Starting phenix.real_space_refine on Tue Mar 3 19:33:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvk_32142/03_2026/7vvk_32142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvk_32142/03_2026/7vvk_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vvk_32142/03_2026/7vvk_32142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvk_32142/03_2026/7vvk_32142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vvk_32142/03_2026/7vvk_32142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvk_32142/03_2026/7vvk_32142.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU: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, 'ASP:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1} 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: {'ARG:plan': 1, 'HIS:plan': 1, 'PHE%COO: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: {'GLU:plan': 9, 'GLN:plan1': 3, 'PHE:plan': 3, 'HIS:plan': 4, 'ARG:plan': 9, 'TRP:plan': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 238 Time building chain proxies: 1.89, per 1000 atoms: 0.22 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: 0.73 Conformation dependent library (CDL) restraints added in 230.3 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: 0.29 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: 1.26 Time building geometry restraints manager: 0.98 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.730 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.280 ------------------------------------------------------------------------------- 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 8691 Z= 1.062 Angle : 1.750 8.681 11805 Z= 1.275 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.027 0.003 ARG B 283 TYR 0.057 0.010 TYR R 297 PHE 0.048 0.009 PHE A 246 TRP 0.064 0.011 TRP A 271 HIS 0.027 0.006 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.01466 ( 8688) covalent geometry : angle 1.74634 (11799) SS BOND : bond 0.01868 ( 3) SS BOND : angle 4.98727 ( 6) hydrogen bonds : bond 0.23614 ( 408) hydrogen bonds : angle 8.44183 ( 1167) *********************** 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 : 0.315 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: 0.6511 (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: 0.5117 (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: 0.7862 (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: 0.6450 (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 222 ILE cc_start: 0.7601 (mm) cc_final: 0.7137 (mt) REVERT: R 224 MET cc_start: 0.6862 (mmm) cc_final: 0.6342 (ttm) REVERT: R 311 PHE cc_start: 0.7180 (m-80) cc_final: 0.6688 (m-80) REVERT: R 312 MET cc_start: 0.7240 (mmm) cc_final: 0.6856 (mtp) REVERT: R 315 PHE cc_start: 0.3986 (t80) cc_final: 0.3657 (t80) REVERT: R 429 TYR cc_start: 0.3934 (m-10) cc_final: 0.3451 (m-80) REVERT: R 458 ILE cc_start: 0.6587 (mt) cc_final: 0.6215 (mm) REVERT: R 474 TRP cc_start: 0.5888 (t60) cc_final: 0.5644 (t60) outliers start: 4 outliers final: 0 residues processed: 224 average time/residue: 0.1192 time to fit residues: 34.3437 Evaluate side-chains 161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 176 GLN B 313 ASN B 340 ASN N 39 GLN P 29 GLN R 223 HIS ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122602 restraints weight = 12164.060| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.14 r_work: 0.3407 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8691 Z= 0.148 Angle : 0.571 7.372 11805 Z= 0.311 Chirality : 0.044 0.227 1345 Planarity : 0.004 0.036 1511 Dihedral : 4.511 30.396 1208 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.12 % Allowed : 11.16 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1095 helix: 1.15 (0.25), residues: 430 sheet: -0.30 (0.36), residues: 214 loop : -0.45 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 49 TYR 0.018 0.002 TYR R 297 PHE 0.020 0.002 PHE R 335 TRP 0.019 0.002 TRP R 298 HIS 0.006 0.002 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8688) covalent geometry : angle 0.57098 (11799) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.17091 ( 6) hydrogen bonds : bond 0.05167 ( 408) hydrogen bonds : angle 5.21724 ( 1167) *********************** 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 194 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7072 (tmmt) cc_final: 0.6716 (mptt) REVERT: A 337 ARG cc_start: 0.7522 (tmt-80) cc_final: 0.7096 (ttm110) REVERT: A 357 VAL cc_start: 0.7229 (p) cc_final: 0.6687 (t) REVERT: B 44 GLN cc_start: 0.6513 (pm20) cc_final: 0.6071 (pm20) REVERT: B 59 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6083 (m-80) REVERT: B 130 GLU cc_start: 0.6232 (mp0) cc_final: 0.6003 (mt-10) REVERT: B 145 TYR cc_start: 0.8205 (p90) cc_final: 0.7667 (p90) REVERT: B 239 ASN cc_start: 0.7880 (m-40) cc_final: 0.7506 (m-40) REVERT: B 298 ASP cc_start: 0.8508 (t0) cc_final: 0.8291 (t70) REVERT: B 322 ASP cc_start: 0.6640 (m-30) cc_final: 0.6249 (m-30) REVERT: N 34 MET cc_start: 0.8159 (mmm) cc_final: 0.7891 (mmm) REVERT: N 105 ARG cc_start: 0.5996 (mmt-90) cc_final: 0.5727 (mtp180) REVERT: N 117 TYR cc_start: 0.7528 (m-80) cc_final: 0.6862 (m-80) REVERT: R 206 VAL cc_start: 0.6307 (t) cc_final: 0.6038 (t) REVERT: R 405 LYS cc_start: 0.6946 (tptt) cc_final: 0.6672 (tptp) REVERT: R 425 MET cc_start: 0.7464 (tmm) cc_final: 0.7047 (tmm) REVERT: R 458 ILE cc_start: 0.6400 (mt) cc_final: 0.5905 (mp) REVERT: R 474 TRP cc_start: 0.5731 (t60) cc_final: 0.4420 (t-100) outliers start: 18 outliers final: 9 residues processed: 186 average time/residue: 0.1131 time to fit residues: 27.4435 Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL 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 104 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 196 SER 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 28 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 313 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123328 restraints weight = 12029.765| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.12 r_work: 0.3421 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8691 Z= 0.151 Angle : 0.541 5.663 11805 Z= 0.293 Chirality : 0.043 0.164 1345 Planarity : 0.004 0.040 1511 Dihedral : 4.458 31.858 1208 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.59 % Allowed : 15.16 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1095 helix: 1.43 (0.25), residues: 434 sheet: -0.31 (0.36), residues: 217 loop : -0.49 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.017 0.002 TYR R 297 PHE 0.022 0.002 PHE R 315 TRP 0.014 0.002 TRP R 298 HIS 0.006 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8688) covalent geometry : angle 0.54054 (11799) SS BOND : bond 0.00238 ( 3) SS BOND : angle 0.74542 ( 6) hydrogen bonds : bond 0.04363 ( 408) hydrogen bonds : angle 4.84683 ( 1167) *********************** 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 170 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7187 (tmmt) cc_final: 0.6666 (mptt) REVERT: A 337 ARG cc_start: 0.7502 (tmt-80) cc_final: 0.7073 (ttm110) REVERT: B 44 GLN cc_start: 0.6482 (pm20) cc_final: 0.6000 (pm20) REVERT: B 130 GLU cc_start: 0.6600 (mp0) cc_final: 0.6232 (mt-10) REVERT: B 145 TYR cc_start: 0.8190 (p90) cc_final: 0.7794 (p90) REVERT: B 175 GLN cc_start: 0.7197 (pt0) cc_final: 0.6977 (pt0) REVERT: B 181 THR cc_start: 0.7663 (p) cc_final: 0.7363 (m) REVERT: B 215 GLU cc_start: 0.6459 (tp30) cc_final: 0.6032 (mm-30) REVERT: B 239 ASN cc_start: 0.8109 (m-40) cc_final: 0.7608 (m-40) REVERT: B 298 ASP cc_start: 0.8480 (t0) cc_final: 0.8152 (t70) REVERT: B 313 ASN cc_start: 0.7177 (OUTLIER) cc_final: 0.6693 (m-40) REVERT: B 322 ASP cc_start: 0.6718 (m-30) cc_final: 0.6345 (m-30) REVERT: N 7 SER cc_start: 0.6739 (t) cc_final: 0.6348 (p) REVERT: N 34 MET cc_start: 0.8006 (mmm) cc_final: 0.7771 (mmm) REVERT: N 91 THR cc_start: 0.7592 (t) cc_final: 0.7108 (m) REVERT: N 105 ARG cc_start: 0.6085 (mmt-90) cc_final: 0.5752 (mtp180) REVERT: N 117 TYR cc_start: 0.7555 (m-80) cc_final: 0.6822 (m-80) REVERT: R 348 ASN cc_start: 0.5993 (t0) cc_final: 0.5440 (t0) REVERT: R 405 LYS cc_start: 0.6892 (tptt) cc_final: 0.6585 (tptp) REVERT: R 458 ILE cc_start: 0.6375 (mt) cc_final: 0.5956 (mp) REVERT: R 474 TRP cc_start: 0.5754 (t60) cc_final: 0.4359 (t-100) outliers start: 22 outliers final: 14 residues processed: 164 average time/residue: 0.1079 time to fit residues: 23.6707 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 : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR 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 G residue 54 VAL Chi-restraints excluded: chain N residue 51 ILE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 0.0050 chunk 81 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126921 restraints weight = 12327.332| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.22 r_work: 0.3437 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8691 Z= 0.103 Angle : 0.472 6.635 11805 Z= 0.258 Chirality : 0.041 0.242 1345 Planarity : 0.003 0.041 1511 Dihedral : 4.124 29.357 1208 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.23 % Allowed : 16.92 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.26), residues: 1095 helix: 1.79 (0.26), residues: 432 sheet: -0.21 (0.36), residues: 224 loop : -0.54 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 213 TYR 0.013 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.013 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8688) covalent geometry : angle 0.47171 (11799) SS BOND : bond 0.00565 ( 3) SS BOND : angle 0.57538 ( 6) hydrogen bonds : bond 0.03595 ( 408) hydrogen bonds : angle 4.47972 ( 1167) *********************** 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: 19 poor density : 152 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7145 (tmmt) cc_final: 0.6682 (mptt) REVERT: A 209 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: A 337 ARG cc_start: 0.7446 (tmt-80) cc_final: 0.7069 (ttm110) REVERT: B 17 GLN cc_start: 0.6533 (tm-30) cc_final: 0.6244 (tm-30) REVERT: B 44 GLN cc_start: 0.6621 (pm20) cc_final: 0.6184 (pm20) REVERT: B 130 GLU cc_start: 0.6726 (mp0) cc_final: 0.6297 (mt-10) REVERT: B 145 TYR cc_start: 0.8263 (p90) cc_final: 0.7924 (p90) REVERT: B 181 THR cc_start: 0.7626 (p) cc_final: 0.7360 (m) REVERT: B 239 ASN cc_start: 0.8158 (m-40) cc_final: 0.7655 (m-40) REVERT: B 298 ASP cc_start: 0.8468 (t0) cc_final: 0.8124 (t70) REVERT: B 322 ASP cc_start: 0.6618 (m-30) cc_final: 0.6314 (m-30) REVERT: G 21 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.4865 (ttm) REVERT: N 7 SER cc_start: 0.6861 (t) cc_final: 0.6517 (p) REVERT: N 34 MET cc_start: 0.7984 (mmm) cc_final: 0.7776 (mmm) REVERT: N 91 THR cc_start: 0.7525 (t) cc_final: 0.6984 (m) REVERT: N 105 ARG cc_start: 0.6311 (mmt-90) cc_final: 0.5826 (mtp180) REVERT: N 117 TYR cc_start: 0.7563 (m-80) cc_final: 0.6806 (m-80) REVERT: R 331 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7248 (tt) REVERT: R 414 MET cc_start: 0.7581 (mtt) cc_final: 0.7349 (mtp) REVERT: R 458 ILE cc_start: 0.6341 (mt) cc_final: 0.5910 (mp) REVERT: R 467 GLN cc_start: 0.6121 (mt0) cc_final: 0.5898 (mt0) REVERT: R 474 TRP cc_start: 0.5635 (t60) cc_final: 0.5269 (t60) outliers start: 19 outliers final: 12 residues processed: 164 average time/residue: 0.1083 time to fit residues: 23.7660 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 160 SER 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 B residue 334 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 70 ILE 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 331 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 B 340 ASN P 14 HIS ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124640 restraints weight = 12267.565| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.16 r_work: 0.3431 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8691 Z= 0.137 Angle : 0.510 5.188 11805 Z= 0.277 Chirality : 0.043 0.260 1345 Planarity : 0.004 0.042 1511 Dihedral : 4.284 31.959 1208 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.29 % Allowed : 17.16 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1095 helix: 1.72 (0.25), residues: 433 sheet: -0.18 (0.36), residues: 217 loop : -0.69 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 19 TYR 0.017 0.001 TYR R 191 PHE 0.017 0.002 PHE A 212 TRP 0.011 0.001 TRP R 298 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8688) covalent geometry : angle 0.50994 (11799) SS BOND : bond 0.00159 ( 3) SS BOND : angle 0.69836 ( 6) hydrogen bonds : bond 0.03805 ( 408) hydrogen bonds : angle 4.51861 ( 1167) *********************** 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 165 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6955 (tmmt) cc_final: 0.6535 (mptt) REVERT: A 209 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: A 337 ARG cc_start: 0.7315 (tmt-80) cc_final: 0.6919 (ttm110) REVERT: B 17 GLN cc_start: 0.6462 (tm-30) cc_final: 0.6190 (tm-30) REVERT: B 44 GLN cc_start: 0.6546 (pm20) cc_final: 0.6115 (pm20) REVERT: B 130 GLU cc_start: 0.6662 (mp0) cc_final: 0.6202 (mt-10) REVERT: B 145 TYR cc_start: 0.8259 (p90) cc_final: 0.7927 (p90) REVERT: B 181 THR cc_start: 0.7397 (p) cc_final: 0.7130 (m) REVERT: B 217 MET cc_start: 0.7162 (ptt) cc_final: 0.6948 (ptt) REVERT: B 298 ASP cc_start: 0.8470 (t0) cc_final: 0.8126 (t70) REVERT: B 322 ASP cc_start: 0.6733 (m-30) cc_final: 0.6401 (m-30) REVERT: G 21 MET cc_start: 0.5422 (OUTLIER) cc_final: 0.4896 (ttm) REVERT: N 7 SER cc_start: 0.6983 (t) cc_final: 0.6659 (p) REVERT: N 19 ARG cc_start: 0.6782 (ttm-80) cc_final: 0.6575 (ttm-80) REVERT: N 34 MET cc_start: 0.7910 (mmm) cc_final: 0.7702 (mmm) REVERT: N 105 ARG cc_start: 0.6286 (mmt-90) cc_final: 0.5806 (mtp180) REVERT: N 117 TYR cc_start: 0.7665 (m-80) cc_final: 0.7003 (m-80) REVERT: R 231 MET cc_start: 0.5948 (mmt) cc_final: 0.5586 (mmp) REVERT: R 302 GLU cc_start: 0.7359 (tt0) cc_final: 0.7134 (tt0) REVERT: R 331 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7335 (tt) REVERT: R 351 CYS cc_start: 0.4694 (t) cc_final: 0.4486 (t) REVERT: R 360 LYS cc_start: 0.5861 (mmtt) cc_final: 0.5542 (mmtp) REVERT: R 405 LYS cc_start: 0.6822 (tptt) cc_final: 0.6527 (tptp) REVERT: R 446 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7246 (tt) REVERT: R 458 ILE cc_start: 0.6392 (mt) cc_final: 0.6008 (mp) REVERT: R 467 GLN cc_start: 0.6110 (mt0) cc_final: 0.5776 (mt0) REVERT: R 472 LYS cc_start: 0.5185 (mtmt) cc_final: 0.4581 (mtpt) REVERT: R 474 TRP cc_start: 0.5692 (t60) cc_final: 0.4330 (t-100) outliers start: 28 outliers final: 20 residues processed: 155 average time/residue: 0.1109 time to fit residues: 22.8341 Evaluate side-chains 156 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 209 GLU 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 213 VAL 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 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 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 2 VAL 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 399 THR 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 42 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 313 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125925 restraints weight = 12143.887| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.23 r_work: 0.3427 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8691 Z= 0.133 Angle : 0.502 6.863 11805 Z= 0.271 Chirality : 0.042 0.244 1345 Planarity : 0.003 0.042 1511 Dihedral : 4.274 35.865 1208 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.88 % Allowed : 17.16 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1095 helix: 1.78 (0.25), residues: 432 sheet: -0.17 (0.36), residues: 209 loop : -0.75 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.015 0.001 TYR R 191 PHE 0.017 0.001 PHE A 212 TRP 0.011 0.001 TRP R 298 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8688) covalent geometry : angle 0.50178 (11799) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.55224 ( 6) hydrogen bonds : bond 0.03685 ( 408) hydrogen bonds : angle 4.44505 ( 1167) *********************** 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 168 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6912 (tmmt) cc_final: 0.6604 (mptt) REVERT: A 209 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: A 337 ARG cc_start: 0.7362 (tmt-80) cc_final: 0.6911 (ttm110) REVERT: B 17 GLN cc_start: 0.6201 (tm-30) cc_final: 0.5900 (tm-30) REVERT: B 44 GLN cc_start: 0.6500 (pm20) cc_final: 0.6114 (pm20) REVERT: B 130 GLU cc_start: 0.6705 (mp0) cc_final: 0.6221 (mt-10) REVERT: B 145 TYR cc_start: 0.8282 (p90) cc_final: 0.8041 (p90) REVERT: B 181 THR cc_start: 0.7402 (p) cc_final: 0.7141 (m) REVERT: N 7 SER cc_start: 0.6760 (t) cc_final: 0.6471 (p) REVERT: N 105 ARG cc_start: 0.6337 (mmt-90) cc_final: 0.5849 (mtp180) REVERT: N 117 TYR cc_start: 0.7654 (m-80) cc_final: 0.6987 (m-80) REVERT: R 189 MET cc_start: 0.5019 (tpp) cc_final: 0.4688 (ptt) REVERT: R 231 MET cc_start: 0.5814 (mmt) cc_final: 0.5466 (mmp) REVERT: R 302 GLU cc_start: 0.7365 (tt0) cc_final: 0.7138 (tt0) REVERT: R 331 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7299 (tt) REVERT: R 405 LYS cc_start: 0.6822 (tptt) cc_final: 0.6517 (tptp) REVERT: R 446 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7345 (tt) REVERT: R 458 ILE cc_start: 0.6371 (mt) cc_final: 0.5989 (mp) REVERT: R 467 GLN cc_start: 0.6075 (mt0) cc_final: 0.5811 (mt0) REVERT: R 472 LYS cc_start: 0.5328 (mtmt) cc_final: 0.4531 (mtpt) REVERT: R 474 TRP cc_start: 0.5697 (t60) cc_final: 0.4142 (t-100) outliers start: 33 outliers final: 23 residues processed: 157 average time/residue: 0.1129 time to fit residues: 23.4891 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET 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 70 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL 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 G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL 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 P residue 2 VAL 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 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 R 295 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 = 0.3861 r_free = 0.3861 target = 0.151451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122458 restraints weight = 12372.494| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.16 r_work: 0.3408 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8691 Z= 0.216 Angle : 0.618 7.849 11805 Z= 0.329 Chirality : 0.046 0.248 1345 Planarity : 0.004 0.044 1511 Dihedral : 4.949 57.354 1208 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.23 % Allowed : 18.33 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1095 helix: 1.35 (0.25), residues: 433 sheet: -0.29 (0.36), residues: 209 loop : -1.02 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 255 TYR 0.016 0.002 TYR R 191 PHE 0.022 0.002 PHE A 212 TRP 0.013 0.002 TRP R 298 HIS 0.006 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 8688) covalent geometry : angle 0.61732 (11799) SS BOND : bond 0.00451 ( 3) SS BOND : angle 1.29190 ( 6) hydrogen bonds : bond 0.04420 ( 408) hydrogen bonds : angle 4.83972 ( 1167) *********************** 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 173 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: A 337 ARG cc_start: 0.7422 (tmt-80) cc_final: 0.6951 (ttm110) REVERT: B 44 GLN cc_start: 0.6476 (pm20) cc_final: 0.6051 (pm20) REVERT: B 130 GLU cc_start: 0.6861 (mp0) cc_final: 0.6335 (mt-10) REVERT: B 145 TYR cc_start: 0.8237 (p90) cc_final: 0.8008 (p90) REVERT: B 181 THR cc_start: 0.7454 (p) cc_final: 0.7150 (m) REVERT: B 219 ARG cc_start: 0.7440 (ptp-110) cc_final: 0.6567 (mtp180) REVERT: B 313 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6870 (m-40) REVERT: N 7 SER cc_start: 0.6516 (t) cc_final: 0.6233 (p) REVERT: N 109 ASP cc_start: 0.7483 (m-30) cc_final: 0.7238 (m-30) REVERT: R 231 MET cc_start: 0.5888 (mmt) cc_final: 0.5577 (mmp) REVERT: R 302 GLU cc_start: 0.7422 (tt0) cc_final: 0.7170 (tt0) REVERT: R 331 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7183 (tt) REVERT: R 348 ASN cc_start: 0.5538 (t0) cc_final: 0.5285 (t0) REVERT: R 360 LYS cc_start: 0.5880 (mmtt) cc_final: 0.5469 (mmtp) REVERT: R 405 LYS cc_start: 0.6808 (tptt) cc_final: 0.6506 (tptp) REVERT: R 446 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7307 (tt) REVERT: R 458 ILE cc_start: 0.6378 (mt) cc_final: 0.6047 (mp) REVERT: R 467 GLN cc_start: 0.6082 (mt0) cc_final: 0.5804 (mt0) REVERT: R 472 LYS cc_start: 0.4700 (mtmt) cc_final: 0.3851 (mtpt) REVERT: R 474 TRP cc_start: 0.5810 (t60) cc_final: 0.4571 (t-100) outliers start: 36 outliers final: 28 residues processed: 162 average time/residue: 0.1091 time to fit residues: 23.4957 Evaluate side-chains 166 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 60 MET 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 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 HIS 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 G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 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 14 HIS 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 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.0040 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN R 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.156038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128910 restraints weight = 12089.184| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.06 r_work: 0.3461 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8691 Z= 0.102 Angle : 0.480 7.118 11805 Z= 0.261 Chirality : 0.041 0.213 1345 Planarity : 0.003 0.042 1511 Dihedral : 4.310 51.068 1208 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.35 % Allowed : 19.98 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1095 helix: 1.88 (0.26), residues: 428 sheet: -0.05 (0.36), residues: 196 loop : -0.97 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 19 TYR 0.014 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.015 0.002 TRP B 297 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 8688) covalent geometry : angle 0.48022 (11799) SS BOND : bond 0.00107 ( 3) SS BOND : angle 0.41263 ( 6) hydrogen bonds : bond 0.03328 ( 408) hydrogen bonds : angle 4.27854 ( 1167) *********************** 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 160 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.332 Fit side-chains REVERT: A 24 LYS cc_start: 0.6885 (tmmt) cc_final: 0.6596 (mptt) REVERT: A 209 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6750 (pm20) REVERT: A 337 ARG cc_start: 0.7284 (tmt-80) cc_final: 0.6854 (ttm110) REVERT: B 17 GLN cc_start: 0.5447 (tm-30) cc_final: 0.5241 (tm-30) REVERT: B 44 GLN cc_start: 0.6456 (pm20) cc_final: 0.6059 (pm20) REVERT: B 130 GLU cc_start: 0.6678 (mp0) cc_final: 0.6156 (mt-10) REVERT: B 181 THR cc_start: 0.7447 (p) cc_final: 0.7162 (m) REVERT: B 233 CYS cc_start: 0.8314 (p) cc_final: 0.7694 (t) REVERT: N 7 SER cc_start: 0.6703 (t) cc_final: 0.6493 (p) REVERT: N 104 THR cc_start: 0.6993 (t) cc_final: 0.6753 (t) REVERT: R 189 MET cc_start: 0.4938 (tpp) cc_final: 0.4608 (ptt) REVERT: R 231 MET cc_start: 0.5862 (mmt) cc_final: 0.5632 (mmp) REVERT: R 302 GLU cc_start: 0.7304 (tt0) cc_final: 0.7082 (tt0) REVERT: R 331 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7223 (tt) REVERT: R 446 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7201 (tt) REVERT: R 458 ILE cc_start: 0.6316 (mt) cc_final: 0.5933 (mp) REVERT: R 467 GLN cc_start: 0.6331 (mt0) cc_final: 0.6077 (mt0) outliers start: 20 outliers final: 13 residues processed: 153 average time/residue: 0.1107 time to fit residues: 22.5734 Evaluate side-chains 147 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 313 ASN P 16 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126829 restraints weight = 12272.057| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.21 r_work: 0.3439 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8691 Z= 0.131 Angle : 0.513 6.704 11805 Z= 0.276 Chirality : 0.042 0.202 1345 Planarity : 0.004 0.043 1511 Dihedral : 4.398 53.879 1208 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.70 % Allowed : 21.03 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1095 helix: 1.91 (0.25), residues: 426 sheet: -0.11 (0.35), residues: 197 loop : -1.02 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 219 TYR 0.015 0.001 TYR R 191 PHE 0.018 0.001 PHE A 212 TRP 0.011 0.002 TRP B 211 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8688) covalent geometry : angle 0.51265 (11799) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.65678 ( 6) hydrogen bonds : bond 0.03531 ( 408) hydrogen bonds : angle 4.33336 ( 1167) *********************** 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 164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.284 Fit side-chains REVERT: A 24 LYS cc_start: 0.6965 (tmmt) cc_final: 0.6653 (mptt) REVERT: A 209 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: A 337 ARG cc_start: 0.7314 (tmt-80) cc_final: 0.6846 (ttm110) REVERT: B 17 GLN cc_start: 0.5342 (tm-30) cc_final: 0.5042 (tm-30) REVERT: B 44 GLN cc_start: 0.6477 (pm20) cc_final: 0.6085 (pm20) REVERT: B 130 GLU cc_start: 0.6685 (mp0) cc_final: 0.6161 (mt-10) REVERT: B 181 THR cc_start: 0.7425 (p) cc_final: 0.7149 (m) REVERT: G 21 MET cc_start: 0.5704 (ptp) cc_final: 0.5486 (ptm) REVERT: R 189 MET cc_start: 0.4927 (tpp) cc_final: 0.4630 (ptt) REVERT: R 302 GLU cc_start: 0.7337 (tt0) cc_final: 0.7090 (tt0) REVERT: R 331 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7285 (tt) REVERT: R 348 ASN cc_start: 0.5916 (t0) cc_final: 0.5495 (t0) REVERT: R 360 LYS cc_start: 0.5309 (mmtt) cc_final: 0.4975 (mmtp) REVERT: R 405 LYS cc_start: 0.6803 (tptt) cc_final: 0.6500 (tptp) REVERT: R 446 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7379 (tt) REVERT: R 458 ILE cc_start: 0.6342 (mt) cc_final: 0.5963 (mp) REVERT: R 467 GLN cc_start: 0.5964 (mt0) cc_final: 0.5737 (mt0) REVERT: R 472 LYS cc_start: 0.4882 (mtmt) cc_final: 0.4022 (mtpt) REVERT: R 474 TRP cc_start: 0.5572 (t60) cc_final: 0.5064 (t60) outliers start: 23 outliers final: 19 residues processed: 155 average time/residue: 0.1140 time to fit residues: 23.4621 Evaluate side-chains 154 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 14 HIS 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 407 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 108 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 50.0000 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 313 ASN P 16 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 = 0.3898 r_free = 0.3898 target = 0.154491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127233 restraints weight = 12156.439| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.17 r_work: 0.3445 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8691 Z= 0.120 Angle : 0.507 6.543 11805 Z= 0.272 Chirality : 0.041 0.191 1345 Planarity : 0.003 0.043 1511 Dihedral : 4.363 54.012 1208 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.47 % Allowed : 21.50 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1095 helix: 1.95 (0.25), residues: 426 sheet: -0.17 (0.35), residues: 198 loop : -1.02 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.015 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.012 0.001 TRP R 298 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8688) covalent geometry : angle 0.50671 (11799) SS BOND : bond 0.00078 ( 3) SS BOND : angle 0.59357 ( 6) hydrogen bonds : bond 0.03445 ( 408) hydrogen bonds : angle 4.29185 ( 1167) ********************** 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 156 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.359 Fit side-chains REVERT: A 24 LYS cc_start: 0.6932 (tmmt) cc_final: 0.6630 (mptt) REVERT: A 209 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: A 337 ARG cc_start: 0.7297 (tmt-80) cc_final: 0.6847 (ttm110) REVERT: B 17 GLN cc_start: 0.5297 (tm-30) cc_final: 0.5000 (tm-30) REVERT: B 44 GLN cc_start: 0.6479 (pm20) cc_final: 0.6076 (pm20) REVERT: B 130 GLU cc_start: 0.6783 (mp0) cc_final: 0.6212 (mt-10) REVERT: B 181 THR cc_start: 0.7420 (p) cc_final: 0.7145 (m) REVERT: G 21 MET cc_start: 0.5700 (ptp) cc_final: 0.5488 (ptm) REVERT: P 19 GLU cc_start: 0.4978 (tm-30) cc_final: 0.4670 (tm-30) REVERT: R 189 MET cc_start: 0.4912 (tpp) cc_final: 0.4694 (ptt) REVERT: R 302 GLU cc_start: 0.7344 (tt0) cc_final: 0.7099 (tt0) REVERT: R 331 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7307 (tt) REVERT: R 348 ASN cc_start: 0.5917 (t0) cc_final: 0.5487 (t0) REVERT: R 360 LYS cc_start: 0.5386 (mmtt) cc_final: 0.5071 (mmtp) REVERT: R 405 LYS cc_start: 0.6792 (tptt) cc_final: 0.6483 (tptp) REVERT: R 446 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7280 (tt) REVERT: R 458 ILE cc_start: 0.6341 (mt) cc_final: 0.5944 (mp) REVERT: R 467 GLN cc_start: 0.5804 (mt0) cc_final: 0.5532 (mt0) REVERT: R 472 LYS cc_start: 0.4910 (mtmt) cc_final: 0.4041 (mtpt) REVERT: R 474 TRP cc_start: 0.5548 (t60) cc_final: 0.5034 (t60) outliers start: 21 outliers final: 17 residues processed: 148 average time/residue: 0.1101 time to fit residues: 21.6654 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 14 HIS 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 407 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 0 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125867 restraints weight = 12186.548| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.14 r_work: 0.3423 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8691 Z= 0.164 Angle : 0.561 6.789 11805 Z= 0.299 Chirality : 0.043 0.194 1345 Planarity : 0.004 0.043 1511 Dihedral : 4.621 55.753 1208 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.94 % Allowed : 21.27 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1095 helix: 1.77 (0.25), residues: 427 sheet: -0.29 (0.35), residues: 200 loop : -1.09 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.016 0.002 TYR A 348 PHE 0.020 0.002 PHE A 212 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.002 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8688) covalent geometry : angle 0.56073 (11799) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.74655 ( 6) hydrogen bonds : bond 0.03791 ( 408) hydrogen bonds : angle 4.47742 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.71 seconds wall clock time: 46 minutes 1.51 seconds (2761.51 seconds total)