Starting phenix.real_space_refine on Wed Mar 12 22:01:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvk_32142/03_2025/7vvk_32142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvk_32142/03_2025/7vvk_32142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vvk_32142/03_2025/7vvk_32142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvk_32142/03_2025/7vvk_32142.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvk_32142/03_2025/7vvk_32142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvk_32142/03_2025/7vvk_32142.cif" } resolution = 3.3 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5405 2.51 5 N 1485 2.21 5 O 1574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8516 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1903 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2544 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 396 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 965 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE%COO:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2457 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 6, 'TRANS': 327} Chain breaks: 6 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 238 Time building chain proxies: 4.79, per 1000 atoms: 0.56 Number of scatterers: 8516 At special positions: 0 Unit cell: (127.267, 99.6003, 122.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1574 8.00 N 1485 7.00 C 5405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.00 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 967.7 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 41.7% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.639A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.573A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.509A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.521A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.573A pdb=" N GLU A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.984A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.974A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.509A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.616A pdb=" N HIS A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.566A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.643A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 44 removed outlier: 3.878A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.659A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 removed outlier: 3.541A pdb=" N GLN P 29 " --> pdb=" O ARG P 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 180 through 212 removed outlier: 4.114A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU R 187 " --> pdb=" O VAL R 183 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET R 189 " --> pdb=" O ASP R 185 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 246 removed outlier: 3.783A pdb=" N ILE R 237 " --> pdb=" O ARG R 233 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 4.232A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 346 removed outlier: 3.907A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU R 346 " --> pdb=" O VAL R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.839A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 removed outlier: 3.620A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.898A pdb=" N SER R 370 " --> pdb=" O PRO R 366 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE R 371 " --> pdb=" O ILE R 367 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL R 372 " --> pdb=" O LEU R 368 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN R 374 " --> pdb=" O SER R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 420 through 424 removed outlier: 3.515A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 449 Processing helix chain 'R' and resid 450 through 461 Processing helix chain 'R' and resid 463 through 478 removed outlier: 3.826A pdb=" N GLU R 469 " --> pdb=" O GLU R 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 9.371A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.670A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.040A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.694A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.096A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.698A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.377A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.779A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.508A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 128 through 130 408 hydrogen bonds defined for protein. 1167 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: 2.24 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1441 1.31 - 1.45: 2405 1.45 - 1.59: 4766 1.59 - 1.73: 0 1.73 - 1.87: 76 Bond restraints: 8688 Sorted by residual: bond pdb=" C ARG B 314 " pdb=" O ARG B 314 " ideal model delta sigma weight residual 1.234 1.304 -0.069 1.20e-02 6.94e+03 3.34e+01 bond pdb=" CE1 HIS R 307 " pdb=" NE2 HIS R 307 " ideal model delta sigma weight residual 1.321 1.376 -0.055 1.00e-02 1.00e+04 3.00e+01 bond pdb=" C SER B 189 " pdb=" O SER B 189 " ideal model delta sigma weight residual 1.234 1.172 0.061 1.24e-02 6.50e+03 2.44e+01 bond pdb=" C ILE B 338 " pdb=" O ILE B 338 " ideal model delta sigma weight residual 1.237 1.185 0.051 1.07e-02 8.73e+03 2.31e+01 bond pdb=" N ILE R 115 " pdb=" CA ILE R 115 " ideal model delta sigma weight residual 1.458 1.498 -0.041 9.00e-03 1.23e+04 2.03e+01 ... (remaining 8683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 6884 1.42 - 2.84: 3694 2.84 - 4.27: 1076 4.27 - 5.69: 124 5.69 - 7.11: 21 Bond angle restraints: 11799 Sorted by residual: angle pdb=" N ILE R 371 " pdb=" CA ILE R 371 " pdb=" C ILE R 371 " ideal model delta sigma weight residual 111.81 106.43 5.38 8.60e-01 1.35e+00 3.92e+01 angle pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " ideal model delta sigma weight residual 112.60 118.42 -5.82 1.00e+00 1.00e+00 3.38e+01 angle pdb=" C THR A 315 " pdb=" CA THR A 315 " pdb=" CB THR A 315 " ideal model delta sigma weight residual 110.33 115.59 -5.26 1.02e+00 9.61e-01 2.66e+01 angle pdb=" N ARG N 67 " pdb=" CA ARG N 67 " pdb=" C ARG N 67 " ideal model delta sigma weight residual 113.55 107.10 6.45 1.26e+00 6.30e-01 2.62e+01 angle pdb=" C SER R 433 " pdb=" N GLY R 434 " pdb=" CA GLY R 434 " ideal model delta sigma weight residual 119.92 124.81 -4.89 9.60e-01 1.09e+00 2.60e+01 ... (remaining 11794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4672 17.99 - 35.97: 365 35.97 - 53.96: 57 53.96 - 71.95: 13 71.95 - 89.93: 6 Dihedral angle restraints: 5113 sinusoidal: 1854 harmonic: 3259 Sorted by residual: 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 93.00 136.96 -43.96 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual 180.00 -156.49 -23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 750 0.068 - 0.137: 445 0.137 - 0.205: 127 0.205 - 0.273: 21 0.273 - 0.342: 2 Chirality restraints: 1345 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB VAL P 31 " pdb=" CA VAL P 31 " pdb=" CG1 VAL P 31 " pdb=" CG2 VAL P 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA VAL A 277 " pdb=" N VAL A 277 " pdb=" C VAL A 277 " pdb=" CB VAL A 277 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1342 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.064 2.00e-02 2.50e+03 3.11e-02 2.42e+01 pdb=" CG TRP A 271 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 329 " -0.047 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP R 329 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP R 329 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP R 329 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP R 329 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP R 329 " -0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP R 329 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 329 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 329 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP R 329 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " -0.060 2.00e-02 2.50e+03 2.79e-02 1.94e+01 pdb=" CG TRP B 99 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " -0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " -0.019 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 743 2.76 - 3.29: 8851 3.29 - 3.83: 13479 3.83 - 4.36: 17823 4.36 - 4.90: 29238 Nonbonded interactions: 70134 Sorted by model distance: nonbonded pdb=" O LEU A 383 " pdb=" OG SER R 409 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.250 3.040 nonbonded pdb=" O ALA R 344 " pdb=" ND2 ASN R 348 " model vdw 2.262 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O GLY B 288 " model vdw 2.264 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.282 3.040 ... (remaining 70129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 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 0.091 8688 Z= 0.971 Angle : 1.746 7.111 11799 Z= 1.274 Chirality : 0.087 0.342 1345 Planarity : 0.008 0.038 1511 Dihedral : 13.866 89.932 2992 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.20 % Favored : 95.62 % Rotamer: Outliers : 0.47 % Allowed : 4.47 % Favored : 95.06 % 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: -0.92 (0.24), residues: 1095 helix: -0.30 (0.24), residues: 422 sheet: -0.46 (0.39), residues: 189 loop : -0.80 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.011 TRP A 271 HIS 0.027 0.006 HIS P 9 PHE 0.048 0.009 PHE A 246 TYR 0.057 0.010 TYR R 297 ARG 0.027 0.003 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7300 (tmmt) cc_final: 0.7097 (tptt) REVERT: A 28 LYS cc_start: 0.6888 (mmpt) cc_final: 0.6513 (ptmm) REVERT: A 32 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6958 (mttm) REVERT: A 253 TYR cc_start: 0.7739 (m-80) cc_final: 0.7518 (m-80) REVERT: A 255 ARG cc_start: 0.6954 (mtp-110) cc_final: 0.6746 (ttm170) REVERT: A 273 ARG cc_start: 0.6823 (ptp-110) cc_final: 0.6585 (ptp-170) REVERT: A 297 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7437 (mtpp) REVERT: A 337 ARG cc_start: 0.7152 (tmt-80) cc_final: 0.6668 (ttm-80) REVERT: A 342 SER cc_start: 0.5333 (p) cc_final: 0.5119 (m) REVERT: B 119 ASN cc_start: 0.7894 (m110) cc_final: 0.7644 (m110) REVERT: B 145 TYR cc_start: 0.8202 (p90) cc_final: 0.7656 (p90) REVERT: B 152 LEU cc_start: 0.8092 (mt) cc_final: 0.7716 (mp) REVERT: B 156 GLN cc_start: 0.7582 (mm110) cc_final: 0.7233 (mt0) REVERT: B 184 THR cc_start: 0.7165 (p) cc_final: 0.6880 (t) REVERT: B 226 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 233 CYS cc_start: 0.8754 (p) cc_final: 0.8276 (t) REVERT: B 239 ASN cc_start: 0.8047 (m-40) cc_final: 0.7651 (m-40) REVERT: B 254 ASP cc_start: 0.7230 (t0) cc_final: 0.6990 (t0) REVERT: B 262 MET cc_start: 0.7388 (ttt) cc_final: 0.7018 (tpp) REVERT: B 291 ASP cc_start: 0.6989 (t70) cc_final: 0.6759 (t0) REVERT: B 298 ASP cc_start: 0.8670 (t0) cc_final: 0.8456 (t70) REVERT: B 301 LYS cc_start: 0.6862 (mmtt) cc_final: 0.6606 (mmtt) REVERT: B 314 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6551 (ttm170) REVERT: B 322 ASP cc_start: 0.7216 (m-30) cc_final: 0.6823 (m-30) REVERT: B 337 LYS cc_start: 0.8292 (mttt) cc_final: 0.8059 (mttm) REVERT: G 38 MET cc_start: 0.6732 (tpt) cc_final: 0.6449 (ttp) REVERT: G 46 LYS cc_start: 0.6996 (mppt) cc_final: 0.6713 (tptp) REVERT: N 34 MET cc_start: 0.8449 (mmm) cc_final: 0.8016 (mmm) REVERT: N 105 ARG cc_start: 0.6339 (mmt-90) cc_final: 0.5470 (mtp180) REVERT: N 117 TYR cc_start: 0.7447 (m-80) cc_final: 0.6866 (m-80) REVERT: N 120 GLN cc_start: 0.7032 (tt0) cc_final: 0.6696 (mm110) REVERT: R 224 MET cc_start: 0.6862 (mmm) cc_final: 0.6352 (ttm) REVERT: R 311 PHE cc_start: 0.7180 (m-80) cc_final: 0.6687 (m-80) REVERT: R 312 MET cc_start: 0.7240 (mmm) cc_final: 0.6861 (mtp) REVERT: R 315 PHE cc_start: 0.3986 (t80) cc_final: 0.3634 (t80) REVERT: R 429 TYR cc_start: 0.3934 (m-10) cc_final: 0.3453 (m-80) REVERT: R 458 ILE cc_start: 0.6587 (mt) cc_final: 0.6212 (mm) REVERT: R 474 TRP cc_start: 0.5888 (t60) cc_final: 0.5640 (t60) outliers start: 4 outliers final: 0 residues processed: 224 average time/residue: 0.2630 time to fit residues: 75.4086 Evaluate side-chains 162 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 156 GLN B 176 GLN B 313 ASN N 39 GLN P 29 GLN R 223 HIS ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.150733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119413 restraints weight = 11816.109| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.29 r_work: 0.3347 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8688 Z= 0.285 Angle : 0.620 7.784 11799 Z= 0.337 Chirality : 0.045 0.254 1345 Planarity : 0.004 0.037 1511 Dihedral : 4.715 32.422 1208 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.23 % Allowed : 10.93 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1095 helix: 0.96 (0.25), residues: 430 sheet: -0.27 (0.36), residues: 217 loop : -0.47 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 298 HIS 0.006 0.002 HIS P 9 PHE 0.020 0.002 PHE R 335 TYR 0.021 0.002 TYR R 297 ARG 0.005 0.001 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7090 (tmmt) cc_final: 0.6733 (mptt) REVERT: A 255 ARG cc_start: 0.7029 (mtp-110) cc_final: 0.6758 (mtp180) REVERT: A 273 ARG cc_start: 0.7069 (ptp-110) cc_final: 0.6836 (ptp-170) REVERT: A 337 ARG cc_start: 0.7458 (tmt-80) cc_final: 0.6936 (ttm-80) REVERT: A 346 ARG cc_start: 0.6276 (mmm-85) cc_final: 0.6048 (mmm-85) REVERT: B 44 GLN cc_start: 0.6492 (pm20) cc_final: 0.5988 (pm20) REVERT: B 59 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: B 145 TYR cc_start: 0.8206 (p90) cc_final: 0.7668 (p90) REVERT: B 156 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7596 (mt0) REVERT: B 239 ASN cc_start: 0.8038 (m-40) cc_final: 0.7685 (m-40) REVERT: B 271 CYS cc_start: 0.6201 (m) cc_final: 0.5918 (p) REVERT: B 298 ASP cc_start: 0.8525 (t0) cc_final: 0.8309 (t70) REVERT: B 301 LYS cc_start: 0.6772 (mmtt) cc_final: 0.6420 (mttp) REVERT: B 322 ASP cc_start: 0.6682 (m-30) cc_final: 0.6198 (m-30) REVERT: N 34 MET cc_start: 0.8192 (mmm) cc_final: 0.7926 (mmm) REVERT: N 46 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: N 105 ARG cc_start: 0.6024 (mmt-90) cc_final: 0.5574 (mtp180) REVERT: N 117 TYR cc_start: 0.7584 (m-80) cc_final: 0.6979 (m-80) REVERT: R 206 VAL cc_start: 0.6269 (t) cc_final: 0.6047 (t) REVERT: R 331 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7421 (tp) REVERT: R 348 ASN cc_start: 0.6089 (t0) cc_final: 0.5573 (t0) REVERT: R 401 GLN cc_start: 0.4433 (tm-30) cc_final: 0.4176 (mt0) REVERT: R 405 LYS cc_start: 0.7000 (tptt) cc_final: 0.6729 (tptp) REVERT: R 425 MET cc_start: 0.7432 (tmm) cc_final: 0.6992 (tmm) REVERT: R 441 MET cc_start: 0.6775 (mmt) cc_final: 0.6530 (tpp) REVERT: R 458 ILE cc_start: 0.6365 (mt) cc_final: 0.5931 (mp) REVERT: R 474 TRP cc_start: 0.5630 (t60) cc_final: 0.4447 (t-100) outliers start: 19 outliers final: 9 residues processed: 179 average time/residue: 0.2468 time to fit residues: 58.2549 Evaluate side-chains 157 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 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 = 0.3880 r_free = 0.3880 target = 0.152909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125001 restraints weight = 12278.087| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.23 r_work: 0.3414 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8688 Z= 0.175 Angle : 0.505 5.204 11799 Z= 0.276 Chirality : 0.042 0.224 1345 Planarity : 0.003 0.041 1511 Dihedral : 4.310 25.452 1208 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.88 % Allowed : 15.16 % Favored : 82.96 % 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: 0.46 (0.26), residues: 1095 helix: 1.51 (0.25), residues: 436 sheet: -0.27 (0.36), residues: 212 loop : -0.54 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.002 PHE R 315 TYR 0.017 0.001 TYR R 191 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.636 Fit side-chains REVERT: A 24 LYS cc_start: 0.7196 (tmmt) cc_final: 0.6671 (mptt) REVERT: A 337 ARG cc_start: 0.7564 (tmt-80) cc_final: 0.7138 (ttm110) REVERT: B 44 GLN cc_start: 0.6497 (pm20) cc_final: 0.6026 (pm20) REVERT: B 130 GLU cc_start: 0.6581 (mp0) cc_final: 0.6197 (mt-10) REVERT: B 145 TYR cc_start: 0.8203 (p90) cc_final: 0.7804 (p90) REVERT: B 181 THR cc_start: 0.7668 (p) cc_final: 0.7363 (m) REVERT: B 239 ASN cc_start: 0.8174 (m-40) cc_final: 0.7734 (m-40) REVERT: B 298 ASP cc_start: 0.8490 (t0) cc_final: 0.8180 (t70) REVERT: B 322 ASP cc_start: 0.6580 (m-30) cc_final: 0.6260 (m-30) REVERT: B 325 MET cc_start: 0.6986 (tpp) cc_final: 0.6674 (tpp) REVERT: N 7 SER cc_start: 0.6765 (t) cc_final: 0.6380 (p) REVERT: N 34 MET cc_start: 0.8043 (mmm) cc_final: 0.7826 (mmm) REVERT: N 46 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: N 91 THR cc_start: 0.7871 (t) cc_final: 0.7342 (m) REVERT: N 105 ARG cc_start: 0.6157 (mmt-90) cc_final: 0.5779 (mtp180) REVERT: N 117 TYR cc_start: 0.7575 (m-80) cc_final: 0.6850 (m-80) REVERT: R 331 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7345 (tp) REVERT: R 405 LYS cc_start: 0.6901 (tptt) cc_final: 0.6592 (tptp) REVERT: R 458 ILE cc_start: 0.6362 (mt) cc_final: 0.5942 (mp) REVERT: R 474 TRP cc_start: 0.5748 (t60) cc_final: 0.4251 (t-100) outliers start: 16 outliers final: 9 residues processed: 173 average time/residue: 0.2875 time to fit residues: 66.3972 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 0.0070 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN B 88 ASN B 176 GLN B 313 ASN R 295 ASN R 448 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121600 restraints weight = 12266.903| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.14 r_work: 0.3390 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8688 Z= 0.335 Angle : 0.629 6.673 11799 Z= 0.340 Chirality : 0.046 0.265 1345 Planarity : 0.005 0.044 1511 Dihedral : 4.934 43.331 1208 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.76 % Allowed : 16.45 % Favored : 79.79 % 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: 0.16 (0.26), residues: 1095 helix: 1.27 (0.25), residues: 431 sheet: -0.30 (0.36), residues: 213 loop : -0.77 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.006 0.002 HIS P 9 PHE 0.022 0.002 PHE A 212 TYR 0.023 0.002 TYR R 297 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: A 337 ARG cc_start: 0.7565 (tmt-80) cc_final: 0.7006 (ttm110) REVERT: B 44 GLN cc_start: 0.6504 (pm20) cc_final: 0.6036 (pm20) REVERT: B 130 GLU cc_start: 0.6722 (mp0) cc_final: 0.6232 (mt-10) REVERT: B 336 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7953 (tt) REVERT: N 7 SER cc_start: 0.6798 (t) cc_final: 0.6410 (p) REVERT: N 34 MET cc_start: 0.7923 (mmm) cc_final: 0.7717 (mmm) REVERT: N 105 ARG cc_start: 0.6256 (mmt-90) cc_final: 0.5796 (mtp180) REVERT: N 117 TYR cc_start: 0.7661 (m-80) cc_final: 0.6961 (m-80) REVERT: R 302 GLU cc_start: 0.7447 (tt0) cc_final: 0.7180 (tt0) REVERT: R 331 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7290 (tp) REVERT: R 348 ASN cc_start: 0.5987 (t0) cc_final: 0.5386 (t0) REVERT: R 405 LYS cc_start: 0.6801 (tptt) cc_final: 0.6506 (tptp) REVERT: R 441 MET cc_start: 0.7259 (tpp) cc_final: 0.6929 (tpp) REVERT: R 446 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7472 (tt) REVERT: R 458 ILE cc_start: 0.6404 (mt) cc_final: 0.6049 (mp) REVERT: R 467 GLN cc_start: 0.6262 (mt0) cc_final: 0.5971 (mt0) REVERT: R 474 TRP cc_start: 0.5864 (t60) cc_final: 0.4306 (t-100) outliers start: 32 outliers final: 22 residues processed: 163 average time/residue: 0.2267 time to fit residues: 49.8412 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 102 optimal weight: 0.0060 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 261 ASN B 313 ASN R 420 HIS R 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125173 restraints weight = 12179.306| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.15 r_work: 0.3445 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8688 Z= 0.163 Angle : 0.495 5.168 11799 Z= 0.270 Chirality : 0.042 0.251 1345 Planarity : 0.004 0.044 1511 Dihedral : 4.427 40.522 1208 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.35 % Allowed : 18.45 % Favored : 79.20 % 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: 0.53 (0.26), residues: 1095 helix: 1.71 (0.25), residues: 431 sheet: -0.12 (0.37), residues: 218 loop : -0.71 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.014 0.001 TYR R 191 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.897 Fit side-chains REVERT: A 24 LYS cc_start: 0.7078 (tmmt) cc_final: 0.6636 (tmmt) REVERT: A 209 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: A 337 ARG cc_start: 0.7346 (tmt-80) cc_final: 0.6881 (ttm110) REVERT: B 17 GLN cc_start: 0.6367 (tm-30) cc_final: 0.6103 (tm-30) REVERT: B 44 GLN cc_start: 0.6486 (pm20) cc_final: 0.6035 (pm20) REVERT: B 130 GLU cc_start: 0.6733 (mp0) cc_final: 0.6222 (mt-10) REVERT: B 181 THR cc_start: 0.7452 (p) cc_final: 0.7153 (m) REVERT: G 21 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.4887 (ttm) REVERT: N 7 SER cc_start: 0.6911 (t) cc_final: 0.6591 (p) REVERT: N 91 THR cc_start: 0.7816 (t) cc_final: 0.7203 (m) REVERT: N 105 ARG cc_start: 0.6281 (mmt-90) cc_final: 0.5774 (mtp180) REVERT: N 117 TYR cc_start: 0.7727 (m-80) cc_final: 0.7014 (m-80) REVERT: R 189 MET cc_start: 0.4915 (tpp) cc_final: 0.4650 (tmm) REVERT: R 231 MET cc_start: 0.5891 (mmt) cc_final: 0.5568 (mmt) REVERT: R 302 GLU cc_start: 0.7343 (tt0) cc_final: 0.7093 (tt0) REVERT: R 331 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7366 (tt) REVERT: R 360 LYS cc_start: 0.5732 (mmtt) cc_final: 0.5438 (mmtp) REVERT: R 441 MET cc_start: 0.7330 (tpp) cc_final: 0.6860 (tpp) REVERT: R 446 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7386 (tt) REVERT: R 458 ILE cc_start: 0.6373 (mt) cc_final: 0.5996 (mp) REVERT: R 467 GLN cc_start: 0.6325 (mt0) cc_final: 0.5982 (mt0) REVERT: R 469 GLU cc_start: 0.3958 (mm-30) cc_final: 0.3668 (mm-30) REVERT: R 472 LYS cc_start: 0.5120 (mtmt) cc_final: 0.4230 (mtpt) REVERT: R 474 TRP cc_start: 0.5765 (t60) cc_final: 0.4475 (t-100) outliers start: 20 outliers final: 11 residues processed: 163 average time/residue: 0.2370 time to fit residues: 51.3252 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 0.0970 chunk 86 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 313 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.152203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123417 restraints weight = 12284.857| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.14 r_work: 0.3422 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8688 Z= 0.254 Angle : 0.551 6.908 11799 Z= 0.298 Chirality : 0.043 0.250 1345 Planarity : 0.004 0.045 1511 Dihedral : 4.652 47.863 1208 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.76 % Allowed : 19.51 % Favored : 76.73 % 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: 0.36 (0.26), residues: 1095 helix: 1.58 (0.25), residues: 433 sheet: -0.16 (0.37), residues: 209 loop : -0.84 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 298 HIS 0.005 0.001 HIS A 220 PHE 0.031 0.002 PHE R 315 TYR 0.015 0.002 TYR R 191 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7227 (tmmt) cc_final: 0.6775 (tmmt) REVERT: A 209 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: A 337 ARG cc_start: 0.7400 (tmt-80) cc_final: 0.6933 (ttm110) REVERT: B 87 THR cc_start: 0.7754 (m) cc_final: 0.7120 (p) REVERT: B 130 GLU cc_start: 0.6742 (mp0) cc_final: 0.6224 (mt-10) REVERT: B 181 THR cc_start: 0.7446 (p) cc_final: 0.7143 (m) REVERT: B 252 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 336 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7950 (tt) REVERT: N 7 SER cc_start: 0.6509 (t) cc_final: 0.6244 (p) REVERT: N 106 ASP cc_start: 0.6479 (p0) cc_final: 0.6220 (p0) REVERT: R 184 PHE cc_start: 0.5623 (m-10) cc_final: 0.4265 (m-80) REVERT: R 231 MET cc_start: 0.5863 (mmt) cc_final: 0.5590 (mmt) REVERT: R 302 GLU cc_start: 0.7409 (tt0) cc_final: 0.7140 (tt0) REVERT: R 331 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7348 (tt) REVERT: R 348 ASN cc_start: 0.5815 (t0) cc_final: 0.5457 (t0) REVERT: R 405 LYS cc_start: 0.6843 (tptt) cc_final: 0.6606 (tptt) REVERT: R 441 MET cc_start: 0.7341 (tpp) cc_final: 0.6961 (tpp) REVERT: R 446 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7439 (tt) REVERT: R 458 ILE cc_start: 0.6373 (mt) cc_final: 0.5984 (mp) REVERT: R 467 GLN cc_start: 0.6346 (mt0) cc_final: 0.6014 (mt0) REVERT: R 469 GLU cc_start: 0.3936 (mm-30) cc_final: 0.3689 (mm-30) REVERT: R 472 LYS cc_start: 0.4794 (mtmt) cc_final: 0.3868 (mtpt) REVERT: R 474 TRP cc_start: 0.5906 (t60) cc_final: 0.4488 (t-100) outliers start: 32 outliers final: 21 residues processed: 160 average time/residue: 0.2364 time to fit residues: 50.2419 Evaluate side-chains 161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 14 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 31 ASN R 420 HIS R 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123120 restraints weight = 12281.468| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.16 r_work: 0.3417 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8688 Z= 0.284 Angle : 0.574 6.508 11799 Z= 0.309 Chirality : 0.044 0.253 1345 Planarity : 0.004 0.045 1511 Dihedral : 4.798 52.634 1208 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.35 % Allowed : 20.33 % Favored : 75.32 % 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: 0.16 (0.26), residues: 1095 helix: 1.46 (0.25), residues: 433 sheet: -0.22 (0.37), residues: 203 loop : -1.03 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 298 HIS 0.005 0.002 HIS B 225 PHE 0.023 0.002 PHE R 315 TYR 0.016 0.002 TYR R 191 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7191 (tmmt) cc_final: 0.6740 (tmmt) REVERT: A 209 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6805 (pm20) REVERT: A 337 ARG cc_start: 0.7443 (tmt-80) cc_final: 0.6957 (ttm110) REVERT: B 87 THR cc_start: 0.7769 (m) cc_final: 0.7147 (p) REVERT: B 130 GLU cc_start: 0.6846 (mp0) cc_final: 0.6312 (mt-10) REVERT: B 181 THR cc_start: 0.7457 (p) cc_final: 0.7148 (m) REVERT: B 192 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8035 (mt) REVERT: B 219 ARG cc_start: 0.7127 (ptp-110) cc_final: 0.6408 (ptp-110) REVERT: B 336 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7939 (tt) REVERT: N 7 SER cc_start: 0.6564 (t) cc_final: 0.6339 (p) REVERT: R 184 PHE cc_start: 0.5594 (m-10) cc_final: 0.4258 (m-80) REVERT: R 189 MET cc_start: 0.4909 (tpp) cc_final: 0.4663 (ptt) REVERT: R 231 MET cc_start: 0.5840 (mmt) cc_final: 0.5595 (mmt) REVERT: R 302 GLU cc_start: 0.7412 (tt0) cc_final: 0.7112 (tt0) REVERT: R 331 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7438 (tp) REVERT: R 348 ASN cc_start: 0.5529 (t0) cc_final: 0.5285 (t0) REVERT: R 360 LYS cc_start: 0.5885 (mmtt) cc_final: 0.5486 (mmtp) REVERT: R 405 LYS cc_start: 0.6843 (tptt) cc_final: 0.6611 (tptt) REVERT: R 441 MET cc_start: 0.7365 (tpp) cc_final: 0.6984 (tpp) REVERT: R 443 TYR cc_start: 0.6462 (OUTLIER) cc_final: 0.5951 (t80) REVERT: R 446 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7513 (tt) REVERT: R 458 ILE cc_start: 0.6376 (mt) cc_final: 0.6002 (mp) REVERT: R 467 GLN cc_start: 0.6296 (mt0) cc_final: 0.5987 (mt0) REVERT: R 472 LYS cc_start: 0.4690 (mtmt) cc_final: 0.3923 (mtpt) REVERT: R 474 TRP cc_start: 0.5889 (t60) cc_final: 0.4516 (t-100) outliers start: 37 outliers final: 25 residues processed: 160 average time/residue: 0.3042 time to fit residues: 66.5501 Evaluate side-chains 164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 443 TYR Chi-restraints excluded: chain R residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN R 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124850 restraints weight = 12467.652| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.23 r_work: 0.3410 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8688 Z= 0.251 Angle : 0.553 6.149 11799 Z= 0.299 Chirality : 0.043 0.240 1345 Planarity : 0.004 0.045 1511 Dihedral : 4.766 52.480 1208 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.82 % Allowed : 20.09 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1095 helix: 1.49 (0.25), residues: 433 sheet: -0.20 (0.36), residues: 203 loop : -1.07 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 298 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.002 PHE R 315 TYR 0.015 0.002 TYR R 191 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 1.274 Fit side-chains REVERT: A 24 LYS cc_start: 0.7128 (tmmt) cc_final: 0.6651 (tmmt) REVERT: A 35 GLN cc_start: 0.6493 (mm-40) cc_final: 0.6154 (mm110) REVERT: A 209 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6569 (pm20) REVERT: A 337 ARG cc_start: 0.7240 (tmt-80) cc_final: 0.6891 (ttm110) REVERT: B 87 THR cc_start: 0.7616 (m) cc_final: 0.7011 (p) REVERT: B 181 THR cc_start: 0.7451 (p) cc_final: 0.7135 (m) REVERT: B 192 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8005 (mt) REVERT: B 219 ARG cc_start: 0.6866 (ptp-110) cc_final: 0.6055 (ptp-110) REVERT: B 336 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7841 (tt) REVERT: R 184 PHE cc_start: 0.5441 (m-10) cc_final: 0.4079 (m-80) REVERT: R 189 MET cc_start: 0.4971 (tpp) cc_final: 0.4660 (tmm) REVERT: R 231 MET cc_start: 0.5599 (mmt) cc_final: 0.5330 (mmt) REVERT: R 302 GLU cc_start: 0.7202 (tt0) cc_final: 0.6889 (tt0) REVERT: R 331 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7412 (tt) REVERT: R 348 ASN cc_start: 0.5435 (t0) cc_final: 0.5212 (t0) REVERT: R 405 LYS cc_start: 0.6764 (tptt) cc_final: 0.6516 (tptt) REVERT: R 443 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.5920 (t80) REVERT: R 446 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7466 (tt) REVERT: R 448 ASN cc_start: 0.7603 (m110) cc_final: 0.7248 (m-40) REVERT: R 458 ILE cc_start: 0.6333 (mt) cc_final: 0.5976 (mp) REVERT: R 467 GLN cc_start: 0.5892 (mt0) cc_final: 0.5688 (mt0) REVERT: R 472 LYS cc_start: 0.4856 (mtmt) cc_final: 0.3995 (mtpt) REVERT: R 474 TRP cc_start: 0.5981 (t60) cc_final: 0.4609 (t-100) outliers start: 41 outliers final: 29 residues processed: 166 average time/residue: 0.3040 time to fit residues: 67.3782 Evaluate side-chains 171 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 443 TYR Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 32 GLN R 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.152552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124715 restraints weight = 12374.319| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.23 r_work: 0.3410 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8688 Z= 0.266 Angle : 0.570 7.775 11799 Z= 0.307 Chirality : 0.043 0.222 1345 Planarity : 0.004 0.044 1511 Dihedral : 4.820 52.778 1208 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.58 % Allowed : 20.09 % Favored : 75.32 % 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: 0.07 (0.26), residues: 1095 helix: 1.45 (0.25), residues: 433 sheet: -0.29 (0.36), residues: 205 loop : -1.14 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 298 HIS 0.005 0.002 HIS P 9 PHE 0.018 0.002 PHE R 315 TYR 0.018 0.002 TYR A 348 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7322 (tmmt) cc_final: 0.6878 (tmmt) REVERT: A 209 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: A 337 ARG cc_start: 0.7475 (tmt-80) cc_final: 0.6980 (ttm110) REVERT: B 87 THR cc_start: 0.7726 (m) cc_final: 0.7240 (p) REVERT: B 181 THR cc_start: 0.7467 (p) cc_final: 0.7159 (m) REVERT: B 192 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7989 (mt) REVERT: B 336 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7963 (tt) REVERT: N 109 ASP cc_start: 0.7515 (m-30) cc_final: 0.7300 (m-30) REVERT: R 184 PHE cc_start: 0.5523 (m-10) cc_final: 0.4144 (m-80) REVERT: R 231 MET cc_start: 0.5829 (mmt) cc_final: 0.5601 (mmt) REVERT: R 302 GLU cc_start: 0.7426 (tt0) cc_final: 0.7115 (tt0) REVERT: R 331 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7445 (tp) REVERT: R 348 ASN cc_start: 0.5510 (t0) cc_final: 0.5280 (t0) REVERT: R 405 LYS cc_start: 0.6855 (tptt) cc_final: 0.6619 (tptt) REVERT: R 443 TYR cc_start: 0.6443 (OUTLIER) cc_final: 0.5883 (t80) REVERT: R 446 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7600 (tt) REVERT: R 448 ASN cc_start: 0.7755 (m110) cc_final: 0.7486 (m-40) REVERT: R 458 ILE cc_start: 0.6378 (mt) cc_final: 0.6021 (mp) REVERT: R 467 GLN cc_start: 0.5874 (mt0) cc_final: 0.5646 (mt0) REVERT: R 472 LYS cc_start: 0.4753 (mtmt) cc_final: 0.3877 (mtpt) outliers start: 39 outliers final: 31 residues processed: 168 average time/residue: 0.2195 time to fit residues: 49.5793 Evaluate side-chains 175 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 443 TYR Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 19 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.0470 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN P 16 ASN R 374 ASN R 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.156134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128626 restraints weight = 12155.481| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.20 r_work: 0.3460 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8688 Z= 0.144 Angle : 0.501 7.694 11799 Z= 0.272 Chirality : 0.041 0.191 1345 Planarity : 0.004 0.044 1511 Dihedral : 4.375 48.487 1208 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.23 % Allowed : 23.15 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1095 helix: 1.80 (0.25), residues: 432 sheet: -0.17 (0.36), residues: 204 loop : -1.03 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.016 0.001 TYR R 191 ARG 0.005 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.911 Fit side-chains REVERT: A 24 LYS cc_start: 0.7066 (tmmt) cc_final: 0.6653 (mptt) REVERT: A 35 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6329 (mm110) REVERT: A 209 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6566 (pm20) REVERT: A 337 ARG cc_start: 0.7075 (tmt-80) cc_final: 0.6775 (ttm110) REVERT: B 181 THR cc_start: 0.7397 (p) cc_final: 0.7102 (m) REVERT: B 215 GLU cc_start: 0.6144 (tp30) cc_final: 0.5841 (mm-30) REVERT: G 21 MET cc_start: 0.5518 (ptp) cc_final: 0.5317 (ptm) REVERT: P 1 SER cc_start: 0.6442 (p) cc_final: 0.6081 (t) REVERT: R 184 PHE cc_start: 0.5736 (m-10) cc_final: 0.4282 (m-80) REVERT: R 231 MET cc_start: 0.5810 (mmt) cc_final: 0.5425 (mmp) REVERT: R 302 GLU cc_start: 0.7122 (tt0) cc_final: 0.6828 (tt0) REVERT: R 331 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7387 (tt) REVERT: R 446 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7195 (tt) REVERT: R 448 ASN cc_start: 0.7596 (m110) cc_final: 0.7236 (m-40) REVERT: R 458 ILE cc_start: 0.6309 (mt) cc_final: 0.5859 (mp) REVERT: R 467 GLN cc_start: 0.6072 (mt0) cc_final: 0.5800 (mt0) REVERT: R 474 TRP cc_start: 0.5556 (t60) cc_final: 0.5245 (t60) outliers start: 19 outliers final: 12 residues processed: 146 average time/residue: 0.2306 time to fit residues: 45.7459 Evaluate side-chains 144 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 0.5980 chunk 16 optimal weight: 0.0000 chunk 40 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN P 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129789 restraints weight = 12299.767| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.02 r_work: 0.3473 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8688 Z= 0.148 Angle : 0.490 7.356 11799 Z= 0.265 Chirality : 0.041 0.175 1345 Planarity : 0.004 0.044 1511 Dihedral : 4.218 44.447 1208 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.88 % Allowed : 23.50 % Favored : 74.62 % 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: 0.49 (0.26), residues: 1095 helix: 1.95 (0.25), residues: 432 sheet: -0.31 (0.35), residues: 201 loop : -0.93 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 437 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.001 PHE R 335 TYR 0.014 0.001 TYR R 191 ARG 0.004 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5397.13 seconds wall clock time: 95 minutes 58.53 seconds (5758.53 seconds total)