Starting phenix.real_space_refine on Mon Mar 11 14:36:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvm_32144/03_2024/7vvm_32144.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvm_32144/03_2024/7vvm_32144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvm_32144/03_2024/7vvm_32144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvm_32144/03_2024/7vvm_32144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvm_32144/03_2024/7vvm_32144.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvm_32144/03_2024/7vvm_32144.pdb" } resolution = 3.2 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= 0.001 sd= 0.008 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 52 5.16 5 C 5405 2.51 5 N 1486 2.21 5 O 1564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 209": "OE1" <-> "OE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1893 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2508 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 389 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 217 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2536 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 409 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 362 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 5, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 284 Time building chain proxies: 5.10, per 1000 atoms: 0.60 Number of scatterers: 8507 At special positions: 0 Unit cell: (127.267, 105.134, 126.16, 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 52 16.00 O 1564 8.00 N 1486 7.00 C 5405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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=2.07 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.04 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 41.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.269A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.503A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.503A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.518A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.945A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.562A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.677A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.575A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.687A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL R 193 " --> pdb=" O MET R 189 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 removed outlier: 3.570A pdb=" N PHE R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.923A pdb=" N VAL R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 347 removed outlier: 3.763A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.619A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 391 removed outlier: 3.570A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.617A pdb=" N LEU R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 418 removed outlier: 3.700A pdb=" N TYR R 403 " --> pdb=" O THR R 399 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET R 414 " --> pdb=" O THR R 410 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.633A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 477 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.611A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.611A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.511A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.691A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.750A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.823A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.711A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.501A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.426A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.604A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.576A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 449 hydrogen bonds defined for protein. 1257 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: 2.55 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1409 1.31 - 1.44: 2401 1.44 - 1.58: 4798 1.58 - 1.72: 0 1.72 - 1.85: 76 Bond restraints: 8684 Sorted by residual: bond pdb=" N VAL R 157 " pdb=" CA VAL R 157 " ideal model delta sigma weight residual 1.460 1.503 -0.043 7.50e-03 1.78e+04 3.30e+01 bond pdb=" C ALA B 287 " pdb=" O ALA B 287 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.21e-02 6.83e+03 2.97e+01 bond pdb=" C VAL B 100 " pdb=" O VAL B 100 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.04e-02 9.25e+03 2.96e+01 bond pdb=" C TYR B 124 " pdb=" O TYR B 124 " ideal model delta sigma weight residual 1.236 1.301 -0.065 1.21e-02 6.83e+03 2.88e+01 bond pdb=" CE1 HIS A 377 " pdb=" NE2 HIS A 377 " ideal model delta sigma weight residual 1.321 1.371 -0.050 1.00e-02 1.00e+04 2.46e+01 ... (remaining 8679 not shown) Histogram of bond angle deviations from ideal: 96.67 - 104.45: 109 104.45 - 112.23: 3867 112.23 - 120.01: 4400 120.01 - 127.79: 3347 127.79 - 135.57: 84 Bond angle restraints: 11807 Sorted by residual: angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 113.57 120.74 -7.17 1.31e+00 5.83e-01 2.99e+01 angle pdb=" N GLN R 451 " pdb=" CA GLN R 451 " pdb=" C GLN R 451 " ideal model delta sigma weight residual 110.97 105.73 5.24 1.09e+00 8.42e-01 2.32e+01 angle pdb=" CA VAL R 439 " pdb=" C VAL R 439 " pdb=" O VAL R 439 " ideal model delta sigma weight residual 121.05 115.76 5.29 1.11e+00 8.12e-01 2.27e+01 angle pdb=" N ILE A 372 " pdb=" CA ILE A 372 " pdb=" C ILE A 372 " ideal model delta sigma weight residual 110.72 106.02 4.70 1.01e+00 9.80e-01 2.16e+01 angle pdb=" C LYS R 34 " pdb=" N GLU R 35 " pdb=" CA GLU R 35 " ideal model delta sigma weight residual 120.54 126.82 -6.28 1.35e+00 5.49e-01 2.16e+01 ... (remaining 11802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 4632 16.64 - 33.28: 396 33.28 - 49.92: 56 49.92 - 66.56: 13 66.56 - 83.20: 14 Dihedral angle restraints: 5111 sinusoidal: 1822 harmonic: 3289 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 172.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+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 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 649 0.058 - 0.117: 466 0.117 - 0.175: 186 0.175 - 0.233: 44 0.233 - 0.291: 7 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA PRO A 351 " pdb=" N PRO A 351 " pdb=" C PRO A 351 " pdb=" CB PRO A 351 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1349 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " 0.013 2.00e-02 2.50e+03 1.04e-02 2.68e+00 pdb=" CG TRP A 234 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 378 " -0.020 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE R 378 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE R 378 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 378 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 378 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 378 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 378 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 352 " 0.015 2.00e-02 2.50e+03 1.20e-02 2.14e+00 pdb=" CG HIS A 352 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS A 352 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 352 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 352 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 352 " 0.007 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 8636 3.28 - 3.82: 13249 3.82 - 4.36: 17850 4.36 - 4.90: 29450 Nonbonded interactions: 69701 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.200 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.300 2.440 nonbonded pdb=" O SER R 356 " pdb=" OG SER R 356 " model vdw 2.304 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.312 2.440 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.322 2.440 ... (remaining 69696 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.140 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.060 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.015 0.101 8684 Z= 0.995 Angle : 1.761 10.650 11807 Z= 1.280 Chirality : 0.086 0.291 1352 Planarity : 0.003 0.012 1514 Dihedral : 13.507 83.200 2972 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.60 % Allowed : 4.06 % Favored : 95.35 % 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: -1.17 (0.24), residues: 1113 helix: -0.46 (0.23), residues: 430 sheet: -0.85 (0.33), residues: 226 loop : -0.84 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP B 297 HIS 0.005 0.001 HIS A 352 PHE 0.020 0.003 PHE R 378 TYR 0.015 0.003 TYR N 60 ARG 0.006 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 0.993 Fit side-chains REVERT: A 16 GLU cc_start: 0.6489 (tp30) cc_final: 0.5699 (tm-30) REVERT: A 216 LYS cc_start: 0.7371 (mptt) cc_final: 0.7127 (mmtt) REVERT: A 221 MET cc_start: 0.7791 (ttt) cc_final: 0.7457 (ttp) REVERT: A 258 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7217 (mp0) REVERT: A 325 THR cc_start: 0.8530 (m) cc_final: 0.8325 (m) REVERT: A 379 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.6980 (ttm110) REVERT: A 382 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6999 (mm-30) REVERT: B 80 ILE cc_start: 0.8221 (mt) cc_final: 0.8021 (mm) REVERT: B 137 ARG cc_start: 0.6551 (ttm110) cc_final: 0.5769 (ttm-80) REVERT: B 181 THR cc_start: 0.7741 (m) cc_final: 0.7530 (p) REVERT: B 197 ARG cc_start: 0.6105 (mmp-170) cc_final: 0.5892 (mmm160) REVERT: B 220 GLN cc_start: 0.7424 (mt0) cc_final: 0.6993 (mt0) REVERT: B 264 TYR cc_start: 0.7883 (m-80) cc_final: 0.7269 (m-80) REVERT: B 277 SER cc_start: 0.8783 (t) cc_final: 0.8316 (m) REVERT: B 289 TYR cc_start: 0.9113 (m-80) cc_final: 0.8723 (m-80) REVERT: B 322 ASP cc_start: 0.7872 (m-30) cc_final: 0.7023 (t0) REVERT: G 42 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6939 (mt-10) REVERT: G 44 HIS cc_start: 0.6819 (m90) cc_final: 0.6608 (m170) REVERT: G 62 ARG cc_start: 0.4738 (pmt-80) cc_final: 0.3603 (mmm160) REVERT: N 3 GLN cc_start: 0.6269 (tt0) cc_final: 0.5545 (tp-100) REVERT: N 19 ARG cc_start: 0.7322 (ttt90) cc_final: 0.7062 (ttt-90) REVERT: N 82 GLN cc_start: 0.6016 (tp40) cc_final: 0.5136 (tp-100) REVERT: N 83 MET cc_start: 0.6351 (mtt) cc_final: 0.5925 (mpp) REVERT: N 93 VAL cc_start: 0.7778 (t) cc_final: 0.7540 (p) REVERT: N 94 TYR cc_start: 0.8466 (m-80) cc_final: 0.7815 (m-80) REVERT: R 282 ARG cc_start: 0.7013 (mpt-90) cc_final: 0.6724 (mmt90) REVERT: R 291 PHE cc_start: 0.8031 (m-10) cc_final: 0.7733 (m-10) REVERT: R 360 LYS cc_start: 0.4708 (ptmt) cc_final: 0.4498 (ptmt) REVERT: R 363 ILE cc_start: 0.7763 (mm) cc_final: 0.7487 (tt) REVERT: R 372 VAL cc_start: 0.7205 (m) cc_final: 0.6989 (t) REVERT: R 383 ARG cc_start: 0.6956 (tmm-80) cc_final: 0.6714 (tmm-80) REVERT: R 391 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7566 (mt-10) REVERT: R 399 THR cc_start: 0.5947 (t) cc_final: 0.5636 (p) REVERT: R 439 VAL cc_start: 0.4753 (p) cc_final: 0.4292 (m) REVERT: R 443 TYR cc_start: 0.7097 (t80) cc_final: 0.6775 (t80) REVERT: R 445 MET cc_start: 0.7668 (mmm) cc_final: 0.7223 (mmp) REVERT: R 462 CYS cc_start: 0.6426 (m) cc_final: 0.6098 (t) REVERT: R 473 SER cc_start: 0.4742 (m) cc_final: 0.4528 (t) outliers start: 5 outliers final: 2 residues processed: 206 average time/residue: 0.2789 time to fit residues: 73.1377 Evaluate side-chains 156 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 213 GLN A 254 ASN B 88 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN P 14 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8684 Z= 0.179 Angle : 0.539 5.867 11807 Z= 0.294 Chirality : 0.041 0.152 1352 Planarity : 0.003 0.027 1514 Dihedral : 4.439 33.238 1217 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.27 % Allowed : 9.79 % Favored : 87.95 % 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 (0.25), residues: 1113 helix: 1.05 (0.25), residues: 433 sheet: -0.47 (0.34), residues: 219 loop : -0.43 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS P 9 PHE 0.016 0.001 PHE R 335 TYR 0.019 0.001 TYR R 191 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6735 (tppt) cc_final: 0.6225 (tmtt) REVERT: A 216 LYS cc_start: 0.7212 (mptt) cc_final: 0.6957 (mmtt) REVERT: A 221 MET cc_start: 0.7711 (ttt) cc_final: 0.7407 (ttp) REVERT: A 258 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7416 (mp0) REVERT: B 68 ARG cc_start: 0.7544 (ttt180) cc_final: 0.7291 (ttt90) REVERT: B 137 ARG cc_start: 0.6476 (ttm110) cc_final: 0.5696 (ttm-80) REVERT: B 220 GLN cc_start: 0.7041 (mt0) cc_final: 0.6821 (tt0) REVERT: B 262 MET cc_start: 0.7315 (tpp) cc_final: 0.7055 (tpt) REVERT: B 264 TYR cc_start: 0.7612 (m-80) cc_final: 0.7030 (m-80) REVERT: B 277 SER cc_start: 0.8805 (t) cc_final: 0.8333 (m) REVERT: B 322 ASP cc_start: 0.7754 (m-30) cc_final: 0.7008 (t0) REVERT: G 42 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6936 (mt-10) REVERT: G 44 HIS cc_start: 0.6549 (m90) cc_final: 0.6214 (m170) REVERT: G 62 ARG cc_start: 0.4363 (pmt-80) cc_final: 0.3330 (mmm-85) REVERT: N 34 MET cc_start: 0.8610 (mmm) cc_final: 0.8390 (mmm) REVERT: N 77 ASN cc_start: 0.6660 (m-40) cc_final: 0.6408 (t0) REVERT: N 93 VAL cc_start: 0.7771 (t) cc_final: 0.7396 (p) REVERT: N 94 TYR cc_start: 0.8295 (m-80) cc_final: 0.7627 (m-80) REVERT: R 360 LYS cc_start: 0.4600 (ptmt) cc_final: 0.4352 (ptmt) REVERT: R 363 ILE cc_start: 0.7626 (mm) cc_final: 0.7367 (tt) REVERT: R 391 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6694 (mt-10) REVERT: R 399 THR cc_start: 0.5549 (t) cc_final: 0.5227 (m) REVERT: R 439 VAL cc_start: 0.4681 (p) cc_final: 0.4161 (m) REVERT: R 441 MET cc_start: 0.6202 (mmt) cc_final: 0.5485 (mmt) REVERT: R 445 MET cc_start: 0.7288 (mmm) cc_final: 0.6899 (mmp) outliers start: 19 outliers final: 12 residues processed: 179 average time/residue: 0.2322 time to fit residues: 55.6431 Evaluate side-chains 148 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 0.0270 chunk 109 optimal weight: 0.0770 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8684 Z= 0.129 Angle : 0.459 5.608 11807 Z= 0.251 Chirality : 0.040 0.154 1352 Planarity : 0.003 0.032 1514 Dihedral : 3.795 16.359 1215 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 11.69 % Favored : 86.28 % 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: 0.69 (0.26), residues: 1113 helix: 1.59 (0.26), residues: 434 sheet: -0.15 (0.34), residues: 225 loop : -0.22 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.009 0.001 HIS P 14 PHE 0.019 0.001 PHE R 315 TYR 0.016 0.001 TYR R 191 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6884 (tppt) cc_final: 0.6321 (tmtt) REVERT: A 59 GLN cc_start: 0.5905 (mm-40) cc_final: 0.5654 (mt0) REVERT: A 216 LYS cc_start: 0.7280 (mptt) cc_final: 0.7018 (mmtt) REVERT: A 258 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7315 (mp0) REVERT: B 68 ARG cc_start: 0.7606 (ttt180) cc_final: 0.7220 (ttt90) REVERT: B 137 ARG cc_start: 0.6540 (ttm110) cc_final: 0.5768 (ttm-80) REVERT: B 274 THR cc_start: 0.8073 (m) cc_final: 0.7724 (p) REVERT: G 42 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7039 (mt-10) REVERT: G 44 HIS cc_start: 0.6490 (m90) cc_final: 0.6167 (m-70) REVERT: G 58 GLU cc_start: 0.6906 (pm20) cc_final: 0.6658 (pm20) REVERT: G 62 ARG cc_start: 0.4189 (pmt-80) cc_final: 0.3457 (mmm160) REVERT: N 29 PHE cc_start: 0.7618 (t80) cc_final: 0.7273 (t80) REVERT: N 93 VAL cc_start: 0.7709 (t) cc_final: 0.7348 (p) REVERT: N 94 TYR cc_start: 0.8227 (m-80) cc_final: 0.7657 (m-80) REVERT: R 230 PHE cc_start: 0.7129 (m-80) cc_final: 0.6899 (m-80) REVERT: R 240 LYS cc_start: 0.5576 (mmmm) cc_final: 0.5337 (tptp) REVERT: R 291 PHE cc_start: 0.7752 (m-10) cc_final: 0.7442 (m-10) REVERT: R 292 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6593 (tp) REVERT: R 360 LYS cc_start: 0.4652 (ptmt) cc_final: 0.4392 (ptmt) REVERT: R 363 ILE cc_start: 0.7553 (mm) cc_final: 0.7303 (tt) REVERT: R 439 VAL cc_start: 0.4671 (p) cc_final: 0.4155 (m) REVERT: R 441 MET cc_start: 0.6127 (mmt) cc_final: 0.5809 (mmt) outliers start: 17 outliers final: 11 residues processed: 174 average time/residue: 0.2263 time to fit residues: 53.2277 Evaluate side-chains 148 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 254 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS R 223 HIS R 374 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8684 Z= 0.217 Angle : 0.493 5.664 11807 Z= 0.269 Chirality : 0.041 0.165 1352 Planarity : 0.003 0.041 1514 Dihedral : 3.965 16.804 1215 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.98 % Allowed : 13.48 % Favored : 83.53 % 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: 0.64 (0.26), residues: 1113 helix: 1.48 (0.25), residues: 435 sheet: -0.05 (0.34), residues: 211 loop : -0.25 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.012 0.002 HIS B 225 PHE 0.018 0.002 PHE R 335 TYR 0.019 0.001 TYR R 191 ARG 0.007 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7229 (mptt) cc_final: 0.6929 (mmtt) REVERT: A 258 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7385 (mp0) REVERT: A 346 ARG cc_start: 0.6219 (mmm160) cc_final: 0.5787 (mtt180) REVERT: A 381 TYR cc_start: 0.6694 (m-80) cc_final: 0.6433 (m-80) REVERT: B 68 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7305 (ttt90) REVERT: B 137 ARG cc_start: 0.6593 (ttm110) cc_final: 0.5824 (ttm-80) REVERT: B 290 ASP cc_start: 0.7050 (m-30) cc_final: 0.6629 (m-30) REVERT: B 322 ASP cc_start: 0.7747 (m-30) cc_final: 0.6817 (t0) REVERT: G 42 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6972 (mt-10) REVERT: G 62 ARG cc_start: 0.4213 (pmt-80) cc_final: 0.3409 (mmm160) REVERT: N 29 PHE cc_start: 0.7645 (t80) cc_final: 0.7413 (t80) REVERT: N 93 VAL cc_start: 0.7850 (t) cc_final: 0.7490 (p) REVERT: N 94 TYR cc_start: 0.8301 (m-80) cc_final: 0.7650 (m-80) REVERT: R 240 LYS cc_start: 0.5572 (mmmm) cc_final: 0.5342 (tptp) REVERT: R 292 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6663 (tp) REVERT: R 363 ILE cc_start: 0.7602 (mm) cc_final: 0.7349 (tp) REVERT: R 391 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6743 (mt-10) REVERT: R 441 MET cc_start: 0.6353 (mmt) cc_final: 0.5798 (mmt) outliers start: 25 outliers final: 20 residues processed: 157 average time/residue: 0.2327 time to fit residues: 48.9552 Evaluate side-chains 148 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 407 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8684 Z= 0.212 Angle : 0.480 5.573 11807 Z= 0.263 Chirality : 0.041 0.168 1352 Planarity : 0.004 0.040 1514 Dihedral : 3.985 15.029 1215 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.34 % Allowed : 15.16 % Favored : 81.50 % 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: 0.61 (0.26), residues: 1113 helix: 1.47 (0.25), residues: 439 sheet: -0.16 (0.34), residues: 214 loop : -0.26 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.010 0.002 HIS B 225 PHE 0.024 0.002 PHE R 315 TYR 0.017 0.001 TYR R 191 ARG 0.004 0.001 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6069 (mm-40) cc_final: 0.5854 (mt0) REVERT: A 216 LYS cc_start: 0.7200 (mptt) cc_final: 0.6899 (mmtt) REVERT: A 258 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7377 (mp0) REVERT: A 346 ARG cc_start: 0.6157 (mmm160) cc_final: 0.5752 (mtt180) REVERT: A 354 THR cc_start: 0.8406 (t) cc_final: 0.8201 (t) REVERT: A 381 TYR cc_start: 0.6643 (m-80) cc_final: 0.6418 (m-80) REVERT: B 68 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7260 (ttt90) REVERT: B 170 ASP cc_start: 0.7374 (t70) cc_final: 0.7147 (t70) REVERT: B 322 ASP cc_start: 0.7892 (m-30) cc_final: 0.6971 (t0) REVERT: G 42 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6977 (mt-10) REVERT: G 62 ARG cc_start: 0.4197 (pmt-80) cc_final: 0.3251 (mmm-85) REVERT: N 93 VAL cc_start: 0.7756 (t) cc_final: 0.7494 (p) REVERT: N 94 TYR cc_start: 0.8336 (m-80) cc_final: 0.7700 (m-80) REVERT: P 5 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6713 (mp) REVERT: R 181 ARG cc_start: 0.5139 (mmt-90) cc_final: 0.4936 (mpt180) REVERT: R 240 LYS cc_start: 0.5598 (mmmm) cc_final: 0.5328 (tptp) REVERT: R 363 ILE cc_start: 0.7599 (mm) cc_final: 0.7351 (tp) REVERT: R 441 MET cc_start: 0.6264 (mmt) cc_final: 0.5854 (mmt) outliers start: 28 outliers final: 22 residues processed: 156 average time/residue: 0.2229 time to fit residues: 47.1931 Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 56 optimal weight: 0.0050 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 overall best weight: 0.9976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 254 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN R 401 GLN R 438 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8684 Z= 0.145 Angle : 0.438 5.572 11807 Z= 0.241 Chirality : 0.039 0.161 1352 Planarity : 0.003 0.038 1514 Dihedral : 3.796 15.651 1215 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.46 % Allowed : 16.11 % Favored : 80.43 % 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: 0.84 (0.26), residues: 1113 helix: 1.77 (0.25), residues: 435 sheet: -0.04 (0.33), residues: 217 loop : -0.24 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS P 14 PHE 0.026 0.001 PHE R 315 TYR 0.018 0.001 TYR R 191 ARG 0.003 0.000 ARG R 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.5920 (mm-40) cc_final: 0.5715 (mt0) REVERT: A 216 LYS cc_start: 0.7177 (mptt) cc_final: 0.6892 (mmtt) REVERT: A 249 ASP cc_start: 0.7331 (t0) cc_final: 0.7084 (t0) REVERT: A 258 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7422 (mp0) REVERT: A 346 ARG cc_start: 0.6127 (mmm160) cc_final: 0.5712 (mtt180) REVERT: A 354 THR cc_start: 0.8261 (t) cc_final: 0.8054 (t) REVERT: A 381 TYR cc_start: 0.6650 (m-80) cc_final: 0.6419 (m-80) REVERT: B 68 ARG cc_start: 0.7583 (ttt180) cc_final: 0.7278 (ttt90) REVERT: B 170 ASP cc_start: 0.7283 (t70) cc_final: 0.6908 (t70) REVERT: B 322 ASP cc_start: 0.7885 (m-30) cc_final: 0.6969 (t0) REVERT: G 42 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7026 (mt-10) REVERT: G 62 ARG cc_start: 0.4058 (pmt-80) cc_final: 0.3275 (mmm-85) REVERT: N 93 VAL cc_start: 0.7723 (t) cc_final: 0.7400 (p) REVERT: N 94 TYR cc_start: 0.8259 (m-80) cc_final: 0.7621 (m-80) REVERT: R 233 ARG cc_start: 0.6796 (ttt180) cc_final: 0.6557 (ttt180) REVERT: R 240 LYS cc_start: 0.5627 (mmmm) cc_final: 0.5421 (tptp) REVERT: R 292 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6539 (tp) REVERT: R 363 ILE cc_start: 0.7418 (mm) cc_final: 0.7158 (tp) REVERT: R 391 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6778 (mt-10) REVERT: R 441 MET cc_start: 0.6269 (mmt) cc_final: 0.5929 (mmt) outliers start: 29 outliers final: 21 residues processed: 157 average time/residue: 0.2355 time to fit residues: 49.2238 Evaluate side-chains 151 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8684 Z= 0.329 Angle : 0.561 6.175 11807 Z= 0.304 Chirality : 0.043 0.174 1352 Planarity : 0.004 0.040 1514 Dihedral : 4.380 15.920 1215 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.18 % Allowed : 16.23 % Favored : 79.59 % 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: 0.34 (0.26), residues: 1113 helix: 1.27 (0.25), residues: 439 sheet: -0.41 (0.33), residues: 216 loop : -0.37 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.011 0.002 HIS B 225 PHE 0.020 0.002 PHE R 315 TYR 0.021 0.002 TYR R 191 ARG 0.005 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7011 (mptt) cc_final: 0.6795 (mmtt) REVERT: A 249 ASP cc_start: 0.7438 (t0) cc_final: 0.7044 (t0) REVERT: A 258 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7417 (mp0) REVERT: A 346 ARG cc_start: 0.6160 (mmm160) cc_final: 0.5662 (mtt180) REVERT: B 170 ASP cc_start: 0.7414 (t70) cc_final: 0.7154 (t70) REVERT: B 259 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6188 (mm110) REVERT: B 322 ASP cc_start: 0.7862 (m-30) cc_final: 0.7001 (t0) REVERT: G 42 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6922 (mt-10) REVERT: N 93 VAL cc_start: 0.7754 (t) cc_final: 0.7501 (p) REVERT: N 94 TYR cc_start: 0.8357 (m-80) cc_final: 0.8147 (m-80) REVERT: N 124 VAL cc_start: 0.7831 (t) cc_final: 0.7621 (p) REVERT: R 240 LYS cc_start: 0.5637 (mmmm) cc_final: 0.5363 (tptp) REVERT: R 363 ILE cc_start: 0.7500 (mm) cc_final: 0.7259 (tp) REVERT: R 441 MET cc_start: 0.6365 (mmt) cc_final: 0.5606 (mmt) outliers start: 35 outliers final: 29 residues processed: 156 average time/residue: 0.2351 time to fit residues: 49.0121 Evaluate side-chains 153 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 374 ASN Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 218 ASN A 254 ASN B 13 GLN B 75 GLN P 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8684 Z= 0.146 Angle : 0.459 6.180 11807 Z= 0.249 Chirality : 0.040 0.158 1352 Planarity : 0.003 0.035 1514 Dihedral : 3.917 16.332 1215 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.34 % Allowed : 17.42 % Favored : 79.24 % 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: 0.63 (0.26), residues: 1113 helix: 1.66 (0.25), residues: 436 sheet: -0.27 (0.32), residues: 226 loop : -0.36 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.009 0.001 HIS P 14 PHE 0.031 0.001 PHE R 315 TYR 0.017 0.001 TYR R 191 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7001 (mptt) cc_final: 0.6770 (mmtt) REVERT: A 249 ASP cc_start: 0.7181 (t0) cc_final: 0.6833 (t0) REVERT: A 258 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7391 (mp0) REVERT: A 346 ARG cc_start: 0.6011 (mmm160) cc_final: 0.5594 (mtt180) REVERT: B 45 MET cc_start: 0.8272 (mtp) cc_final: 0.7415 (ttm) REVERT: B 68 ARG cc_start: 0.7642 (ttt180) cc_final: 0.7334 (ttt90) REVERT: B 170 ASP cc_start: 0.7283 (t70) cc_final: 0.7069 (t70) REVERT: B 259 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6188 (mm110) REVERT: B 264 TYR cc_start: 0.7419 (m-80) cc_final: 0.6844 (m-80) REVERT: B 322 ASP cc_start: 0.7911 (m-30) cc_final: 0.6992 (t0) REVERT: G 42 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7000 (mt-10) REVERT: G 62 ARG cc_start: 0.4207 (pmt-80) cc_final: 0.3219 (mmm160) REVERT: N 93 VAL cc_start: 0.7719 (t) cc_final: 0.7390 (p) REVERT: N 94 TYR cc_start: 0.8269 (m-80) cc_final: 0.7701 (m-80) REVERT: R 231 MET cc_start: 0.6779 (mtp) cc_final: 0.6530 (mtp) REVERT: R 240 LYS cc_start: 0.5704 (mmmm) cc_final: 0.5486 (tptp) REVERT: R 363 ILE cc_start: 0.7382 (mm) cc_final: 0.7176 (tp) REVERT: R 441 MET cc_start: 0.6289 (mmt) cc_final: 0.5766 (mmt) outliers start: 28 outliers final: 22 residues processed: 147 average time/residue: 0.2312 time to fit residues: 45.6811 Evaluate side-chains 144 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 0.0870 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8684 Z= 0.133 Angle : 0.441 5.783 11807 Z= 0.240 Chirality : 0.040 0.186 1352 Planarity : 0.003 0.036 1514 Dihedral : 3.722 17.668 1215 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.98 % Allowed : 18.26 % Favored : 78.76 % 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: 0.81 (0.26), residues: 1113 helix: 1.76 (0.25), residues: 440 sheet: -0.12 (0.32), residues: 231 loop : -0.26 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.028 0.001 PHE R 315 TYR 0.019 0.001 TYR R 191 ARG 0.005 0.000 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7075 (mptt) cc_final: 0.6856 (mmtt) REVERT: A 249 ASP cc_start: 0.7156 (t0) cc_final: 0.6871 (t0) REVERT: A 258 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7413 (mp0) REVERT: A 346 ARG cc_start: 0.6096 (mmm160) cc_final: 0.5517 (mmt-90) REVERT: B 45 MET cc_start: 0.8244 (mtp) cc_final: 0.7399 (ttm) REVERT: B 68 ARG cc_start: 0.7520 (ttt180) cc_final: 0.7222 (ttt90) REVERT: B 259 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.6222 (mm110) REVERT: B 322 ASP cc_start: 0.7872 (m-30) cc_final: 0.6962 (t0) REVERT: G 42 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7046 (mt-10) REVERT: G 62 ARG cc_start: 0.4186 (pmt-80) cc_final: 0.3327 (mmm-85) REVERT: N 7 SER cc_start: 0.6564 (m) cc_final: 0.6272 (t) REVERT: N 93 VAL cc_start: 0.7681 (t) cc_final: 0.7339 (p) REVERT: N 94 TYR cc_start: 0.8240 (m-80) cc_final: 0.7738 (m-80) REVERT: R 231 MET cc_start: 0.6947 (mtp) cc_final: 0.6684 (mtp) REVERT: R 292 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6451 (tp) REVERT: R 441 MET cc_start: 0.5997 (mmt) cc_final: 0.5714 (mmt) outliers start: 25 outliers final: 19 residues processed: 148 average time/residue: 0.2271 time to fit residues: 45.3606 Evaluate side-chains 146 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 75 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8684 Z= 0.206 Angle : 0.494 7.537 11807 Z= 0.264 Chirality : 0.041 0.169 1352 Planarity : 0.004 0.039 1514 Dihedral : 3.918 14.636 1215 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.86 % Allowed : 18.85 % 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: 0.63 (0.26), residues: 1113 helix: 1.64 (0.25), residues: 439 sheet: -0.32 (0.32), residues: 226 loop : -0.33 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.008 0.002 HIS P 9 PHE 0.030 0.002 PHE R 315 TYR 0.020 0.001 TYR R 191 ARG 0.002 0.000 ARG R 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7005 (mptt) cc_final: 0.6770 (mmtt) REVERT: A 249 ASP cc_start: 0.7233 (t0) cc_final: 0.6923 (t0) REVERT: A 258 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7416 (mp0) REVERT: A 346 ARG cc_start: 0.5950 (mmm160) cc_final: 0.5558 (mtt180) REVERT: B 45 MET cc_start: 0.8301 (mtp) cc_final: 0.7467 (ttm) REVERT: B 68 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7295 (ttt90) REVERT: B 170 ASP cc_start: 0.7248 (t70) cc_final: 0.7004 (t70) REVERT: B 259 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6204 (mm110) REVERT: B 322 ASP cc_start: 0.7809 (m-30) cc_final: 0.6965 (t0) REVERT: G 42 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6614 (tm-30) REVERT: G 62 ARG cc_start: 0.4158 (pmt-80) cc_final: 0.3184 (mmm160) REVERT: N 7 SER cc_start: 0.6618 (m) cc_final: 0.6189 (t) REVERT: N 93 VAL cc_start: 0.7722 (t) cc_final: 0.7443 (p) REVERT: N 94 TYR cc_start: 0.8267 (m-80) cc_final: 0.7651 (m-80) REVERT: R 231 MET cc_start: 0.6998 (mtp) cc_final: 0.6771 (mtp) REVERT: R 441 MET cc_start: 0.6222 (mmt) cc_final: 0.5798 (mmt) outliers start: 24 outliers final: 21 residues processed: 141 average time/residue: 0.2229 time to fit residues: 42.7242 Evaluate side-chains 145 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 30.0000 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 75 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134459 restraints weight = 11006.670| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.10 r_work: 0.3523 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8684 Z= 0.161 Angle : 0.463 5.873 11807 Z= 0.252 Chirality : 0.040 0.162 1352 Planarity : 0.003 0.039 1514 Dihedral : 3.840 15.382 1215 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.98 % Allowed : 18.97 % Favored : 78.04 % 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: 0.71 (0.26), residues: 1113 helix: 1.71 (0.25), residues: 439 sheet: -0.20 (0.32), residues: 226 loop : -0.34 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.011 0.001 HIS P 9 PHE 0.030 0.001 PHE R 315 TYR 0.020 0.001 TYR R 191 ARG 0.002 0.000 ARG R 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.20 seconds wall clock time: 40 minutes 17.22 seconds (2417.22 seconds total)