Starting phenix.real_space_refine on Wed Feb 14 07:40:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/02_2024/7wv9_32850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/02_2024/7wv9_32850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/02_2024/7wv9_32850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/02_2024/7wv9_32850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/02_2024/7wv9_32850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv9_32850/02_2024/7wv9_32850.pdb" } resolution = 3.36 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= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 26 atoms to isotropic. 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 66 5.16 5 C 5660 2.51 5 N 1508 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8848 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1732 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2583 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2306 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1740 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'7IC': 1, '9GF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.13, per 1000 atoms: 0.58 Number of scatterers: 8848 At special positions: 0 Unit cell: (130.05, 113.9, 109.65, 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 66 16.00 O 1614 8.00 N 1508 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.756A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.563A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.509A pdb=" N CYS A 215 " --> pdb=" O TRP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.999A pdb=" N ALA A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.993A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 283 through 288 removed outlier: 4.271A pdb=" N CYS A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.144A pdb=" N ALA A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.595A pdb=" N LYS A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.658A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.890A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.889A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.609A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 142 removed outlier: 4.134A pdb=" N ALA R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 149 Processing helix chain 'R' and resid 150 through 179 removed outlier: 3.620A pdb=" N HIS R 154 " --> pdb=" O ARG R 150 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 220 removed outlier: 4.043A pdb=" N GLY R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 removed outlier: 3.507A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 255 Proline residue: R 251 - end of helix removed outlier: 3.654A pdb=" N GLY R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 312 removed outlier: 3.605A pdb=" N TRP R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY R 312 " --> pdb=" O MET R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 357 removed outlier: 4.397A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU R 349 " --> pdb=" O LEU R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 369 removed outlier: 4.064A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 398 removed outlier: 4.259A pdb=" N LYS R 376 " --> pdb=" O ASN R 372 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR R 377 " --> pdb=" O LYS R 373 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 401 through 411 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.220A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 74 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.753A pdb=" N VAL A 34 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.135A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.136A 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: 6.015A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.153A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.605A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.697A 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: 4.086A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.569A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 317 removed outlier: 3.997A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 removed outlier: 4.318A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.150A pdb=" N MET S 93 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR S 59 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'S' and resid 173 through 174 387 hydrogen bonds defined for protein. 1092 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: 2.61 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1404 1.30 - 1.43: 2415 1.43 - 1.56: 5114 1.56 - 1.68: 3 1.68 - 1.81: 98 Bond restraints: 9034 Sorted by residual: bond pdb=" N2 7IC R 502 " pdb=" O1 7IC R 502 " ideal model delta sigma weight residual 1.220 1.402 -0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C16 7IC R 502 " pdb=" C7 7IC R 502 " ideal model delta sigma weight residual 1.463 1.384 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" N TRP R 356 " pdb=" CA TRP R 356 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.16e-02 7.43e+03 1.41e+01 bond pdb=" C ALA A 13 " pdb=" O ALA A 13 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.34e-02 5.57e+03 8.80e+00 bond pdb=" C7 7IC R 502 " pdb=" N8 7IC R 502 " ideal model delta sigma weight residual 1.382 1.323 0.059 2.00e-02 2.50e+03 8.77e+00 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 88.68 - 97.81: 2 97.81 - 106.95: 211 106.95 - 116.08: 5775 116.08 - 125.21: 6105 125.21 - 134.35: 153 Bond angle restraints: 12246 Sorted by residual: angle pdb=" CAM 9GF R 501 " pdb=" CAN 9GF R 501 " pdb=" CAO 9GF R 501 " ideal model delta sigma weight residual 110.47 88.68 21.79 3.00e+00 1.11e-01 5.28e+01 angle pdb=" N GLU A 14 " pdb=" CA GLU A 14 " pdb=" C GLU A 14 " ideal model delta sigma weight residual 113.50 105.96 7.54 1.23e+00 6.61e-01 3.75e+01 angle pdb=" N MET A 248 " pdb=" CA MET A 248 " pdb=" C MET A 248 " ideal model delta sigma weight residual 111.07 105.48 5.59 1.07e+00 8.73e-01 2.73e+01 angle pdb=" CAM 9GF R 501 " pdb=" CAN 9GF R 501 " pdb=" CAT 9GF R 501 " ideal model delta sigma weight residual 112.87 127.31 -14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" N ALA A 13 " pdb=" CA ALA A 13 " pdb=" C ALA A 13 " ideal model delta sigma weight residual 112.92 107.02 5.90 1.23e+00 6.61e-01 2.30e+01 ... (remaining 12241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 5218 32.69 - 65.37: 122 65.37 - 98.06: 17 98.06 - 130.75: 0 130.75 - 163.43: 7 Dihedral angle restraints: 5364 sinusoidal: 2053 harmonic: 3311 Sorted by residual: dihedral pdb=" CA THR B 164 " pdb=" C THR B 164 " pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta harmonic sigma weight residual -180.00 -153.66 -26.34 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CAF 9GF R 501 " pdb=" CAG 9GF R 501 " pdb=" CAJ 9GF R 501 " pdb=" CAK 9GF R 501 " ideal model delta sinusoidal sigma weight residual -124.02 39.41 -163.43 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CAF 9GF R 501 " pdb=" CAG 9GF R 501 " pdb=" CAJ 9GF R 501 " pdb=" CBA 9GF R 501 " ideal model delta sinusoidal sigma weight residual 56.56 -140.73 -162.71 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 5361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1218 0.062 - 0.125: 167 0.125 - 0.187: 19 0.187 - 0.249: 3 0.249 - 0.312: 2 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA ASN A 47 " pdb=" N ASN A 47 " pdb=" C ASN A 47 " pdb=" CB ASN A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA MET A 248 " pdb=" N MET A 248 " pdb=" C MET A 248 " pdb=" CB MET A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASP S 74 " pdb=" N ASP S 74 " pdb=" C ASP S 74 " pdb=" CB ASP S 74 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1406 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 12 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.83e+00 pdb=" CD GLU B 12 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU B 12 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU B 12 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 356 " -0.021 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP R 356 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP R 356 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP R 356 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 356 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP R 356 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 356 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 356 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 356 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 356 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 305 " 0.011 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C GLN A 305 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 305 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 306 " 0.012 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 774 2.74 - 3.28: 8934 3.28 - 3.82: 14226 3.82 - 4.36: 16330 4.36 - 4.90: 28162 Nonbonded interactions: 68426 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR S 95 " pdb=" O GLN S 171 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.259 2.440 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.263 2.520 nonbonded pdb=" OG SER A 6 " pdb=" OH TYR S 161 " model vdw 2.264 2.440 ... (remaining 68421 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.180 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 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 : 0.004 0.182 9034 Z= 0.260 Angle : 0.729 21.789 12246 Z= 0.400 Chirality : 0.046 0.312 1409 Planarity : 0.004 0.047 1532 Dihedral : 16.047 163.433 3221 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 0.53 % Allowed : 0.43 % Favored : 99.04 % 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: -0.80 (0.25), residues: 1125 helix: 0.99 (0.28), residues: 358 sheet: -0.61 (0.34), residues: 236 loop : -1.56 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 356 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.001 PHE S 80 TYR 0.015 0.001 TYR S 102 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.6911 (ttt) cc_final: 0.6700 (ttm) REVERT: A 248 MET cc_start: 0.7274 (ttm) cc_final: 0.6304 (mmt) REVERT: A 278 LYS cc_start: 0.7320 (pttm) cc_final: 0.7026 (pttt) REVERT: A 288 PHE cc_start: 0.5862 (p90) cc_final: 0.5443 (p90) REVERT: S 18 ARG cc_start: 0.4698 (ttt180) cc_final: 0.4435 (ttm170) REVERT: S 65 LYS cc_start: 0.7451 (mppt) cc_final: 0.7011 (mptt) outliers start: 5 outliers final: 2 residues processed: 178 average time/residue: 0.1871 time to fit residues: 47.5167 Evaluate side-chains 139 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0070 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9034 Z= 0.205 Angle : 0.569 7.734 12246 Z= 0.302 Chirality : 0.042 0.183 1409 Planarity : 0.004 0.049 1532 Dihedral : 13.803 158.408 1282 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.13 % Allowed : 9.81 % Favored : 88.06 % 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: -0.77 (0.25), residues: 1125 helix: 1.18 (0.27), residues: 363 sheet: -0.85 (0.33), residues: 259 loop : -1.59 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.010 0.001 HIS B 91 PHE 0.017 0.002 PHE S 80 TYR 0.011 0.001 TYR S 178 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6691 (mmt) cc_final: 0.5988 (mmt) REVERT: A 248 MET cc_start: 0.7268 (ttm) cc_final: 0.6308 (mmt) REVERT: A 278 LYS cc_start: 0.7377 (pttm) cc_final: 0.7105 (pttt) REVERT: R 371 MET cc_start: 0.7691 (mmm) cc_final: 0.7099 (mmm) REVERT: S 18 ARG cc_start: 0.4727 (ttt180) cc_final: 0.4410 (ttm170) outliers start: 20 outliers final: 17 residues processed: 154 average time/residue: 0.1859 time to fit residues: 41.0734 Evaluate side-chains 152 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.0040 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 17 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9034 Z= 0.167 Angle : 0.525 7.183 12246 Z= 0.281 Chirality : 0.042 0.204 1409 Planarity : 0.003 0.044 1532 Dihedral : 13.038 151.895 1280 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.92 % Allowed : 14.93 % Favored : 83.16 % 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: 1125 helix: 1.37 (0.27), residues: 363 sheet: -0.89 (0.32), residues: 278 loop : -1.50 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS B 91 PHE 0.015 0.001 PHE A 190 TYR 0.014 0.001 TYR S 216 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6803 (mmt) cc_final: 0.6367 (mmt) REVERT: A 248 MET cc_start: 0.7189 (ttm) cc_final: 0.6317 (mmt) REVERT: A 278 LYS cc_start: 0.7381 (pttm) cc_final: 0.7180 (pttt) REVERT: S 18 ARG cc_start: 0.4669 (ttt180) cc_final: 0.4308 (ttm170) outliers start: 18 outliers final: 17 residues processed: 148 average time/residue: 0.1980 time to fit residues: 42.2525 Evaluate side-chains 140 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9034 Z= 0.190 Angle : 0.538 7.769 12246 Z= 0.286 Chirality : 0.042 0.198 1409 Planarity : 0.004 0.044 1532 Dihedral : 12.530 149.349 1280 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.52 % Allowed : 15.35 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1125 helix: 1.27 (0.27), residues: 362 sheet: -0.94 (0.34), residues: 251 loop : -1.61 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.010 0.001 HIS B 91 PHE 0.015 0.001 PHE A 190 TYR 0.010 0.001 TYR S 178 ARG 0.003 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: A 244 MET cc_start: 0.6960 (mmt) cc_final: 0.6542 (mmt) REVERT: A 248 MET cc_start: 0.7203 (ttm) cc_final: 0.6346 (mmt) REVERT: A 278 LYS cc_start: 0.7430 (pttm) cc_final: 0.7217 (pttt) REVERT: A 298 ASP cc_start: 0.6609 (m-30) cc_final: 0.6336 (m-30) REVERT: B 273 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 26 ASP cc_start: 0.7320 (t0) cc_final: 0.6986 (t0) REVERT: R 371 MET cc_start: 0.7794 (mmm) cc_final: 0.7240 (mmm) REVERT: S 18 ARG cc_start: 0.4659 (ttt180) cc_final: 0.4310 (ttm170) outliers start: 33 outliers final: 23 residues processed: 158 average time/residue: 0.1892 time to fit residues: 42.7933 Evaluate side-chains 146 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 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 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9034 Z= 0.210 Angle : 0.564 8.153 12246 Z= 0.297 Chirality : 0.042 0.198 1409 Planarity : 0.004 0.042 1532 Dihedral : 11.924 144.415 1280 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 3.41 % Allowed : 17.80 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1125 helix: 1.31 (0.28), residues: 363 sheet: -0.91 (0.34), residues: 238 loop : -1.64 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 36 HIS 0.011 0.001 HIS B 91 PHE 0.019 0.002 PHE A 308 TYR 0.012 0.001 TYR A 303 ARG 0.008 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: A 244 MET cc_start: 0.6996 (mmt) cc_final: 0.6622 (mmt) REVERT: A 248 MET cc_start: 0.7240 (ttm) cc_final: 0.6335 (mmt) REVERT: A 278 LYS cc_start: 0.7462 (pttm) cc_final: 0.7250 (pttt) REVERT: B 273 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8643 (mp) REVERT: C 26 ASP cc_start: 0.7352 (t0) cc_final: 0.6991 (t0) REVERT: R 178 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.6335 (m-70) REVERT: S 18 ARG cc_start: 0.4682 (ttt180) cc_final: 0.4344 (ttm170) outliers start: 32 outliers final: 25 residues processed: 163 average time/residue: 0.1903 time to fit residues: 44.4267 Evaluate side-chains 158 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 110 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9034 Z= 0.291 Angle : 0.618 8.217 12246 Z= 0.328 Chirality : 0.044 0.206 1409 Planarity : 0.004 0.042 1532 Dihedral : 11.732 140.583 1280 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.30 % Allowed : 19.72 % Favored : 76.97 % 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: -1.04 (0.25), residues: 1125 helix: 1.04 (0.27), residues: 364 sheet: -1.11 (0.34), residues: 239 loop : -1.74 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 36 HIS 0.017 0.002 HIS B 91 PHE 0.030 0.002 PHE A 308 TYR 0.015 0.002 TYR A 303 ARG 0.007 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: A 248 MET cc_start: 0.7269 (ttm) cc_final: 0.6320 (mmt) REVERT: B 291 ASP cc_start: 0.6946 (t0) cc_final: 0.6686 (t0) REVERT: C 26 ASP cc_start: 0.7354 (t0) cc_final: 0.6987 (t0) REVERT: R 178 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6410 (m-70) REVERT: R 371 MET cc_start: 0.7887 (mmm) cc_final: 0.7203 (mmm) outliers start: 31 outliers final: 25 residues processed: 158 average time/residue: 0.1931 time to fit residues: 43.3185 Evaluate side-chains 157 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9034 Z= 0.199 Angle : 0.583 9.244 12246 Z= 0.304 Chirality : 0.042 0.211 1409 Planarity : 0.004 0.041 1532 Dihedral : 11.021 136.724 1280 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.30 % Allowed : 20.04 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1125 helix: 1.19 (0.27), residues: 364 sheet: -0.92 (0.34), residues: 240 loop : -1.71 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.010 0.001 HIS B 91 PHE 0.017 0.001 PHE A 308 TYR 0.014 0.001 TYR A 303 ARG 0.005 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: A 244 MET cc_start: 0.6943 (mmt) cc_final: 0.6488 (mmt) REVERT: A 248 MET cc_start: 0.7254 (ttm) cc_final: 0.6306 (mmt) REVERT: B 291 ASP cc_start: 0.6868 (t0) cc_final: 0.6621 (t0) REVERT: C 26 ASP cc_start: 0.7342 (t0) cc_final: 0.6972 (t0) REVERT: R 178 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.6339 (m-70) REVERT: S 18 ARG cc_start: 0.4976 (ttt180) cc_final: 0.4477 (ttm170) REVERT: S 70 ILE cc_start: 0.4310 (OUTLIER) cc_final: 0.3945 (mm) REVERT: S 151 LYS cc_start: 0.6746 (ptmt) cc_final: 0.6404 (ptpt) outliers start: 31 outliers final: 25 residues processed: 161 average time/residue: 0.1923 time to fit residues: 43.8856 Evaluate side-chains 160 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9034 Z= 0.196 Angle : 0.584 9.090 12246 Z= 0.305 Chirality : 0.042 0.215 1409 Planarity : 0.004 0.039 1532 Dihedral : 10.429 133.606 1279 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.26 % Allowed : 19.94 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.25), residues: 1125 helix: 1.21 (0.27), residues: 363 sheet: -0.94 (0.33), residues: 240 loop : -1.72 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.010 0.001 HIS B 91 PHE 0.017 0.001 PHE A 308 TYR 0.015 0.001 TYR S 103 ARG 0.004 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6905 (mmt) cc_final: 0.6497 (mmt) REVERT: A 248 MET cc_start: 0.7212 (ttm) cc_final: 0.6281 (mmt) REVERT: B 234 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: B 291 ASP cc_start: 0.6863 (t0) cc_final: 0.6569 (t0) REVERT: C 26 ASP cc_start: 0.7343 (t0) cc_final: 0.6972 (t0) REVERT: R 178 HIS cc_start: 0.6637 (OUTLIER) cc_final: 0.6324 (m-70) REVERT: R 341 LEU cc_start: 0.3865 (OUTLIER) cc_final: 0.3497 (mt) REVERT: R 371 MET cc_start: 0.7763 (mmm) cc_final: 0.7310 (mmm) REVERT: S 39 GLN cc_start: 0.5867 (tp40) cc_final: 0.5611 (tp40) REVERT: S 70 ILE cc_start: 0.4333 (OUTLIER) cc_final: 0.4112 (mm) REVERT: S 151 LYS cc_start: 0.6807 (ptmt) cc_final: 0.6541 (ptpt) outliers start: 40 outliers final: 30 residues processed: 168 average time/residue: 0.1935 time to fit residues: 45.9002 Evaluate side-chains 166 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.0050 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9034 Z= 0.170 Angle : 0.587 10.416 12246 Z= 0.305 Chirality : 0.042 0.246 1409 Planarity : 0.003 0.039 1532 Dihedral : 9.901 131.295 1279 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.30 % Allowed : 20.79 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1125 helix: 1.23 (0.27), residues: 368 sheet: -0.77 (0.33), residues: 249 loop : -1.74 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.008 0.001 HIS B 91 PHE 0.016 0.001 PHE A 190 TYR 0.014 0.001 TYR S 103 ARG 0.004 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6868 (mmt) cc_final: 0.6525 (mmt) REVERT: A 248 MET cc_start: 0.7213 (ttm) cc_final: 0.6295 (mmt) REVERT: B 234 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: C 26 ASP cc_start: 0.7336 (t0) cc_final: 0.6972 (t0) REVERT: C 60 PRO cc_start: 0.5718 (Cg_endo) cc_final: 0.5202 (Cg_exo) REVERT: R 178 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6314 (m-70) REVERT: R 341 LEU cc_start: 0.3838 (OUTLIER) cc_final: 0.3472 (mt) REVERT: R 371 MET cc_start: 0.7747 (mmm) cc_final: 0.7293 (mmm) REVERT: S 39 GLN cc_start: 0.5875 (tp40) cc_final: 0.5575 (tp40) REVERT: S 70 ILE cc_start: 0.4326 (OUTLIER) cc_final: 0.4038 (mm) REVERT: S 151 LYS cc_start: 0.6846 (ptmt) cc_final: 0.6531 (ptpt) REVERT: S 156 SER cc_start: 0.5532 (t) cc_final: 0.5280 (m) outliers start: 31 outliers final: 25 residues processed: 167 average time/residue: 0.1942 time to fit residues: 45.7055 Evaluate side-chains 164 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS R 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9034 Z= 0.412 Angle : 0.747 9.700 12246 Z= 0.392 Chirality : 0.049 0.285 1409 Planarity : 0.005 0.040 1532 Dihedral : 10.638 133.736 1279 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.30 % Allowed : 21.00 % Favored : 75.69 % 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: -1.44 (0.24), residues: 1125 helix: 0.68 (0.27), residues: 363 sheet: -1.46 (0.33), residues: 235 loop : -1.89 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 339 HIS 0.024 0.002 HIS B 91 PHE 0.034 0.003 PHE A 308 TYR 0.019 0.002 TYR B 105 ARG 0.005 0.001 ARG S 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 248 MET cc_start: 0.7427 (ttm) cc_final: 0.6397 (mmt) REVERT: B 234 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: B 291 ASP cc_start: 0.7027 (t0) cc_final: 0.6783 (t0) REVERT: C 26 ASP cc_start: 0.7391 (t0) cc_final: 0.7080 (t0) REVERT: R 341 LEU cc_start: 0.3989 (OUTLIER) cc_final: 0.3583 (tp) REVERT: S 39 GLN cc_start: 0.5860 (tp40) cc_final: 0.5543 (tp40) REVERT: S 70 ILE cc_start: 0.4362 (OUTLIER) cc_final: 0.4046 (mm) REVERT: S 151 LYS cc_start: 0.7007 (ptmt) cc_final: 0.6664 (ptpt) outliers start: 31 outliers final: 25 residues processed: 158 average time/residue: 0.1964 time to fit residues: 43.9875 Evaluate side-chains 156 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.211855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.173996 restraints weight = 12356.499| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.81 r_work: 0.3884 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9034 Z= 0.213 Angle : 0.632 9.569 12246 Z= 0.326 Chirality : 0.044 0.215 1409 Planarity : 0.004 0.039 1532 Dihedral : 9.879 131.720 1279 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.30 % Allowed : 21.96 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1125 helix: 1.04 (0.27), residues: 362 sheet: -1.15 (0.33), residues: 240 loop : -1.82 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.010 0.001 HIS B 91 PHE 0.017 0.002 PHE A 190 TYR 0.019 0.002 TYR S 103 ARG 0.005 0.000 ARG S 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2026.87 seconds wall clock time: 37 minutes 36.57 seconds (2256.57 seconds total)