Starting phenix.real_space_refine on Wed Feb 14 07:35:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvj_32141/02_2024/7vvj_32141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvj_32141/02_2024/7vvj_32141.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/7vvj_32141/02_2024/7vvj_32141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvj_32141/02_2024/7vvj_32141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvj_32141/02_2024/7vvj_32141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvj_32141/02_2024/7vvj_32141.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= 0.000 sd= 0.006 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 51 5.16 5 C 5630 2.51 5 N 1559 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 137": "OD1" <-> "OD2" Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1932 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 424 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 249 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2734 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 11, 'TRANS': 354} Chain breaks: 3 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 200 Time building chain proxies: 5.36, per 1000 atoms: 0.60 Number of scatterers: 8872 At special positions: 0 Unit cell: (130.725, 104.58, 127.82, 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 51 16.00 O 1632 8.00 N 1559 7.00 C 5630 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=2.09 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=2.02 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 41.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.582A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.927A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.627A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.991A pdb=" N ARG A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.585A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.180A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.603A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.578A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.791A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.371A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.798A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.864A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.793A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 52 Processing helix chain 'R' and resid 182 through 212 removed outlier: 3.637A pdb=" N GLY R 194 " --> pdb=" O ILE R 190 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU R 202 " --> pdb=" O SER R 198 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.570A 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 219 through 245 Processing helix chain 'R' and resid 277 through 312 removed outlier: 4.406A pdb=" N CYS R 281 " --> pdb=" O GLY R 277 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET R 312 " --> pdb=" O SER R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'R' and resid 329 through 346 removed outlier: 3.979A pdb=" N ALA R 333 " --> pdb=" O TRP R 329 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.555A pdb=" N THR R 387 " --> pdb=" O ARG R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 402 through 417 removed outlier: 3.585A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.108A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 480 removed outlier: 3.575A pdb=" N GLU R 469 " --> pdb=" O GLU R 465 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER R 475 " --> pdb=" O LYS R 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 4.007A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.817A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.587A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.213A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.787A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.215A 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: 3.617A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.876A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.785A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 439 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: 2.94 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1449 1.30 - 1.43: 2504 1.43 - 1.57: 5032 1.57 - 1.70: 0 1.70 - 1.84: 74 Bond restraints: 9059 Sorted by residual: bond pdb=" C VAL B 327 " pdb=" O VAL B 327 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.00e-02 1.00e+04 3.79e+01 bond pdb=" C PRO A 351 " pdb=" O PRO A 351 " ideal model delta sigma weight residual 1.233 1.167 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" C ARG B 137 " pdb=" O ARG B 137 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.22e-02 6.72e+03 3.59e+01 bond pdb=" C ASP N 109 " pdb=" O ASP N 109 " ideal model delta sigma weight residual 1.232 1.170 0.062 1.12e-02 7.97e+03 3.03e+01 bond pdb=" C LEU R 187 " pdb=" O LEU R 187 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.17e-02 7.31e+03 2.75e+01 ... (remaining 9054 not shown) Histogram of bond angle deviations from ideal: 98.73 - 106.02: 187 106.02 - 113.31: 4638 113.31 - 120.60: 4266 120.60 - 127.89: 3112 127.89 - 135.18: 86 Bond angle restraints: 12289 Sorted by residual: angle pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" O CYS N 107 " ideal model delta sigma weight residual 120.36 113.06 7.30 1.08e+00 8.57e-01 4.56e+01 angle pdb=" CA ILE B 80 " pdb=" C ILE B 80 " pdb=" O ILE B 80 " ideal model delta sigma weight residual 120.39 113.60 6.79 1.05e+00 9.07e-01 4.19e+01 angle pdb=" CA GLY N 121 " pdb=" C GLY N 121 " pdb=" O GLY N 121 " ideal model delta sigma weight residual 122.22 118.35 3.87 6.50e-01 2.37e+00 3.55e+01 angle pdb=" CA VAL R 384 " pdb=" C VAL R 384 " pdb=" O VAL R 384 " ideal model delta sigma weight residual 119.29 114.79 4.50 8.40e-01 1.42e+00 2.86e+01 angle pdb=" N VAL R 419 " pdb=" CA VAL R 419 " pdb=" C VAL R 419 " ideal model delta sigma weight residual 111.90 107.69 4.21 8.10e-01 1.52e+00 2.70e+01 ... (remaining 12284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 4796 17.21 - 34.42: 446 34.42 - 51.63: 78 51.63 - 68.84: 22 68.84 - 86.05: 10 Dihedral angle restraints: 5352 sinusoidal: 2002 harmonic: 3350 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 -86.00 -165.05 79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 29.98 63.02 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 150.03 -57.03 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 5349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 863 0.081 - 0.162: 442 0.162 - 0.243: 69 0.243 - 0.325: 8 0.325 - 0.406: 1 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CA LEU A 378 " pdb=" N LEU A 378 " pdb=" C LEU A 378 " pdb=" CB LEU A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA PHE N 108 " pdb=" N PHE N 108 " pdb=" C PHE N 108 " pdb=" CB PHE N 108 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA LEU B 318 " pdb=" N LEU B 318 " pdb=" C LEU B 318 " pdb=" CB LEU B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1380 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.058 2.00e-02 2.50e+03 3.14e-02 2.47e+01 pdb=" CG TRP A 271 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 335 " 0.059 2.00e-02 2.50e+03 3.64e-02 2.31e+01 pdb=" CG PHE B 335 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 335 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE B 335 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 335 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE B 335 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 335 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.037 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR B 59 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.009 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 618 2.74 - 3.28: 8973 3.28 - 3.82: 13778 3.82 - 4.36: 18956 4.36 - 4.90: 30834 Nonbonded interactions: 73159 Sorted by model distance: nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.205 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.231 2.440 nonbonded pdb=" O MET R 445 " pdb=" OG SER R 449 " model vdw 2.254 2.440 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.279 2.520 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.291 2.440 ... (remaining 73154 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: 0.020 Extract box with map and model: 1.440 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.720 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 0.080 9059 Z= 0.999 Angle : 1.783 7.673 12289 Z= 1.297 Chirality : 0.088 0.406 1383 Planarity : 0.009 0.037 1576 Dihedral : 14.241 86.051 3177 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 1.77 % Allowed : 5.53 % Favored : 92.70 % Cbeta Deviations : 0.09 % 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: -1.52 (0.23), residues: 1134 helix: -0.87 (0.23), residues: 427 sheet: -0.90 (0.35), residues: 214 loop : -1.01 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.013 TRP A 271 HIS 0.019 0.006 HIS A 352 PHE 0.059 0.010 PHE B 335 TYR 0.058 0.011 TYR B 59 ARG 0.021 0.003 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.008 Fit side-chains REVERT: A 50 ASN cc_start: 0.6210 (m110) cc_final: 0.6007 (p0) REVERT: A 221 MET cc_start: 0.8718 (ttp) cc_final: 0.8488 (ttp) REVERT: A 295 LYS cc_start: 0.7681 (mmpt) cc_final: 0.7309 (mmtp) REVERT: A 376 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: B 161 SER cc_start: 0.9017 (m) cc_final: 0.8771 (m) REVERT: B 175 GLN cc_start: 0.7910 (pm20) cc_final: 0.7364 (pm20) REVERT: B 189 SER cc_start: 0.8980 (m) cc_final: 0.8658 (p) REVERT: N 53 GLN cc_start: 0.8005 (mp10) cc_final: 0.7740 (mp10) REVERT: R 218 THR cc_start: 0.8349 (t) cc_final: 0.8127 (t) REVERT: R 219 ARG cc_start: 0.7075 (ptt90) cc_final: 0.6591 (ptp90) REVERT: R 441 MET cc_start: 0.8456 (mmt) cc_final: 0.7986 (mmt) REVERT: R 443 TYR cc_start: 0.7926 (t80) cc_final: 0.7508 (t80) REVERT: R 445 MET cc_start: 0.8168 (mmm) cc_final: 0.7771 (mmm) REVERT: R 465 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7564 (mt-10) outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 0.2887 time to fit residues: 63.9695 Evaluate side-chains 133 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 25 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN R 402 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9059 Z= 0.263 Angle : 0.578 8.699 12289 Z= 0.313 Chirality : 0.044 0.166 1383 Planarity : 0.004 0.034 1576 Dihedral : 5.696 57.588 1262 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.10 % Allowed : 11.73 % Favored : 86.17 % 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: -0.09 (0.25), residues: 1134 helix: 0.82 (0.25), residues: 432 sheet: -0.66 (0.34), residues: 226 loop : -0.44 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 298 HIS 0.006 0.001 HIS B 91 PHE 0.021 0.002 PHE A 212 TYR 0.027 0.002 TYR R 191 ARG 0.006 0.001 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.155 Fit side-chains REVERT: A 28 LYS cc_start: 0.8280 (pptt) cc_final: 0.7678 (tptt) REVERT: A 295 LYS cc_start: 0.7591 (mmpt) cc_final: 0.7192 (mptt) REVERT: B 45 MET cc_start: 0.8525 (mtt) cc_final: 0.8314 (mtt) REVERT: B 175 GLN cc_start: 0.8047 (pm20) cc_final: 0.7467 (pm20) REVERT: B 189 SER cc_start: 0.8895 (m) cc_final: 0.8675 (p) REVERT: B 262 MET cc_start: 0.8884 (ttm) cc_final: 0.8543 (ttm) REVERT: B 275 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8405 (p) REVERT: G 21 MET cc_start: 0.6449 (ttm) cc_final: 0.6144 (mtt) REVERT: N 53 GLN cc_start: 0.7945 (mp10) cc_final: 0.7657 (mp10) REVERT: N 105 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7261 (mtm-85) REVERT: N 106 ASP cc_start: 0.8770 (p0) cc_final: 0.8498 (p0) REVERT: R 39 PHE cc_start: 0.6732 (t80) cc_final: 0.6192 (t80) REVERT: R 390 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.7341 (ttt-90) REVERT: R 441 MET cc_start: 0.8133 (mmt) cc_final: 0.7815 (mmt) outliers start: 19 outliers final: 15 residues processed: 155 average time/residue: 0.2959 time to fit residues: 58.4070 Evaluate side-chains 146 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 217 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9059 Z= 0.195 Angle : 0.505 7.448 12289 Z= 0.274 Chirality : 0.042 0.142 1383 Planarity : 0.003 0.036 1576 Dihedral : 4.982 58.362 1255 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.88 % Allowed : 12.28 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1134 helix: 1.37 (0.25), residues: 434 sheet: -0.46 (0.33), residues: 232 loop : -0.37 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.004 0.001 HIS A 347 PHE 0.017 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.145 Fit side-chains REVERT: A 24 LYS cc_start: 0.7181 (tptt) cc_final: 0.6844 (tptt) REVERT: B 161 SER cc_start: 0.8885 (m) cc_final: 0.8673 (m) REVERT: B 175 GLN cc_start: 0.8008 (pm20) cc_final: 0.7395 (pm20) REVERT: B 217 MET cc_start: 0.7232 (ppp) cc_final: 0.6977 (ppp) REVERT: B 275 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8400 (p) REVERT: N 53 GLN cc_start: 0.8017 (mp10) cc_final: 0.7705 (mp10) REVERT: N 105 ARG cc_start: 0.7752 (mtm180) cc_final: 0.7143 (mtm-85) REVERT: R 39 PHE cc_start: 0.6504 (t80) cc_final: 0.6102 (t80) REVERT: R 364 GLN cc_start: 0.7779 (pt0) cc_final: 0.7539 (pt0) REVERT: R 409 SER cc_start: 0.7457 (p) cc_final: 0.7199 (m) REVERT: R 443 TYR cc_start: 0.7839 (t80) cc_final: 0.7201 (t80) outliers start: 26 outliers final: 19 residues processed: 157 average time/residue: 0.2988 time to fit residues: 60.1788 Evaluate side-chains 151 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 431 GLU Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 213 GLN B 340 ASN G 59 ASN N 31 ASN R 220 ASN R 358 ASN R 374 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9059 Z= 0.400 Angle : 0.620 7.805 12289 Z= 0.334 Chirality : 0.047 0.217 1383 Planarity : 0.004 0.040 1576 Dihedral : 5.160 49.383 1253 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.31 % Allowed : 13.38 % Favored : 82.30 % 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 (0.25), residues: 1134 helix: 1.07 (0.25), residues: 435 sheet: -0.56 (0.33), residues: 214 loop : -0.59 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 298 HIS 0.006 0.001 HIS A 347 PHE 0.019 0.002 PHE R 335 TYR 0.032 0.002 TYR R 191 ARG 0.005 0.001 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.025 Fit side-chains REVERT: A 24 LYS cc_start: 0.7293 (tptt) cc_final: 0.6965 (tptt) REVERT: A 28 LYS cc_start: 0.8317 (pptt) cc_final: 0.7594 (tptt) REVERT: B 175 GLN cc_start: 0.8019 (pm20) cc_final: 0.7404 (pm20) REVERT: B 217 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7090 (ppp) REVERT: B 275 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8421 (p) REVERT: N 105 ARG cc_start: 0.7861 (mtm180) cc_final: 0.7112 (mtm-85) REVERT: R 409 SER cc_start: 0.7509 (p) cc_final: 0.7255 (m) REVERT: R 443 TYR cc_start: 0.7920 (t80) cc_final: 0.7486 (t80) outliers start: 39 outliers final: 29 residues processed: 159 average time/residue: 0.2797 time to fit residues: 57.3368 Evaluate side-chains 157 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 92 optimal weight: 0.0040 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN R 220 ASN R 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9059 Z= 0.310 Angle : 0.583 10.262 12289 Z= 0.314 Chirality : 0.044 0.172 1383 Planarity : 0.004 0.040 1576 Dihedral : 5.338 54.598 1253 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.42 % Allowed : 15.27 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1134 helix: 1.39 (0.25), residues: 423 sheet: -0.50 (0.32), residues: 212 loop : -0.52 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 298 HIS 0.005 0.001 HIS A 347 PHE 0.019 0.002 PHE R 335 TYR 0.026 0.002 TYR R 191 ARG 0.006 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 0.965 Fit side-chains REVERT: A 24 LYS cc_start: 0.7270 (tptt) cc_final: 0.6942 (tptt) REVERT: A 28 LYS cc_start: 0.8319 (pptt) cc_final: 0.7576 (tptt) REVERT: B 175 GLN cc_start: 0.8022 (pm20) cc_final: 0.7395 (pm20) REVERT: B 217 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7051 (ppp) REVERT: B 275 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8399 (p) REVERT: N 83 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8129 (mtp) REVERT: R 190 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6830 (tt) REVERT: R 321 LEU cc_start: 0.7112 (tp) cc_final: 0.6767 (tt) REVERT: R 409 SER cc_start: 0.7393 (p) cc_final: 0.7158 (m) REVERT: R 443 TYR cc_start: 0.7895 (t80) cc_final: 0.7474 (t80) outliers start: 40 outliers final: 28 residues processed: 158 average time/residue: 0.2738 time to fit residues: 55.7713 Evaluate side-chains 160 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 374 ASN Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 220 ASN R 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9059 Z= 0.177 Angle : 0.506 8.034 12289 Z= 0.273 Chirality : 0.041 0.154 1383 Planarity : 0.003 0.037 1576 Dihedral : 4.701 50.022 1250 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.21 % Allowed : 16.59 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.50 (0.25), residues: 1134 helix: 1.66 (0.25), residues: 431 sheet: -0.36 (0.33), residues: 203 loop : -0.49 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 0.973 Fit side-chains REVERT: A 15 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6622 (tp30) REVERT: A 24 LYS cc_start: 0.7241 (tptt) cc_final: 0.6882 (tptt) REVERT: B 161 SER cc_start: 0.8835 (m) cc_final: 0.8627 (m) REVERT: B 175 GLN cc_start: 0.8049 (pm20) cc_final: 0.7427 (pm20) REVERT: B 217 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7269 (ppp) REVERT: B 275 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8393 (p) REVERT: R 190 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6863 (tt) REVERT: R 321 LEU cc_start: 0.7123 (tp) cc_final: 0.6791 (tt) REVERT: R 409 SER cc_start: 0.7192 (p) cc_final: 0.6991 (m) REVERT: R 443 TYR cc_start: 0.7906 (t80) cc_final: 0.7473 (t80) outliers start: 29 outliers final: 20 residues processed: 144 average time/residue: 0.2810 time to fit residues: 52.2466 Evaluate side-chains 149 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 107 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9059 Z= 0.174 Angle : 0.490 7.460 12289 Z= 0.265 Chirality : 0.041 0.153 1383 Planarity : 0.003 0.037 1576 Dihedral : 4.502 45.183 1250 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.10 % Allowed : 17.04 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1134 helix: 1.99 (0.25), residues: 424 sheet: -0.24 (0.32), residues: 225 loop : -0.33 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 0.924 Fit side-chains REVERT: A 15 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6601 (tp30) REVERT: A 24 LYS cc_start: 0.7265 (tptt) cc_final: 0.6913 (tptt) REVERT: A 379 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7850 (ttp-170) REVERT: B 161 SER cc_start: 0.8812 (m) cc_final: 0.8605 (m) REVERT: B 175 GLN cc_start: 0.8108 (pm20) cc_final: 0.7491 (pm20) REVERT: B 217 MET cc_start: 0.7454 (ppp) cc_final: 0.7230 (ppp) REVERT: B 275 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8417 (p) REVERT: R 186 ARG cc_start: 0.6291 (tmm-80) cc_final: 0.5982 (ttm-80) REVERT: R 321 LEU cc_start: 0.7147 (tp) cc_final: 0.6818 (tt) outliers start: 28 outliers final: 23 residues processed: 153 average time/residue: 0.2656 time to fit residues: 53.0891 Evaluate side-chains 162 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9059 Z= 0.199 Angle : 0.507 7.465 12289 Z= 0.272 Chirality : 0.041 0.154 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.473 42.068 1250 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.32 % Allowed : 17.04 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1134 helix: 1.99 (0.26), residues: 429 sheet: -0.29 (0.33), residues: 209 loop : -0.35 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.027 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.009 Fit side-chains REVERT: A 15 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6607 (tp30) REVERT: A 24 LYS cc_start: 0.7251 (tptt) cc_final: 0.6871 (tptt) REVERT: A 360 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: B 161 SER cc_start: 0.8839 (m) cc_final: 0.8592 (m) REVERT: B 175 GLN cc_start: 0.8114 (pm20) cc_final: 0.7489 (pm20) REVERT: B 262 MET cc_start: 0.8876 (ttm) cc_final: 0.8537 (ttm) REVERT: B 275 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8400 (p) REVERT: N 83 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: R 321 LEU cc_start: 0.7145 (tp) cc_final: 0.6808 (tt) REVERT: R 443 TYR cc_start: 0.7744 (t80) cc_final: 0.7364 (t80) outliers start: 30 outliers final: 23 residues processed: 153 average time/residue: 0.2681 time to fit residues: 53.4618 Evaluate side-chains 157 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9059 Z= 0.219 Angle : 0.516 7.494 12289 Z= 0.277 Chirality : 0.041 0.152 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.505 39.703 1250 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.99 % Allowed : 17.59 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.76 (0.25), residues: 1134 helix: 1.98 (0.25), residues: 431 sheet: -0.33 (0.33), residues: 211 loop : -0.39 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 298 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.983 Fit side-chains REVERT: A 15 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6583 (tp30) REVERT: A 24 LYS cc_start: 0.7250 (tptt) cc_final: 0.6870 (tptt) REVERT: A 360 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6367 (pm20) REVERT: B 161 SER cc_start: 0.8872 (m) cc_final: 0.8633 (m) REVERT: B 175 GLN cc_start: 0.8156 (pm20) cc_final: 0.7536 (pm20) REVERT: B 262 MET cc_start: 0.8873 (ttm) cc_final: 0.8540 (ttm) REVERT: B 275 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8383 (p) REVERT: N 83 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8074 (mtp) REVERT: R 189 MET cc_start: 0.6626 (tmm) cc_final: 0.6318 (tmm) REVERT: R 321 LEU cc_start: 0.7171 (tp) cc_final: 0.6815 (tt) outliers start: 27 outliers final: 23 residues processed: 145 average time/residue: 0.2722 time to fit residues: 51.3718 Evaluate side-chains 154 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9059 Z= 0.256 Angle : 0.541 7.890 12289 Z= 0.290 Chirality : 0.042 0.158 1383 Planarity : 0.003 0.039 1576 Dihedral : 4.610 39.417 1250 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.10 % Allowed : 17.59 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.74 (0.25), residues: 1134 helix: 1.97 (0.25), residues: 429 sheet: -0.30 (0.32), residues: 210 loop : -0.42 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.004 0.001 HIS A 347 PHE 0.019 0.001 PHE R 335 TYR 0.027 0.001 TYR R 191 ARG 0.007 0.000 ARG R 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.901 Fit side-chains REVERT: A 15 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6549 (tp30) REVERT: A 24 LYS cc_start: 0.7265 (tptt) cc_final: 0.6886 (tptt) REVERT: A 360 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6452 (pm20) REVERT: B 161 SER cc_start: 0.8919 (m) cc_final: 0.8675 (m) REVERT: B 175 GLN cc_start: 0.8131 (pm20) cc_final: 0.7510 (pm20) REVERT: B 262 MET cc_start: 0.8875 (ttm) cc_final: 0.8539 (ttm) REVERT: B 275 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8387 (p) REVERT: N 7 SER cc_start: 0.8289 (t) cc_final: 0.8083 (p) REVERT: N 83 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8119 (mtp) REVERT: R 186 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5847 (ttm-80) REVERT: R 189 MET cc_start: 0.6559 (tmm) cc_final: 0.6233 (tmm) REVERT: R 321 LEU cc_start: 0.7173 (tp) cc_final: 0.6811 (tt) REVERT: R 443 TYR cc_start: 0.7734 (t80) cc_final: 0.7243 (t80) outliers start: 28 outliers final: 24 residues processed: 147 average time/residue: 0.2698 time to fit residues: 51.6616 Evaluate side-chains 158 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 186 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118798 restraints weight = 10877.914| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.68 r_work: 0.3255 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9059 Z= 0.167 Angle : 0.494 7.417 12289 Z= 0.265 Chirality : 0.040 0.146 1383 Planarity : 0.003 0.037 1576 Dihedral : 4.342 36.277 1250 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.65 % Allowed : 18.14 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 1.02 (0.25), residues: 1134 helix: 2.27 (0.25), residues: 425 sheet: -0.17 (0.32), residues: 224 loop : -0.30 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.008 0.000 ARG R 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.52 seconds wall clock time: 40 minutes 9.01 seconds (2409.01 seconds total)