Starting phenix.real_space_refine on Mon Mar 11 11:23:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvn_32145/03_2024/7vvn_32145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvn_32145/03_2024/7vvn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvn_32145/03_2024/7vvn_32145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvn_32145/03_2024/7vvn_32145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvn_32145/03_2024/7vvn_32145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvn_32145/03_2024/7vvn_32145.pdb" } 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 Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 19": "OE1" <-> "OE2" Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.75, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.08 Conformation dependent library (CDL) restraints added in 1.5 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: 0.87 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: 2.15 Time building geometry restraints manager: 3.36 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: 96.45 - 104.05: 61 104.05 - 111.64: 3192 111.64 - 119.23: 4383 119.23 - 126.82: 3517 126.82 - 134.42: 98 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 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.254 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.266 2.440 nonbonded pdb=" O SER N 30 " pdb=" NE2 GLN N 53 " model vdw 2.286 2.520 ... (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 ========== 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: 0.130 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: 1.130 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.930 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 0.914 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: 0.2307 time to fit residues: 62.0595 Evaluate side-chains 139 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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: 0.6980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8282 Z= 0.232 Angle : 0.606 7.657 11251 Z= 0.321 Chirality : 0.041 0.146 1301 Planarity : 0.004 0.029 1446 Dihedral : 5.159 36.029 1163 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.12 % Allowed : 13.48 % Favored : 84.39 % 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: -0.99 (0.25), residues: 1054 helix: 0.55 (0.25), residues: 409 sheet: -1.64 (0.33), residues: 207 loop : -1.20 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.007 0.001 HIS A 347 PHE 0.021 0.002 PHE R 454 TYR 0.014 0.002 TYR B 105 ARG 0.005 0.001 ARG N 105 *********************** 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 172 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8033 (tttm) cc_final: 0.7690 (ttmm) REVERT: A 37 TYR cc_start: 0.8514 (t80) cc_final: 0.8280 (t80) REVERT: A 60 MET cc_start: 0.7760 (mpp) cc_final: 0.7031 (mpp) REVERT: A 255 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7173 (mmt90) REVERT: A 270 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.8072 (ttm110) REVERT: A 297 LYS cc_start: 0.8297 (ptpp) cc_final: 0.7901 (ptmt) REVERT: A 360 GLU cc_start: 0.7233 (mm-30) cc_final: 0.7004 (tp30) REVERT: B 23 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7054 (mmtm) REVERT: B 52 ARG cc_start: 0.7703 (mtt90) cc_final: 0.7077 (mmt90) REVERT: B 217 MET cc_start: 0.7664 (ppp) cc_final: 0.7249 (ppp) REVERT: B 219 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7706 (ttp-170) REVERT: B 261 LEU cc_start: 0.7221 (mm) cc_final: 0.6836 (mp) REVERT: B 268 ASN cc_start: 0.8428 (m-40) cc_final: 0.8108 (t0) REVERT: B 286 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8778 (pp) REVERT: B 325 MET cc_start: 0.6761 (mmm) cc_final: 0.6536 (mmm) REVERT: N 32 TYR cc_start: 0.7914 (m-80) cc_final: 0.7686 (m-80) REVERT: N 46 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8476 (mm-30) REVERT: N 95 TYR cc_start: 0.7855 (m-80) cc_final: 0.7635 (m-80) REVERT: P 10 ASN cc_start: 0.5652 (m-40) cc_final: 0.5008 (m110) REVERT: R 408 LYS cc_start: 0.6661 (tttp) cc_final: 0.6407 (tmtt) REVERT: R 444 GLU cc_start: 0.8393 (tp30) cc_final: 0.8063 (tt0) REVERT: R 466 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7843 (t) REVERT: R 470 ILE cc_start: 0.8170 (tt) cc_final: 0.7928 (pt) outliers start: 17 outliers final: 8 residues processed: 166 average time/residue: 0.2393 time to fit residues: 52.6203 Evaluate side-chains 149 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER 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 R residue 310 ILE Chi-restraints excluded: chain R residue 389 LEU 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 53 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 26 optimal weight: 0.0270 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 R 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8282 Z= 0.144 Angle : 0.499 5.800 11251 Z= 0.266 Chirality : 0.039 0.135 1301 Planarity : 0.003 0.026 1446 Dihedral : 4.382 21.132 1159 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.87 % Allowed : 18.23 % Favored : 79.90 % 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: -0.42 (0.26), residues: 1054 helix: 0.99 (0.26), residues: 410 sheet: -1.15 (0.34), residues: 197 loop : -0.99 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.016 0.001 PHE A 212 TYR 0.009 0.001 TYR R 459 ARG 0.003 0.000 ARG B 68 *********************** 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 174 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6910 (mm-30) REVERT: A 28 LYS cc_start: 0.7972 (tttm) cc_final: 0.7610 (ttmm) REVERT: A 37 TYR cc_start: 0.8540 (t80) cc_final: 0.8298 (t80) REVERT: A 60 MET cc_start: 0.7760 (mpp) cc_final: 0.7099 (mpp) REVERT: A 218 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.7118 (p0) REVERT: A 255 ARG cc_start: 0.7460 (mmm-85) cc_final: 0.7156 (mmt-90) REVERT: A 270 ARG cc_start: 0.8285 (mtp-110) cc_final: 0.7973 (ttm110) REVERT: A 297 LYS cc_start: 0.8361 (ptpp) cc_final: 0.7770 (ptmt) REVERT: A 360 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6787 (tp30) REVERT: B 6 GLN cc_start: 0.4052 (tm-30) cc_final: 0.3687 (pt0) REVERT: B 52 ARG cc_start: 0.7747 (mtt90) cc_final: 0.7163 (mmt90) REVERT: B 217 MET cc_start: 0.7699 (ppp) cc_final: 0.7400 (ppp) REVERT: B 261 LEU cc_start: 0.7453 (mm) cc_final: 0.7144 (mp) REVERT: B 268 ASN cc_start: 0.8343 (m-40) cc_final: 0.7960 (t0) REVERT: B 286 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8763 (pp) REVERT: N 32 TYR cc_start: 0.7806 (m-80) cc_final: 0.7580 (m-80) REVERT: N 80 TYR cc_start: 0.8198 (m-80) cc_final: 0.7919 (m-80) REVERT: N 105 ARG cc_start: 0.7349 (mtt90) cc_final: 0.6958 (mtp-110) REVERT: P 10 ASN cc_start: 0.5655 (m-40) cc_final: 0.4987 (m110) REVERT: R 312 MET cc_start: 0.6397 (mmt) cc_final: 0.5649 (ptp) REVERT: R 470 ILE cc_start: 0.8136 (tt) cc_final: 0.7901 (pt) outliers start: 15 outliers final: 9 residues processed: 170 average time/residue: 0.2217 time to fit residues: 49.9079 Evaluate side-chains 150 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 450 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0270 chunk 72 optimal weight: 9.9990 chunk 50 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 85 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8282 Z= 0.134 Angle : 0.485 6.577 11251 Z= 0.255 Chirality : 0.038 0.129 1301 Planarity : 0.003 0.028 1446 Dihedral : 4.085 20.548 1159 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.75 % Allowed : 18.98 % Favored : 78.28 % 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 (0.26), residues: 1054 helix: 1.15 (0.26), residues: 411 sheet: -0.77 (0.35), residues: 205 loop : -0.84 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.005 0.000 HIS A 347 PHE 0.033 0.001 PHE B 199 TYR 0.011 0.001 TYR B 264 ARG 0.003 0.000 ARG B 219 *********************** 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 171 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8047 (tttm) cc_final: 0.7708 (ttmm) REVERT: A 37 TYR cc_start: 0.8489 (t80) cc_final: 0.8242 (t80) REVERT: A 60 MET cc_start: 0.7737 (mpp) cc_final: 0.7135 (mpp) REVERT: A 255 ARG cc_start: 0.7308 (mmm-85) cc_final: 0.7055 (mmt-90) REVERT: A 270 ARG cc_start: 0.8255 (mtp-110) cc_final: 0.7967 (ttm110) REVERT: A 297 LYS cc_start: 0.8351 (ptpp) cc_final: 0.7736 (ptmt) REVERT: A 360 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6658 (tp30) REVERT: B 6 GLN cc_start: 0.4369 (tm-30) cc_final: 0.4078 (pt0) REVERT: B 52 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7367 (mmt90) REVERT: B 217 MET cc_start: 0.7695 (ppp) cc_final: 0.7419 (ppp) REVERT: B 261 LEU cc_start: 0.7521 (mm) cc_final: 0.7208 (mp) REVERT: B 268 ASN cc_start: 0.8309 (m-40) cc_final: 0.7932 (t0) REVERT: B 286 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8656 (pp) REVERT: N 52 SER cc_start: 0.8343 (t) cc_final: 0.8134 (m) REVERT: N 80 TYR cc_start: 0.8173 (m-80) cc_final: 0.7932 (m-80) REVERT: N 105 ARG cc_start: 0.7336 (mtt90) cc_final: 0.6969 (mtp-110) REVERT: R 312 MET cc_start: 0.6003 (mmt) cc_final: 0.5436 (ptp) REVERT: R 443 TYR cc_start: 0.6998 (t80) cc_final: 0.6705 (t80) REVERT: R 470 ILE cc_start: 0.8130 (tt) cc_final: 0.7901 (pt) outliers start: 22 outliers final: 12 residues processed: 164 average time/residue: 0.2163 time to fit residues: 47.6575 Evaluate side-chains 147 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 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 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 450 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 0.0070 chunk 25 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- 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 N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8282 Z= 0.282 Angle : 0.572 7.785 11251 Z= 0.304 Chirality : 0.041 0.148 1301 Planarity : 0.004 0.031 1446 Dihedral : 4.542 28.412 1159 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.87 % Allowed : 20.10 % Favored : 76.03 % 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: 1.06 (0.26), residues: 400 sheet: -0.89 (0.35), residues: 202 loop : -0.96 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.008 0.001 HIS A 347 PHE 0.026 0.002 PHE B 199 TYR 0.019 0.002 TYR B 105 ARG 0.004 0.001 ARG B 314 *********************** 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 161 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7996 (tttm) cc_final: 0.7635 (ttmm) REVERT: A 60 MET cc_start: 0.7906 (mpp) cc_final: 0.7360 (mpp) REVERT: A 270 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.8042 (ttm110) REVERT: A 360 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6934 (mm-30) REVERT: B 52 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7200 (mmt90) REVERT: B 217 MET cc_start: 0.7749 (ppp) cc_final: 0.7476 (ppp) REVERT: B 261 LEU cc_start: 0.7666 (mm) cc_final: 0.7301 (mp) REVERT: B 268 ASN cc_start: 0.8560 (m-40) cc_final: 0.8054 (t0) REVERT: B 284 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8276 (tt) REVERT: N 53 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: P 10 ASN cc_start: 0.5444 (m-40) cc_final: 0.4842 (m110) REVERT: R 192 THR cc_start: 0.8406 (m) cc_final: 0.8156 (p) REVERT: R 312 MET cc_start: 0.6215 (mmt) cc_final: 0.5387 (ptp) REVERT: R 470 ILE cc_start: 0.8198 (tt) cc_final: 0.7981 (pt) outliers start: 31 outliers final: 20 residues processed: 150 average time/residue: 0.2051 time to fit residues: 42.1601 Evaluate side-chains 137 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 284 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 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 410 THR Chi-restraints excluded: chain R residue 450 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 0.0170 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8282 Z= 0.149 Angle : 0.514 8.630 11251 Z= 0.267 Chirality : 0.038 0.134 1301 Planarity : 0.003 0.033 1446 Dihedral : 4.204 20.140 1159 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.00 % Allowed : 21.35 % Favored : 75.66 % 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: 0.02 (0.26), residues: 1054 helix: 1.25 (0.26), residues: 405 sheet: -0.65 (0.36), residues: 204 loop : -0.74 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.022 0.001 PHE B 199 TYR 0.011 0.001 TYR B 264 ARG 0.007 0.000 ARG A 255 *********************** 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 157 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7991 (tttm) cc_final: 0.7647 (ttmm) REVERT: A 60 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7326 (mpp) REVERT: A 252 ASP cc_start: 0.8017 (t0) cc_final: 0.7660 (t0) REVERT: A 270 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.8042 (ttm110) REVERT: A 297 LYS cc_start: 0.8342 (ptpp) cc_final: 0.7752 (ptmm) REVERT: B 6 GLN cc_start: 0.4360 (tm-30) cc_final: 0.4068 (pt0) REVERT: B 52 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7244 (mmt90) REVERT: B 217 MET cc_start: 0.7733 (ppp) cc_final: 0.7482 (ppp) REVERT: B 261 LEU cc_start: 0.7631 (mm) cc_final: 0.7285 (mp) REVERT: B 268 ASN cc_start: 0.8381 (m-40) cc_final: 0.7912 (t0) REVERT: B 284 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8426 (tt) REVERT: N 53 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7741 (tp40) REVERT: P 10 ASN cc_start: 0.5443 (m-40) cc_final: 0.4796 (m110) REVERT: R 312 MET cc_start: 0.5961 (mmt) cc_final: 0.5351 (ptp) REVERT: R 470 ILE cc_start: 0.8109 (tt) cc_final: 0.7888 (pt) outliers start: 24 outliers final: 16 residues processed: 147 average time/residue: 0.2041 time to fit residues: 40.6163 Evaluate side-chains 144 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 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 N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 440 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 142 HIS B 237 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3667 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= 0.337 Angle : 0.631 8.955 11251 Z= 0.332 Chirality : 0.042 0.159 1301 Planarity : 0.004 0.039 1446 Dihedral : 4.845 31.227 1159 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.37 % Allowed : 20.60 % 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: -0.37 (0.26), residues: 1054 helix: 0.83 (0.26), residues: 404 sheet: -0.99 (0.34), residues: 214 loop : -0.76 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.009 0.001 HIS A 347 PHE 0.025 0.002 PHE R 454 TYR 0.020 0.002 TYR B 105 ARG 0.005 0.001 ARG A 255 *********************** 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 159 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8032 (tttm) cc_final: 0.7675 (ttmm) REVERT: A 60 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7269 (mpp) REVERT: A 252 ASP cc_start: 0.8013 (t0) cc_final: 0.7635 (t0) REVERT: A 270 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.8091 (ttm110) REVERT: B 23 LYS cc_start: 0.7658 (tttp) cc_final: 0.7019 (mmtp) REVERT: B 52 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7181 (mmt90) REVERT: B 217 MET cc_start: 0.7767 (ppp) cc_final: 0.7492 (ppp) REVERT: B 234 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: B 261 LEU cc_start: 0.7623 (mm) cc_final: 0.7292 (mp) REVERT: B 268 ASN cc_start: 0.8674 (m-40) cc_final: 0.8162 (t0) REVERT: B 284 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8338 (tt) REVERT: N 46 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8346 (mm-30) REVERT: N 53 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7640 (tp40) REVERT: P 10 ASN cc_start: 0.5343 (m-40) cc_final: 0.4939 (m110) REVERT: R 192 THR cc_start: 0.8364 (m) cc_final: 0.8114 (p) REVERT: R 312 MET cc_start: 0.6104 (mmt) cc_final: 0.5210 (ptp) REVERT: R 327 PHE cc_start: 0.7647 (t80) cc_final: 0.7382 (t80) REVERT: R 470 ILE cc_start: 0.8230 (tt) cc_final: 0.8016 (pt) outliers start: 35 outliers final: 24 residues processed: 150 average time/residue: 0.1973 time to fit residues: 40.8363 Evaluate side-chains 144 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 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 53 GLN 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 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 407 LEU Chi-restraints excluded: chain R residue 410 THR Chi-restraints excluded: chain R residue 440 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 19 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 80 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8282 Z= 0.236 Angle : 0.578 8.665 11251 Z= 0.301 Chirality : 0.040 0.152 1301 Planarity : 0.003 0.040 1446 Dihedral : 4.729 32.159 1159 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.24 % Allowed : 21.72 % Favored : 74.03 % 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: -0.19 (0.26), residues: 1054 helix: 1.03 (0.26), residues: 392 sheet: -0.95 (0.33), residues: 214 loop : -0.64 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS A 347 PHE 0.022 0.002 PHE B 199 TYR 0.015 0.002 TYR B 264 ARG 0.005 0.000 ARG A 255 *********************** 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 156 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7982 (tttm) cc_final: 0.7624 (ttmm) REVERT: A 60 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7386 (mpp) REVERT: A 230 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8110 (mp0) REVERT: A 252 ASP cc_start: 0.8010 (t0) cc_final: 0.7675 (t0) REVERT: A 270 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.8113 (ttm110) REVERT: B 23 LYS cc_start: 0.7663 (tttp) cc_final: 0.7018 (mmtp) REVERT: B 52 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7221 (mmt90) REVERT: B 217 MET cc_start: 0.7752 (ppp) cc_final: 0.7479 (ppp) REVERT: B 234 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: B 261 LEU cc_start: 0.7621 (mm) cc_final: 0.7274 (mp) REVERT: B 268 ASN cc_start: 0.8671 (m-40) cc_final: 0.8184 (t0) REVERT: N 46 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8370 (mm-30) REVERT: N 53 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7961 (tp40) REVERT: P 10 ASN cc_start: 0.5414 (m-40) cc_final: 0.5021 (m110) REVERT: R 192 THR cc_start: 0.8232 (m) cc_final: 0.7992 (p) REVERT: R 231 MET cc_start: 0.7424 (mmp) cc_final: 0.6865 (mtt) REVERT: R 312 MET cc_start: 0.6078 (mmt) cc_final: 0.5265 (ptp) REVERT: R 327 PHE cc_start: 0.7630 (t80) cc_final: 0.7374 (t80) REVERT: R 470 ILE cc_start: 0.8203 (tt) cc_final: 0.7993 (pt) outliers start: 34 outliers final: 22 residues processed: 148 average time/residue: 0.2046 time to fit residues: 41.8182 Evaluate side-chains 144 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE 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 54 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS 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 410 THR Chi-restraints excluded: chain R residue 440 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0060 chunk 97 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8282 Z= 0.229 Angle : 0.591 11.368 11251 Z= 0.303 Chirality : 0.040 0.193 1301 Planarity : 0.003 0.041 1446 Dihedral : 4.664 31.131 1159 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.24 % Allowed : 21.72 % Favored : 74.03 % 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: -0.17 (0.26), residues: 1054 helix: 1.05 (0.26), residues: 392 sheet: -0.94 (0.33), residues: 214 loop : -0.62 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS A 347 PHE 0.021 0.002 PHE B 199 TYR 0.014 0.001 TYR B 264 ARG 0.005 0.000 ARG A 255 *********************** 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 159 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7980 (tttm) cc_final: 0.7619 (ttmm) REVERT: A 60 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7401 (mpp) REVERT: A 230 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8106 (mp0) REVERT: A 252 ASP cc_start: 0.7849 (t0) cc_final: 0.7524 (t0) REVERT: A 270 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.8197 (ttm110) REVERT: B 23 LYS cc_start: 0.7669 (tttp) cc_final: 0.7022 (mmtp) REVERT: B 45 MET cc_start: 0.8368 (mtp) cc_final: 0.7659 (mtp) REVERT: B 52 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7186 (mmt90) REVERT: B 217 MET cc_start: 0.7711 (ppp) cc_final: 0.7434 (ppp) REVERT: B 234 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: B 261 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7242 (mp) REVERT: B 268 ASN cc_start: 0.8659 (m-40) cc_final: 0.8126 (t0) REVERT: N 46 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8369 (mm-30) REVERT: N 53 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: P 10 ASN cc_start: 0.5357 (m-40) cc_final: 0.4968 (m110) REVERT: R 192 THR cc_start: 0.8308 (m) cc_final: 0.8065 (p) REVERT: R 327 PHE cc_start: 0.7672 (t80) cc_final: 0.7405 (t80) REVERT: R 470 ILE cc_start: 0.8206 (tt) cc_final: 0.7997 (pt) outliers start: 34 outliers final: 25 residues processed: 151 average time/residue: 0.1915 time to fit residues: 40.0553 Evaluate side-chains 144 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 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 54 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 237 ILE 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 410 THR Chi-restraints excluded: chain R residue 440 GLN 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 61 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3995 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= 0.265 Angle : 0.611 9.896 11251 Z= 0.317 Chirality : 0.041 0.198 1301 Planarity : 0.004 0.041 1446 Dihedral : 4.778 32.054 1159 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.87 % Allowed : 22.60 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1054 helix: 0.93 (0.26), residues: 391 sheet: -0.98 (0.33), residues: 214 loop : -0.64 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS A 347 PHE 0.022 0.002 PHE B 199 TYR 0.015 0.002 TYR B 264 ARG 0.005 0.000 ARG A 255 ********************** 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 151 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8021 (tttm) cc_final: 0.7665 (ttmm) REVERT: A 60 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7416 (mpp) REVERT: A 230 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8109 (mp0) REVERT: A 252 ASP cc_start: 0.7919 (t0) cc_final: 0.7539 (t0) REVERT: A 270 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8168 (ttm110) REVERT: B 52 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7181 (mmt90) REVERT: B 217 MET cc_start: 0.7693 (ppp) cc_final: 0.7409 (ppp) REVERT: B 234 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.6305 (m-80) REVERT: B 261 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7247 (mp) REVERT: B 268 ASN cc_start: 0.8655 (m-40) cc_final: 0.8136 (t0) REVERT: N 46 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8347 (mm-30) REVERT: N 53 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7750 (tp40) REVERT: P 10 ASN cc_start: 0.5319 (m-40) cc_final: 0.4959 (m110) REVERT: R 192 THR cc_start: 0.8281 (m) cc_final: 0.8034 (p) REVERT: R 327 PHE cc_start: 0.7670 (t80) cc_final: 0.7407 (t80) REVERT: R 444 GLU cc_start: 0.8051 (tp30) cc_final: 0.7813 (tt0) outliers start: 31 outliers final: 26 residues processed: 143 average time/residue: 0.1979 time to fit residues: 38.9200 Evaluate side-chains 146 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 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 B residue 340 ASN 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 53 GLN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 237 ILE 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 410 THR Chi-restraints excluded: chain R residue 440 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3898 r_free = 0.3898 target = 0.142538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124574 restraints weight = 14151.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124045 restraints weight = 10958.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125493 restraints weight = 10044.014| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8282 Z= 0.228 Angle : 0.596 10.075 11251 Z= 0.307 Chirality : 0.040 0.192 1301 Planarity : 0.003 0.041 1446 Dihedral : 4.689 30.589 1159 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.00 % Allowed : 22.22 % Favored : 73.78 % 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: -0.22 (0.26), residues: 1054 helix: 0.99 (0.26), residues: 389 sheet: -0.90 (0.34), residues: 214 loop : -0.66 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.021 0.002 PHE B 199 TYR 0.013 0.001 TYR B 264 ARG 0.005 0.000 ARG A 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.02 seconds wall clock time: 32 minutes 51.93 seconds (1971.93 seconds total)