Starting phenix.real_space_refine on Wed Mar 4 08:46:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lxw_30008/03_2026/6lxw_30008.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lxw_30008/03_2026/6lxw_30008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lxw_30008/03_2026/6lxw_30008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lxw_30008/03_2026/6lxw_30008.map" model { file = "/net/cci-nas-00/data/ceres_data/6lxw_30008/03_2026/6lxw_30008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lxw_30008/03_2026/6lxw_30008.cif" } resolution = 3.27 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= 0.000 sd= 0.002 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 67 5.16 5 C 7740 2.51 5 N 2118 2.21 5 O 2374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s 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: 12299 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1707 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 16, 'TRANS': 208} Chain breaks: 1 Chain: "B" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1660 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 16, 'TRANS': 201} Chain breaks: 1 Chain: "C" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 17, 'TRANS': 203} Chain: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1740 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 17, 'TRANS': 211} Chain: "J" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1016 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Chain: "P" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3988 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 489} Chain breaks: 4 Chain: "S" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 506 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain breaks: 1 Time building chain proxies: 2.49, per 1000 atoms: 0.20 Number of scatterers: 12299 At special positions: 0 Unit cell: (139.932, 102.672, 160.632, 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 67 16.00 O 2374 8.00 N 2118 7.00 C 7740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.01 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS J 68 " distance=2.02 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 323 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 311 " - pdb=" SG CYS P 468 " distance=2.05 Simple disulfide: pdb=" SG CYS D 369 " - pdb=" SG CYS D 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS J 14 " distance=2.02 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.02 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 38 " - pdb=" SG CYS P 46 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 202 " distance=2.03 Simple disulfide: pdb=" SG CYS P 239 " - pdb=" SG CYS P 307 " distance=2.03 Simple disulfide: pdb=" SG CYS P 253 " - pdb=" SG CYS P 261 " distance=2.04 Simple disulfide: pdb=" SG CYS P 353 " - pdb=" SG CYS P 423 " distance=2.03 Simple disulfide: pdb=" SG CYS P 367 " - pdb=" SG CYS P 377 " distance=2.03 Simple disulfide: pdb=" SG CYS P 464 " - pdb=" SG CYS P 526 " distance=2.06 Simple disulfide: pdb=" SG CYS P 478 " - pdb=" SG CYS P 485 " 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: 0.81 Conformation dependent library (CDL) restraints added in 567.9 milliseconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 37 sheets defined 8.6% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.544A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 421 through 427 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.706A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.564A pdb=" N LEU C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.791A pdb=" N ASN C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 311 through 316 removed outlier: 4.565A pdb=" N TRP D 315 " --> pdb=" O CYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.646A pdb=" N LEU D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 427 removed outlier: 3.708A pdb=" N GLY D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 removed outlier: 3.607A pdb=" N LEU J 67 " --> pdb=" O LEU J 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 170 removed outlier: 3.946A pdb=" N THR P 170 " --> pdb=" O PRO P 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 167 through 170' Processing helix chain 'P' and resid 193 through 197 removed outlier: 3.825A pdb=" N ASP P 196 " --> pdb=" O ARG P 193 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA P 197 " --> pdb=" O LEU P 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 193 through 197' Processing helix chain 'P' and resid 467 through 471 Processing helix chain 'S' and resid 184 through 195 removed outlier: 3.533A pdb=" N LYS S 189 " --> pdb=" O GLU S 185 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS S 191 " --> pdb=" O LYS S 187 " (cutoff:3.500A) Processing helix chain 'S' and resid 209 through 220 Processing helix chain 'S' and resid 255 through 268 removed outlier: 3.580A pdb=" N GLU S 259 " --> pdb=" O ALA S 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 249 removed outlier: 3.694A pdb=" N VAL A 304 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 removed outlier: 6.299A pdb=" N TYR A 327 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR A 332 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 297 removed outlier: 3.608A pdb=" N GLY A 300 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.375A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.375A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 461 through 463 removed outlier: 3.687A pdb=" N PHE J 60 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 245 through 249 removed outlier: 5.532A pdb=" N TYR B 302 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 281 Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 352 Processing sheet with id=AB2, first strand: chain 'B' and resid 349 through 352 Processing sheet with id=AB3, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'C' and resid 247 through 249 removed outlier: 3.911A pdb=" N THR C 265 " --> pdb=" O HIS C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AB6, first strand: chain 'C' and resid 348 through 352 Processing sheet with id=AB7, first strand: chain 'C' and resid 348 through 352 removed outlier: 4.671A pdb=" N THR C 410 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB9, first strand: chain 'C' and resid 461 through 463 removed outlier: 6.980A pdb=" N SER C 461 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET D 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 463 " --> pdb=" O MET D 464 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN D 459 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 245 through 248 removed outlier: 4.144A pdb=" N GLY D 270 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR D 302 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 278 through 281 Processing sheet with id=AC3, first strand: chain 'D' and resid 348 through 352 removed outlier: 5.312A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 348 through 352 removed outlier: 5.312A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR D 410 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'J' and resid 74 through 78 Processing sheet with id=AC7, first strand: chain 'J' and resid 110 through 115 Processing sheet with id=AC8, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.601A pdb=" N VAL P 10 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER P 110 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER P 12 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG P 89 " --> pdb=" O GLN P 40 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS P 35 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER P 51 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP P 37 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 17 through 23 Processing sheet with id=AD1, first strand: chain 'P' and resid 121 through 125 removed outlier: 6.634A pdb=" N TYR P 122 " --> pdb=" O GLN P 218 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU P 220 " --> pdb=" O TYR P 122 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL P 124 " --> pdb=" O LEU P 220 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN P 199 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN P 150 " --> pdb=" O GLN P 199 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU P 147 " --> pdb=" O VAL P 158 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL P 158 " --> pdb=" O LEU P 147 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR P 164 " --> pdb=" O ASP P 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 130 through 133 Processing sheet with id=AD3, first strand: chain 'P' and resid 225 through 230 removed outlier: 6.218A pdb=" N GLU P 225 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE P 327 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL P 227 " --> pdb=" O PHE P 327 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASN P 329 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU P 229 " --> pdb=" O ASN P 329 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG P 304 " --> pdb=" O GLN P 255 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS P 250 " --> pdb=" O ASN P 266 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN P 266 " --> pdb=" O LYS P 250 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU P 252 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP P 262 " --> pdb=" O ARG P 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 234 through 239 removed outlier: 3.967A pdb=" N PHE P 290 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 340 through 344 Processing sheet with id=AD6, first strand: chain 'P' and resid 348 through 354 Processing sheet with id=AD7, first strand: chain 'P' and resid 365 through 367 removed outlier: 6.961A pdb=" N TRP P 366 " --> pdb=" O LEU P 380 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 460 through 465 removed outlier: 3.847A pdb=" N LEU P 508 " --> pdb=" O ASP P 503 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 474 through 475 Processing sheet with id=AE1, first strand: chain 'P' and resid 478 through 479 removed outlier: 4.023A pdb=" N GLY P 522 " --> pdb=" O VAL P 542 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL P 542 " --> pdb=" O GLY P 522 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3486 1.33 - 1.46: 3072 1.46 - 1.58: 5931 1.58 - 1.71: 1 1.71 - 1.84: 75 Bond restraints: 12565 Sorted by residual: bond pdb=" C GLN C 402 " pdb=" N GLU C 403 " ideal model delta sigma weight residual 1.331 1.202 0.129 2.07e-02 2.33e+03 3.85e+01 bond pdb=" C ARG P 278 " pdb=" N ILE P 279 " ideal model delta sigma weight residual 1.329 1.262 0.067 1.63e-02 3.76e+03 1.70e+01 bond pdb=" CB VAL P 265 " pdb=" CG2 VAL P 265 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.46e+01 bond pdb=" CB CYS P 367 " pdb=" SG CYS P 367 " ideal model delta sigma weight residual 1.808 1.710 0.098 3.30e-02 9.18e+02 8.80e+00 bond pdb=" CB VAL A 379 " pdb=" CG1 VAL A 379 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.76e+00 ... (remaining 12560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 16456 2.88 - 5.77: 548 5.77 - 8.65: 70 8.65 - 11.54: 17 11.54 - 14.42: 5 Bond angle restraints: 17096 Sorted by residual: angle pdb=" C ALA C 312 " pdb=" N GLU C 313 " pdb=" CA GLU C 313 " ideal model delta sigma weight residual 120.06 125.95 -5.89 1.19e+00 7.06e-01 2.45e+01 angle pdb=" N ASN P 426 " pdb=" CA ASN P 426 " pdb=" C ASN P 426 " ideal model delta sigma weight residual 111.30 104.36 6.94 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C SER J 88 " pdb=" N ASN J 89 " pdb=" CA ASN J 89 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" CA ASP J 131 " pdb=" CB ASP J 131 " pdb=" CG ASP J 131 " ideal model delta sigma weight residual 112.60 117.11 -4.51 1.00e+00 1.00e+00 2.04e+01 angle pdb=" C ALA P 42 " pdb=" N ARG P 43 " pdb=" CA ARG P 43 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 ... (remaining 17091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6630 17.74 - 35.49: 847 35.49 - 53.23: 140 53.23 - 70.97: 20 70.97 - 88.71: 10 Dihedral angle restraints: 7647 sinusoidal: 3053 harmonic: 4594 Sorted by residual: dihedral pdb=" CA ASP A 273 " pdb=" C ASP A 273 " pdb=" N ALA A 274 " pdb=" CA ALA A 274 " ideal model delta harmonic sigma weight residual 180.00 145.12 34.88 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CB CYS P 478 " pdb=" SG CYS P 478 " pdb=" SG CYS P 485 " pdb=" CB CYS P 485 " ideal model delta sinusoidal sigma weight residual 93.00 37.94 55.06 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CB CYS P 367 " pdb=" SG CYS P 367 " pdb=" SG CYS P 377 " pdb=" CB CYS P 377 " ideal model delta sinusoidal sigma weight residual 93.00 144.86 -51.86 1 1.00e+01 1.00e-02 3.67e+01 ... (remaining 7644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1562 0.083 - 0.165: 344 0.165 - 0.248: 42 0.248 - 0.331: 13 0.331 - 0.413: 1 Chirality restraints: 1962 Sorted by residual: chirality pdb=" CB VAL P 265 " pdb=" CA VAL P 265 " pdb=" CG1 VAL P 265 " pdb=" CG2 VAL P 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB VAL J 76 " pdb=" CA VAL J 76 " pdb=" CG1 VAL J 76 " pdb=" CG2 VAL J 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ASP J 131 " pdb=" N ASP J 131 " pdb=" C ASP J 131 " pdb=" CB ASP J 131 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1959 not shown) Planarity restraints: 2195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG P 43 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ARG P 43 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG P 43 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY P 44 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG J 35 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ARG J 35 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG J 35 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN J 36 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 313 " -0.047 5.00e-02 4.00e+02 6.98e-02 7.81e+00 pdb=" N PRO D 314 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 314 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 314 " -0.040 5.00e-02 4.00e+02 ... (remaining 2192 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2554 2.77 - 3.30: 10058 3.30 - 3.84: 19264 3.84 - 4.37: 22109 4.37 - 4.90: 40596 Nonbonded interactions: 94581 Sorted by model distance: nonbonded pdb=" O SER P 52 " pdb=" OG SER P 52 " model vdw 2.241 3.040 nonbonded pdb=" O GLU P 400 " pdb=" OG1 THR P 407 " model vdw 2.248 3.040 nonbonded pdb=" OG SER A 431 " pdb=" OG1 THR A 447 " model vdw 2.266 3.040 nonbonded pdb=" O THR S 208 " pdb=" OG1 THR S 208 " model vdw 2.277 3.040 nonbonded pdb=" O GLU S 259 " pdb=" OG1 THR S 263 " model vdw 2.283 3.040 ... (remaining 94576 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 244 through 452 or resid 462)) selection = (chain 'B' and (resid 244 through 452 or resid 462)) selection = (chain 'C' and (resid 244 through 452 or resid 458)) selection = (chain 'D' and (resid 244 through 452 or resid 462)) } 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.000 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 0.129 12588 Z= 0.600 Angle : 1.270 14.423 17142 Z= 0.663 Chirality : 0.070 0.413 1962 Planarity : 0.009 0.070 2195 Dihedral : 15.581 88.714 4610 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.16 % Favored : 86.71 % Rotamer: Outliers : 1.82 % Allowed : 16.15 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.21 (0.18), residues: 1565 helix: -4.71 (0.19), residues: 122 sheet: -1.88 (0.20), residues: 615 loop : -3.28 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 38 TYR 0.037 0.005 TYR D 327 PHE 0.036 0.004 PHE D 374 TRP 0.031 0.004 TRP P 477 HIS 0.011 0.003 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.01462 (12565) covalent geometry : angle 1.26507 (17096) SS BOND : bond 0.00907 ( 23) SS BOND : angle 2.45146 ( 46) hydrogen bonds : bond 0.17453 ( 372) hydrogen bonds : angle 8.27598 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 378 ASP cc_start: 0.8011 (m-30) cc_final: 0.7777 (m-30) REVERT: B 392 ARG cc_start: 0.8152 (ptp-170) cc_final: 0.7718 (tpt90) REVERT: C 357 GLU cc_start: 0.7445 (mp0) cc_final: 0.6939 (mp0) REVERT: D 428 ASP cc_start: 0.8150 (m-30) cc_final: 0.7897 (m-30) REVERT: J 5 ILE cc_start: 0.8237 (pt) cc_final: 0.8025 (pt) REVERT: J 20 ARG cc_start: 0.7442 (ttp-170) cc_final: 0.7235 (ptm160) REVERT: J 70 LYS cc_start: 0.8137 (mttp) cc_final: 0.7637 (mmtm) REVERT: P 416 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7069 (mpp-170) outliers start: 25 outliers final: 17 residues processed: 201 average time/residue: 0.1605 time to fit residues: 42.2495 Evaluate side-chains 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN B 459 ASN D 249 HIS D 317 HIS J 36 ASN J 89 ASN P 32 HIS P 356 ASN P 481 ASN P 530 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.192934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156812 restraints weight = 14453.767| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.18 r_work: 0.3686 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12588 Z= 0.153 Angle : 0.682 11.931 17142 Z= 0.344 Chirality : 0.043 0.175 1962 Planarity : 0.006 0.057 2195 Dihedral : 6.620 38.502 1729 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.42 % Allowed : 18.04 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -3.43 (0.19), residues: 1565 helix: -3.63 (0.32), residues: 118 sheet: -1.39 (0.20), residues: 616 loop : -2.82 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.015 0.002 TYR A 472 PHE 0.012 0.001 PHE D 374 TRP 0.016 0.002 TRP P 477 HIS 0.004 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00369 (12565) covalent geometry : angle 0.68074 (17096) SS BOND : bond 0.00448 ( 23) SS BOND : angle 1.09162 ( 46) hydrogen bonds : bond 0.03669 ( 372) hydrogen bonds : angle 5.85102 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 265 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6487 (p) REVERT: B 392 ARG cc_start: 0.8251 (ptp-170) cc_final: 0.7308 (tpt170) REVERT: B 459 ASN cc_start: 0.7824 (t0) cc_final: 0.7478 (t0) REVERT: C 357 GLU cc_start: 0.7682 (mp0) cc_final: 0.7029 (tt0) REVERT: C 422 GLU cc_start: 0.7766 (pp20) cc_final: 0.6686 (pm20) REVERT: C 423 ASP cc_start: 0.8250 (t0) cc_final: 0.8026 (t0) REVERT: C 433 MET cc_start: 0.8043 (ptm) cc_final: 0.7811 (ptt) REVERT: D 428 ASP cc_start: 0.8569 (m-30) cc_final: 0.8324 (m-30) REVERT: J 20 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7450 (ptm160) REVERT: J 29 ASN cc_start: 0.7347 (p0) cc_final: 0.7103 (p0) REVERT: J 38 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8211 (tmm-80) REVERT: J 49 ILE cc_start: 0.8646 (tp) cc_final: 0.8112 (pt) REVERT: J 70 LYS cc_start: 0.8063 (mttp) cc_final: 0.7081 (mmtm) REVERT: J 131 ASP cc_start: 0.8562 (p0) cc_final: 0.8296 (p0) REVERT: P 536 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7010 (tm-30) outliers start: 47 outliers final: 31 residues processed: 217 average time/residue: 0.1438 time to fit residues: 41.7526 Evaluate side-chains 187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN J 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.195405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.160066 restraints weight = 14638.743| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.25 r_work: 0.3705 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12588 Z= 0.128 Angle : 0.633 10.899 17142 Z= 0.317 Chirality : 0.042 0.177 1962 Planarity : 0.005 0.058 2195 Dihedral : 5.953 37.379 1725 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.15 % Allowed : 19.42 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -2.85 (0.20), residues: 1565 helix: -2.73 (0.39), residues: 118 sheet: -1.04 (0.20), residues: 623 loop : -2.49 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 418 TYR 0.013 0.001 TYR P 164 PHE 0.022 0.001 PHE D 279 TRP 0.020 0.001 TRP P 366 HIS 0.004 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00310 (12565) covalent geometry : angle 0.63152 (17096) SS BOND : bond 0.00313 ( 23) SS BOND : angle 1.12941 ( 46) hydrogen bonds : bond 0.03293 ( 372) hydrogen bonds : angle 5.31055 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: B 245 ARG cc_start: 0.6793 (mmm-85) cc_final: 0.6548 (mmm160) REVERT: B 265 THR cc_start: 0.6836 (OUTLIER) cc_final: 0.6483 (p) REVERT: B 392 ARG cc_start: 0.8195 (ptp-170) cc_final: 0.7183 (tpt90) REVERT: C 357 GLU cc_start: 0.7641 (mp0) cc_final: 0.6969 (tt0) REVERT: C 422 GLU cc_start: 0.7707 (pp20) cc_final: 0.6661 (pm20) REVERT: C 423 ASP cc_start: 0.8247 (t0) cc_final: 0.7967 (t0) REVERT: C 433 MET cc_start: 0.8002 (ptm) cc_final: 0.7742 (ptt) REVERT: J 20 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7428 (ptm160) REVERT: J 29 ASN cc_start: 0.7298 (p0) cc_final: 0.7005 (p0) REVERT: J 38 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8233 (tmm-80) REVERT: J 49 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8023 (pt) REVERT: J 70 LYS cc_start: 0.8018 (mttp) cc_final: 0.7018 (mmtm) REVERT: J 131 ASP cc_start: 0.8629 (p0) cc_final: 0.8340 (p0) REVERT: P 536 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: S 262 LYS cc_start: 0.7106 (ttmt) cc_final: 0.6775 (ttmm) outliers start: 57 outliers final: 37 residues processed: 212 average time/residue: 0.1319 time to fit residues: 38.2891 Evaluate side-chains 191 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 445 GLN D 362 ASN P 316 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.195208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159121 restraints weight = 14466.444| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.17 r_work: 0.3709 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12588 Z= 0.138 Angle : 0.623 11.575 17142 Z= 0.311 Chirality : 0.042 0.172 1962 Planarity : 0.005 0.057 2195 Dihedral : 5.757 40.459 1724 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.53 % Allowed : 19.78 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -2.49 (0.20), residues: 1565 helix: -2.14 (0.43), residues: 118 sheet: -0.84 (0.21), residues: 632 loop : -2.27 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 418 TYR 0.013 0.001 TYR P 164 PHE 0.019 0.001 PHE D 279 TRP 0.011 0.001 TRP P 366 HIS 0.004 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00338 (12565) covalent geometry : angle 0.62094 (17096) SS BOND : bond 0.00308 ( 23) SS BOND : angle 1.06677 ( 46) hydrogen bonds : bond 0.03165 ( 372) hydrogen bonds : angle 5.12162 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 155 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8035 (mp) REVERT: B 245 ARG cc_start: 0.6771 (mmm-85) cc_final: 0.6516 (mmm160) REVERT: B 265 THR cc_start: 0.6795 (OUTLIER) cc_final: 0.6456 (p) REVERT: B 392 ARG cc_start: 0.8238 (ptp-170) cc_final: 0.7271 (tpt170) REVERT: C 357 GLU cc_start: 0.7646 (mp0) cc_final: 0.6955 (tt0) REVERT: C 358 GLU cc_start: 0.7406 (tt0) cc_final: 0.7174 (tt0) REVERT: C 433 MET cc_start: 0.7948 (ptm) cc_final: 0.7709 (ptt) REVERT: C 443 PHE cc_start: 0.7626 (m-80) cc_final: 0.7393 (m-80) REVERT: J 20 ARG cc_start: 0.7827 (ttp-170) cc_final: 0.7464 (ptm160) REVERT: J 29 ASN cc_start: 0.7236 (p0) cc_final: 0.6977 (p0) REVERT: J 38 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8320 (tmm-80) REVERT: J 70 LYS cc_start: 0.7971 (mttp) cc_final: 0.7035 (mmtm) REVERT: J 131 ASP cc_start: 0.8726 (p0) cc_final: 0.8439 (p0) REVERT: P 536 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: S 199 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7460 (mmt180) outliers start: 76 outliers final: 51 residues processed: 212 average time/residue: 0.1296 time to fit residues: 37.5114 Evaluate side-chains 200 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.192670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156584 restraints weight = 14450.262| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.15 r_work: 0.3674 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12588 Z= 0.192 Angle : 0.654 11.244 17142 Z= 0.327 Chirality : 0.044 0.175 1962 Planarity : 0.005 0.058 2195 Dihedral : 5.927 45.510 1724 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.67 % Allowed : 21.09 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -2.40 (0.20), residues: 1565 helix: -1.94 (0.44), residues: 119 sheet: -0.78 (0.21), residues: 628 loop : -2.23 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 59 TYR 0.014 0.002 TYR P 164 PHE 0.019 0.001 PHE D 279 TRP 0.029 0.002 TRP P 366 HIS 0.005 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00472 (12565) covalent geometry : angle 0.65233 (17096) SS BOND : bond 0.00359 ( 23) SS BOND : angle 1.17888 ( 46) hydrogen bonds : bond 0.03328 ( 372) hydrogen bonds : angle 5.19913 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 146 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8043 (mp) REVERT: B 265 THR cc_start: 0.6804 (OUTLIER) cc_final: 0.6475 (p) REVERT: B 392 ARG cc_start: 0.8284 (ptp-170) cc_final: 0.7289 (tpt90) REVERT: C 357 GLU cc_start: 0.7692 (mp0) cc_final: 0.7030 (tt0) REVERT: C 433 MET cc_start: 0.8016 (ptm) cc_final: 0.7767 (ptt) REVERT: J 20 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7474 (ptm160) REVERT: J 29 ASN cc_start: 0.7238 (p0) cc_final: 0.6998 (p0) REVERT: J 38 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8441 (ttp-170) REVERT: J 70 LYS cc_start: 0.8100 (mttp) cc_final: 0.7152 (mmtm) REVERT: J 131 ASP cc_start: 0.8767 (p0) cc_final: 0.8438 (p0) REVERT: P 536 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: S 199 ARG cc_start: 0.8017 (mmt180) cc_final: 0.7467 (mmt180) outliers start: 78 outliers final: 58 residues processed: 206 average time/residue: 0.1269 time to fit residues: 36.0135 Evaluate side-chains 202 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 426 ASN Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 258 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 119 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.192916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157140 restraints weight = 14580.733| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.24 r_work: 0.3674 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12588 Z= 0.182 Angle : 0.652 10.915 17142 Z= 0.325 Chirality : 0.044 0.207 1962 Planarity : 0.005 0.060 2195 Dihedral : 5.970 50.104 1724 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 5.38 % Allowed : 22.76 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -2.28 (0.21), residues: 1565 helix: -1.75 (0.44), residues: 119 sheet: -0.70 (0.21), residues: 622 loop : -2.16 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 89 TYR 0.013 0.002 TYR P 164 PHE 0.018 0.001 PHE D 279 TRP 0.020 0.002 TRP P 366 HIS 0.005 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00447 (12565) covalent geometry : angle 0.64970 (17096) SS BOND : bond 0.00366 ( 23) SS BOND : angle 1.22604 ( 46) hydrogen bonds : bond 0.03255 ( 372) hydrogen bonds : angle 5.15819 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 148 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8063 (mp) REVERT: B 265 THR cc_start: 0.6804 (OUTLIER) cc_final: 0.6478 (p) REVERT: B 392 ARG cc_start: 0.8269 (ptp-170) cc_final: 0.7288 (tpt90) REVERT: C 357 GLU cc_start: 0.7719 (mp0) cc_final: 0.7067 (tt0) REVERT: C 433 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7813 (ptt) REVERT: J 20 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7479 (ptm160) REVERT: J 29 ASN cc_start: 0.7241 (p0) cc_final: 0.7006 (p0) REVERT: J 38 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8476 (ttp-170) REVERT: J 49 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8012 (pt) REVERT: J 70 LYS cc_start: 0.8130 (mttp) cc_final: 0.7163 (mmtm) REVERT: J 131 ASP cc_start: 0.8764 (p0) cc_final: 0.8424 (p0) REVERT: P 536 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7038 (tm-30) outliers start: 74 outliers final: 55 residues processed: 203 average time/residue: 0.1185 time to fit residues: 33.4142 Evaluate side-chains 201 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 140 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 426 ASN Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS C 350 HIS P 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.195544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159800 restraints weight = 14434.834| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.18 r_work: 0.3705 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12588 Z= 0.132 Angle : 0.608 10.525 17142 Z= 0.303 Chirality : 0.042 0.169 1962 Planarity : 0.005 0.063 2195 Dihedral : 5.652 56.344 1724 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 5.16 % Allowed : 23.35 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -2.08 (0.21), residues: 1565 helix: -1.46 (0.45), residues: 119 sheet: -0.57 (0.21), residues: 622 loop : -2.04 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 418 TYR 0.012 0.001 TYR D 327 PHE 0.020 0.001 PHE D 279 TRP 0.015 0.001 TRP P 366 HIS 0.004 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00324 (12565) covalent geometry : angle 0.60590 (17096) SS BOND : bond 0.00305 ( 23) SS BOND : angle 1.05454 ( 46) hydrogen bonds : bond 0.02990 ( 372) hydrogen bonds : angle 4.98667 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 155 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 245 ARG cc_start: 0.6917 (mmm-85) cc_final: 0.6710 (mmm-85) REVERT: B 265 THR cc_start: 0.6846 (OUTLIER) cc_final: 0.6523 (p) REVERT: B 392 ARG cc_start: 0.8197 (ptp-170) cc_final: 0.7210 (tpt90) REVERT: C 357 GLU cc_start: 0.7678 (mp0) cc_final: 0.7010 (tt0) REVERT: C 433 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7785 (ptt) REVERT: J 20 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7455 (ptm160) REVERT: J 29 ASN cc_start: 0.7239 (p0) cc_final: 0.7029 (p0) REVERT: J 38 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8420 (ttp-170) REVERT: J 70 LYS cc_start: 0.8147 (mttp) cc_final: 0.7348 (mmmt) REVERT: J 131 ASP cc_start: 0.8745 (p0) cc_final: 0.8431 (p0) REVERT: P 262 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: P 536 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7188 (tm-30) REVERT: S 199 ARG cc_start: 0.7917 (mmt180) cc_final: 0.7491 (mmt180) outliers start: 71 outliers final: 53 residues processed: 210 average time/residue: 0.1331 time to fit residues: 38.4126 Evaluate side-chains 207 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 148 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 258 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.0040 chunk 68 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 115 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.199640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164752 restraints weight = 14463.044| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.14 r_work: 0.3770 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12588 Z= 0.103 Angle : 0.579 9.965 17142 Z= 0.289 Chirality : 0.041 0.166 1962 Planarity : 0.004 0.064 2195 Dihedral : 5.247 56.510 1724 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.42 % Allowed : 25.53 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -1.83 (0.21), residues: 1565 helix: -1.08 (0.47), residues: 118 sheet: -0.39 (0.21), residues: 621 loop : -1.92 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 418 TYR 0.011 0.001 TYR P 148 PHE 0.018 0.001 PHE D 279 TRP 0.011 0.001 TRP P 324 HIS 0.003 0.000 HIS D 436 Details of bonding type rmsd covalent geometry : bond 0.00251 (12565) covalent geometry : angle 0.57771 (17096) SS BOND : bond 0.00286 ( 23) SS BOND : angle 0.92341 ( 46) hydrogen bonds : bond 0.02810 ( 372) hydrogen bonds : angle 4.75263 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 245 ARG cc_start: 0.7123 (mmm-85) cc_final: 0.6909 (mmm-85) REVERT: B 265 THR cc_start: 0.6767 (OUTLIER) cc_final: 0.6438 (p) REVERT: B 392 ARG cc_start: 0.8120 (ptp-170) cc_final: 0.7224 (tpt90) REVERT: C 357 GLU cc_start: 0.7612 (mp0) cc_final: 0.7008 (tt0) REVERT: C 433 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7696 (ptt) REVERT: J 20 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7433 (ptm160) REVERT: J 29 ASN cc_start: 0.7205 (p0) cc_final: 0.7002 (p0) REVERT: J 38 ARG cc_start: 0.8522 (tmm160) cc_final: 0.8294 (tmm-80) REVERT: P 262 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7396 (m-30) outliers start: 47 outliers final: 37 residues processed: 200 average time/residue: 0.1338 time to fit residues: 36.3713 Evaluate side-chains 196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 78 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.198507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164364 restraints weight = 14413.831| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.11 r_work: 0.3752 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12588 Z= 0.113 Angle : 0.596 9.622 17142 Z= 0.296 Chirality : 0.042 0.168 1962 Planarity : 0.004 0.064 2195 Dihedral : 5.099 50.851 1721 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.49 % Allowed : 25.75 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -1.68 (0.21), residues: 1565 helix: -0.88 (0.48), residues: 118 sheet: -0.28 (0.21), residues: 621 loop : -1.85 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 336 TYR 0.011 0.001 TYR D 327 PHE 0.017 0.001 PHE D 279 TRP 0.012 0.001 TRP P 386 HIS 0.004 0.000 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00279 (12565) covalent geometry : angle 0.59430 (17096) SS BOND : bond 0.00373 ( 23) SS BOND : angle 1.10351 ( 46) hydrogen bonds : bond 0.02794 ( 372) hydrogen bonds : angle 4.72651 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 245 ARG cc_start: 0.7069 (mmm-85) cc_final: 0.6866 (mmm-85) REVERT: B 265 THR cc_start: 0.6817 (OUTLIER) cc_final: 0.6490 (p) REVERT: B 392 ARG cc_start: 0.8163 (ptp-170) cc_final: 0.7227 (tpt90) REVERT: C 357 GLU cc_start: 0.7629 (mp0) cc_final: 0.6995 (tt0) REVERT: C 433 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7738 (ptt) REVERT: J 20 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7465 (ptm160) REVERT: J 38 ARG cc_start: 0.8591 (tmm160) cc_final: 0.8365 (ttp-170) REVERT: P 262 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: P 536 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7351 (tm-30) outliers start: 48 outliers final: 40 residues processed: 188 average time/residue: 0.1342 time to fit residues: 33.7825 Evaluate side-chains 191 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.195473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.161207 restraints weight = 14531.426| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.08 r_work: 0.3716 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12588 Z= 0.159 Angle : 0.635 9.836 17142 Z= 0.315 Chirality : 0.043 0.196 1962 Planarity : 0.005 0.068 2195 Dihedral : 5.324 41.275 1721 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.93 % Allowed : 25.38 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -1.67 (0.21), residues: 1565 helix: -0.82 (0.48), residues: 118 sheet: -0.26 (0.22), residues: 619 loop : -1.86 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 336 TYR 0.013 0.002 TYR D 327 PHE 0.017 0.001 PHE D 279 TRP 0.012 0.001 TRP A 315 HIS 0.005 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00393 (12565) covalent geometry : angle 0.63238 (17096) SS BOND : bond 0.00356 ( 23) SS BOND : angle 1.24806 ( 46) hydrogen bonds : bond 0.02999 ( 372) hydrogen bonds : angle 4.83838 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 148 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 464 MET cc_start: 0.8665 (mmm) cc_final: 0.8361 (mmm) REVERT: B 265 THR cc_start: 0.6872 (OUTLIER) cc_final: 0.6537 (p) REVERT: B 308 LEU cc_start: 0.6072 (tt) cc_final: 0.5864 (tt) REVERT: B 392 ARG cc_start: 0.8205 (ptp-170) cc_final: 0.7307 (tpt90) REVERT: C 357 GLU cc_start: 0.7725 (mp0) cc_final: 0.7075 (tt0) REVERT: C 433 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7766 (ptt) REVERT: J 20 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7410 (ptm160) REVERT: J 38 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8478 (ttp-170) REVERT: P 262 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: P 536 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7231 (tm-30) outliers start: 54 outliers final: 44 residues processed: 191 average time/residue: 0.1274 time to fit residues: 33.4045 Evaluate side-chains 196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 19 optimal weight: 0.0040 chunk 140 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.197654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162566 restraints weight = 14441.799| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.13 r_work: 0.3749 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12588 Z= 0.120 Angle : 0.602 9.765 17142 Z= 0.300 Chirality : 0.042 0.171 1962 Planarity : 0.004 0.066 2195 Dihedral : 5.082 34.247 1721 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.71 % Allowed : 25.67 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -1.56 (0.21), residues: 1565 helix: -0.87 (0.47), residues: 123 sheet: -0.16 (0.22), residues: 618 loop : -1.79 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 336 TYR 0.011 0.001 TYR D 327 PHE 0.017 0.001 PHE D 279 TRP 0.010 0.001 TRP P 477 HIS 0.004 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00296 (12565) covalent geometry : angle 0.60062 (17096) SS BOND : bond 0.00288 ( 23) SS BOND : angle 1.08063 ( 46) hydrogen bonds : bond 0.02812 ( 372) hydrogen bonds : angle 4.73366 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.92 seconds wall clock time: 59 minutes 37.16 seconds (3577.16 seconds total)