 restraints weight = 10767.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130594 restraints weight = 8086.898| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8282 Z= 0.159 Angle : 0.558 9.494 11251 Z= 0.287 Chirality : 0.039 0.136 1301 Planarity : 0.003 0.029 1446 Dihedral : 4.344 28.716 1159 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.00 % Allowed : 23.10 % Favored : 72.91 % 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: -0.08 (0.26), residues: 1054 helix: 1.01 (0.26), residues: 398 sheet: -0.82 (0.34), residues: 210 loop : -0.52 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.001 PHE A 212 TYR 0.010 0.001 TYR R 459 ARG 0.004 0.000 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7335 (mm-40) cc_final: 0.7053 (tm-30) REVERT: A 38 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7559 (mmm-85) REVERT: B 23 LYS cc_start: 0.7270 (mmmt) cc_final: 0.6919 (tttp) REVERT: B 45 MET cc_start: 0.6938 (mtp) cc_final: 0.6599 (mtp) REVERT: B 52 ARG cc_start: 0.7154 (mmt90) cc_final: 0.6517 (mmt180) REVERT: B 217 MET cc_start: 0.6933 (ppp) cc_final: 0.6691 (ppp) REVERT: B 234 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: B 261 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6124 (mp) REVERT: B 317 CYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7403 (p) REVERT: P 15 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6434 (tt) REVERT: R 192 THR cc_start: 0.7585 (m) cc_final: 0.7243 (p) REVERT: R 231 MET cc_start: 0.7762 (mmp) cc_final: 0.6487 (mtt) REVERT: R 292 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7865 (tp) REVERT: R 327 PHE cc_start: 0.7459 (t80) cc_final: 0.7228 (t80) outliers start: 32 outliers final: 26 residues processed: 150 average time/residue: 0.2005 time to fit residues: 41.7329 Evaluate side-chains 150 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 444 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN P 10 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122357 restraints weight = 14232.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123294 restraints weight = 11474.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124287 restraints weight = 8654.434| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8282 Z= 0.301 Angle : 0.640 9.637 11251 Z= 0.332 Chirality : 0.042 0.183 1301 Planarity : 0.004 0.030 1446 Dihedral : 4.781 32.631 1159 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.37 % Allowed : 23.22 % Favored : 72.41 % 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: -0.39 (0.26), residues: 1054 helix: 0.87 (0.26), residues: 395 sheet: -0.97 (0.33), residues: 209 loop : -0.83 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.007 0.001 HIS A 347 PHE 0.026 0.002 PHE A 212 TYR 0.014 0.002 TYR B 105 ARG 0.005 0.001 ARG A 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2427.17 seconds wall clock time: 43 minutes 1.99 seconds (2581.99 seconds total)