Starting phenix.real_space_refine on Wed Jul 30 11:07:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lxw_30008/07_2025/6lxw_30008.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lxw_30008/07_2025/6lxw_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_30008/07_2025/6lxw_30008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lxw_30008/07_2025/6lxw_30008.map" model { file = "/net/cci-nas-00/data/ceres_data/6lxw_30008/07_2025/6lxw_30008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lxw_30008/07_2025/6lxw_30008.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.90, per 1000 atoms: 0.64 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.82 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: 4.34 Time building geometry restraints manager: 3.41 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.730 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- 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 : 6.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.004 TRP P 477 HIS 0.011 0.003 HIS P 465 PHE 0.036 0.004 PHE D 374 TYR 0.037 0.005 TYR D 327 ARG 0.018 0.001 ARG J 38 Details of bonding type rmsd hydrogen bonds : bond 0.17453 ( 372) hydrogen bonds : angle 8.27598 ( 1092) SS BOND : bond 0.00907 ( 23) SS BOND : angle 2.45146 ( 46) covalent geometry : bond 0.01462 (12565) covalent geometry : angle 1.26507 (17096) *********************** 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 : 1.406 Fit side-chains revert: symmetry clash REVERT: B 378 ASP cc_start: 0.8011 (m-30) cc_final: 0.7773 (m-30) REVERT: B 392 ARG cc_start: 0.8152 (ptp-170) cc_final: 0.7716 (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: 0.7636 (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: 0.3610 time to fit residues: 96.0253 Evaluate side-chains 160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 131 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 S 193 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.193976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157977 restraints weight = 14317.036| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.17 r_work: 0.3699 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12588 Z= 0.136 Angle : 0.671 11.875 17142 Z= 0.339 Chirality : 0.043 0.174 1962 Planarity : 0.006 0.056 2195 Dihedral : 6.513 38.335 1729 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.27 % Allowed : 17.82 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.19), residues: 1565 helix: -3.62 (0.32), residues: 118 sheet: -1.35 (0.20), residues: 615 loop : -2.81 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 477 HIS 0.004 0.001 HIS P 465 PHE 0.012 0.001 PHE B 279 TYR 0.015 0.001 TYR A 472 ARG 0.003 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 372) hydrogen bonds : angle 5.81201 ( 1092) SS BOND : bond 0.00288 ( 23) SS BOND : angle 1.06794 ( 46) covalent geometry : bond 0.00321 (12565) covalent geometry : angle 0.67009 (17096) *********************** 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 233 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8305 (tt0) cc_final: 0.7941 (tt0) REVERT: B 245 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.6950 (mmm160) REVERT: B 265 THR cc_start: 0.6826 (OUTLIER) cc_final: 0.6474 (p) REVERT: B 392 ARG cc_start: 0.8213 (ptp-170) cc_final: 0.7262 (tpt170) REVERT: C 357 GLU cc_start: 0.7668 (mp0) cc_final: 0.7006 (tt0) REVERT: C 422 GLU cc_start: 0.7773 (pp20) cc_final: 0.6673 (pm20) REVERT: C 423 ASP cc_start: 0.8254 (t0) cc_final: 0.8006 (t0) REVERT: C 433 MET cc_start: 0.8025 (ptm) cc_final: 0.7797 (ptt) REVERT: C 450 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.8058 (ttt90) REVERT: D 428 ASP cc_start: 0.8544 (m-30) cc_final: 0.8294 (m-30) REVERT: J 20 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7494 (ptm160) REVERT: J 29 ASN cc_start: 0.7338 (p0) cc_final: 0.7075 (p0) REVERT: J 38 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8185 (tmm-80) REVERT: J 49 ILE cc_start: 0.8633 (tp) cc_final: 0.8118 (pt) REVERT: J 70 LYS cc_start: 0.8041 (mttp) cc_final: 0.7057 (mmtm) REVERT: J 131 ASP cc_start: 0.8588 (p0) cc_final: 0.8316 (p0) REVERT: P 536 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: S 262 LYS cc_start: 0.7337 (ttpt) cc_final: 0.7122 (ttmt) outliers start: 45 outliers final: 29 residues processed: 223 average time/residue: 0.3278 time to fit residues: 97.2987 Evaluate side-chains 188 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL 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 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 57 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 459 ASN D 249 HIS J 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.194161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158023 restraints weight = 14416.613| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.20 r_work: 0.3694 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12588 Z= 0.148 Angle : 0.651 11.015 17142 Z= 0.326 Chirality : 0.043 0.177 1962 Planarity : 0.005 0.057 2195 Dihedral : 6.078 37.036 1724 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 4.29 % Allowed : 19.56 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.20), residues: 1565 helix: -2.75 (0.39), residues: 119 sheet: -1.06 (0.20), residues: 612 loop : -2.51 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 366 HIS 0.005 0.001 HIS P 465 PHE 0.022 0.001 PHE D 279 TYR 0.013 0.002 TYR D 327 ARG 0.005 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 372) hydrogen bonds : angle 5.38823 ( 1092) SS BOND : bond 0.00398 ( 23) SS BOND : angle 1.09237 ( 46) covalent geometry : bond 0.00362 (12565) covalent geometry : angle 0.64943 (17096) *********************** 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 216 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 157 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: B 265 THR cc_start: 0.6776 (OUTLIER) cc_final: 0.6441 (p) REVERT: B 392 ARG cc_start: 0.8225 (ptp-170) cc_final: 0.7266 (tpt170) REVERT: C 357 GLU cc_start: 0.7664 (mp0) cc_final: 0.7006 (tt0) REVERT: C 358 GLU cc_start: 0.7437 (tt0) cc_final: 0.7206 (tt0) REVERT: C 422 GLU cc_start: 0.7692 (pp20) cc_final: 0.6646 (pm20) REVERT: C 423 ASP cc_start: 0.8243 (t0) cc_final: 0.7977 (t0) REVERT: C 433 MET cc_start: 0.7935 (ptm) cc_final: 0.7691 (ptt) REVERT: J 20 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7447 (ptm160) REVERT: J 29 ASN cc_start: 0.7280 (p0) cc_final: 0.7024 (p0) REVERT: J 38 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8254 (tmm-80) REVERT: J 49 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8028 (pt) REVERT: J 70 LYS cc_start: 0.8064 (mttp) cc_final: 0.7071 (mmtm) REVERT: J 131 ASP cc_start: 0.8666 (p0) cc_final: 0.8390 (p0) REVERT: P 536 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: S 262 LYS cc_start: 0.7351 (ttpt) cc_final: 0.7131 (ttmt) outliers start: 59 outliers final: 36 residues processed: 203 average time/residue: 0.3364 time to fit residues: 93.1000 Evaluate side-chains 186 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 368 THR 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 54 optimal weight: 0.0970 chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 115 optimal weight: 0.0170 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.199141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163523 restraints weight = 14338.150| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.10 r_work: 0.3759 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12588 Z= 0.102 Angle : 0.588 11.589 17142 Z= 0.293 Chirality : 0.041 0.181 1962 Planarity : 0.005 0.055 2195 Dihedral : 5.409 37.669 1724 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.58 % Allowed : 20.44 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1565 helix: -2.04 (0.44), residues: 118 sheet: -0.77 (0.21), residues: 632 loop : -2.22 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 366 HIS 0.004 0.000 HIS P 465 PHE 0.020 0.001 PHE D 279 TYR 0.011 0.001 TYR A 472 ARG 0.008 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.02927 ( 372) hydrogen bonds : angle 4.97224 ( 1092) SS BOND : bond 0.00244 ( 23) SS BOND : angle 0.89820 ( 46) covalent geometry : bond 0.00246 (12565) covalent geometry : angle 0.58682 (17096) *********************** 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 236 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 394 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8285 (mmtm) REVERT: B 245 ARG cc_start: 0.6892 (mmm-85) cc_final: 0.6649 (mmm160) REVERT: B 265 THR cc_start: 0.6823 (OUTLIER) cc_final: 0.6485 (p) REVERT: B 392 ARG cc_start: 0.8106 (ptp-170) cc_final: 0.7087 (tpt90) REVERT: C 357 GLU cc_start: 0.7550 (mp0) cc_final: 0.7049 (mp0) REVERT: C 433 MET cc_start: 0.7936 (ptm) cc_final: 0.7677 (ptt) REVERT: J 20 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7454 (ptm160) REVERT: J 29 ASN cc_start: 0.7224 (p0) cc_final: 0.6961 (p0) REVERT: J 38 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8172 (tmm-80) REVERT: J 49 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.7912 (pt) REVERT: J 70 LYS cc_start: 0.7984 (mttp) cc_final: 0.7047 (mmtm) REVERT: J 131 ASP cc_start: 0.8630 (p0) cc_final: 0.8356 (p0) REVERT: P 471 SER cc_start: 0.8570 (m) cc_final: 0.8162 (m) REVERT: S 262 LYS cc_start: 0.7255 (ttpt) cc_final: 0.7048 (ttmt) outliers start: 63 outliers final: 37 residues processed: 220 average time/residue: 0.2996 time to fit residues: 89.7220 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 : 1.417 ------------------------------------------------------------------------------- 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 423 ASP Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 445 GLN 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 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 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 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 277 VAL 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 378 ASP 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 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 435 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 249 HIS D 362 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.196774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.161534 restraints weight = 14384.809| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.15 r_work: 0.3735 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2311 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= 0.137 Angle : 0.607 10.357 17142 Z= 0.302 Chirality : 0.042 0.170 1962 Planarity : 0.005 0.057 2195 Dihedral : 5.373 38.713 1721 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.02 % Allowed : 21.45 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.21), residues: 1565 helix: -1.75 (0.44), residues: 118 sheet: -0.64 (0.21), residues: 630 loop : -2.12 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 477 HIS 0.004 0.001 HIS P 465 PHE 0.020 0.001 PHE B 279 TYR 0.011 0.001 TYR D 327 ARG 0.005 0.000 ARG P 89 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 372) hydrogen bonds : angle 4.97404 ( 1092) SS BOND : bond 0.00348 ( 23) SS BOND : angle 1.08318 ( 46) covalent geometry : bond 0.00336 (12565) covalent geometry : angle 0.60496 (17096) *********************** 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 225 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 156 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8032 (mp) REVERT: B 245 ARG cc_start: 0.6952 (mmm-85) cc_final: 0.6565 (mmm160) REVERT: B 265 THR cc_start: 0.6821 (OUTLIER) cc_final: 0.6484 (p) REVERT: B 392 ARG cc_start: 0.8148 (ptp-170) cc_final: 0.7218 (tpt90) REVERT: C 357 GLU cc_start: 0.7630 (mp0) cc_final: 0.6963 (tt0) REVERT: C 433 MET cc_start: 0.7947 (ptm) cc_final: 0.7681 (ptt) REVERT: J 20 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7432 (ptm160) REVERT: J 29 ASN cc_start: 0.7220 (p0) cc_final: 0.6976 (p0) REVERT: J 38 ARG cc_start: 0.8559 (tmm160) cc_final: 0.8337 (tmm-80) REVERT: J 70 LYS cc_start: 0.8123 (mttp) cc_final: 0.7278 (mmmt) REVERT: J 131 ASP cc_start: 0.8663 (p0) cc_final: 0.8405 (p0) REVERT: P 536 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7247 (tm-30) outliers start: 69 outliers final: 48 residues processed: 208 average time/residue: 0.2905 time to fit residues: 83.1180 Evaluate side-chains 198 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 322 THR Chi-restraints excluded: chain A residue 361 LEU 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 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 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 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 49 ILE Chi-restraints excluded: chain J residue 58 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.197844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162599 restraints weight = 14479.885| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.17 r_work: 0.3741 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2432 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= 0.120 Angle : 0.597 10.544 17142 Z= 0.296 Chirality : 0.042 0.206 1962 Planarity : 0.004 0.059 2195 Dihedral : 5.291 41.307 1721 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.44 % Allowed : 22.55 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.21), residues: 1565 helix: -1.39 (0.46), residues: 117 sheet: -0.49 (0.21), residues: 617 loop : -1.99 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 366 HIS 0.004 0.000 HIS P 465 PHE 0.019 0.001 PHE D 279 TYR 0.011 0.001 TYR D 327 ARG 0.004 0.000 ARG P 89 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 372) hydrogen bonds : angle 4.86926 ( 1092) SS BOND : bond 0.00262 ( 23) SS BOND : angle 1.03837 ( 46) covalent geometry : bond 0.00295 (12565) covalent geometry : angle 0.59523 (17096) *********************** 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 216 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8038 (mp) REVERT: B 245 ARG cc_start: 0.7117 (mmm-85) cc_final: 0.6613 (mmm160) REVERT: B 265 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6485 (p) REVERT: B 392 ARG cc_start: 0.8152 (ptp-170) cc_final: 0.7220 (tpt90) REVERT: C 357 GLU cc_start: 0.7644 (mp0) cc_final: 0.7018 (tt0) REVERT: C 433 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7694 (ptt) REVERT: J 20 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7468 (ptm160) REVERT: J 29 ASN cc_start: 0.7232 (p0) cc_final: 0.6986 (p0) REVERT: J 38 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8306 (tmm-80) REVERT: J 70 LYS cc_start: 0.8102 (mttp) cc_final: 0.7321 (mmmt) REVERT: J 131 ASP cc_start: 0.8671 (p0) cc_final: 0.8413 (p0) REVERT: P 536 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: S 199 ARG cc_start: 0.7961 (mmt180) cc_final: 0.7509 (mmt180) outliers start: 61 outliers final: 46 residues processed: 200 average time/residue: 0.2806 time to fit residues: 76.8742 Evaluate side-chains 200 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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 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 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 429 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 441 LEU 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 364 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP 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 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 319 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 0.0040 chunk 142 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.198261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.162727 restraints weight = 14378.303| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.08 r_work: 0.3748 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2504 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= 0.122 Angle : 0.592 10.269 17142 Z= 0.294 Chirality : 0.042 0.179 1962 Planarity : 0.004 0.063 2195 Dihedral : 5.224 45.407 1721 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.87 % Allowed : 22.33 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.21), residues: 1565 helix: -1.13 (0.47), residues: 117 sheet: -0.42 (0.21), residues: 621 loop : -1.91 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 366 HIS 0.004 0.000 HIS P 465 PHE 0.020 0.001 PHE D 279 TYR 0.011 0.001 TYR D 327 ARG 0.004 0.000 ARG J 59 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 372) hydrogen bonds : angle 4.79008 ( 1092) SS BOND : bond 0.00304 ( 23) SS BOND : angle 1.03145 ( 46) covalent geometry : bond 0.00298 (12565) covalent geometry : angle 0.59035 (17096) *********************** 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 222 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 155 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 245 ARG cc_start: 0.7114 (mmm-85) cc_final: 0.6544 (mmm160) REVERT: B 265 THR cc_start: 0.6823 (OUTLIER) cc_final: 0.6486 (p) REVERT: B 392 ARG cc_start: 0.8183 (ptp-170) cc_final: 0.7242 (tpt90) REVERT: C 357 GLU cc_start: 0.7669 (mp0) cc_final: 0.7014 (tt0) REVERT: C 433 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7677 (ptt) REVERT: D 357 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: J 20 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7434 (ptm160) REVERT: J 29 ASN cc_start: 0.7231 (p0) cc_final: 0.6988 (p0) REVERT: J 38 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8354 (tmm-80) REVERT: J 70 LYS cc_start: 0.8135 (mttp) cc_final: 0.7165 (mmtm) REVERT: J 131 ASP cc_start: 0.8702 (p0) cc_final: 0.8433 (p0) REVERT: P 536 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: S 199 ARG cc_start: 0.7940 (mmt180) cc_final: 0.7509 (mmt180) outliers start: 67 outliers final: 49 residues processed: 204 average time/residue: 0.2942 time to fit residues: 81.8567 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 : 1.266 ------------------------------------------------------------------------------- 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 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 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 282 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 C residue 448 ILE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 267 THR 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 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 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 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 13 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 67 optimal weight: 0.1980 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.197117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.162286 restraints weight = 14437.587| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.02 r_work: 0.3754 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2582 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= 0.121 Angle : 0.591 10.027 17142 Z= 0.295 Chirality : 0.042 0.180 1962 Planarity : 0.004 0.064 2195 Dihedral : 5.203 49.515 1721 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.58 % Allowed : 22.62 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1565 helix: -1.16 (0.46), residues: 124 sheet: -0.33 (0.21), residues: 618 loop : -1.87 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 366 HIS 0.004 0.000 HIS P 465 PHE 0.019 0.001 PHE D 279 TYR 0.011 0.001 TYR D 327 ARG 0.007 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 372) hydrogen bonds : angle 4.75012 ( 1092) SS BOND : bond 0.00277 ( 23) SS BOND : angle 1.03072 ( 46) covalent geometry : bond 0.00298 (12565) covalent geometry : angle 0.58961 (17096) *********************** 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 215 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 152 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7978 (mp) REVERT: A 464 MET cc_start: 0.8615 (mmm) cc_final: 0.8327 (mmm) REVERT: B 245 ARG cc_start: 0.7111 (mmm-85) cc_final: 0.6535 (mmm160) REVERT: B 392 ARG cc_start: 0.8176 (ptp-170) cc_final: 0.7268 (tpt90) REVERT: C 357 GLU cc_start: 0.7651 (mp0) cc_final: 0.6996 (tt0) REVERT: C 433 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7681 (ptt) REVERT: J 20 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7414 (ptm160) REVERT: J 29 ASN cc_start: 0.7206 (p0) cc_final: 0.6965 (p0) REVERT: J 38 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8338 (tmm-80) REVERT: J 131 ASP cc_start: 0.8700 (p0) cc_final: 0.8420 (p0) REVERT: P 536 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: S 199 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7517 (mmt180) outliers start: 63 outliers final: 52 residues processed: 196 average time/residue: 0.3109 time to fit residues: 83.3552 Evaluate side-chains 202 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 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 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 282 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 C residue 448 ILE 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 378 ASP 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 ASN P 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.194670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.159412 restraints weight = 14425.050| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.12 r_work: 0.3715 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2488 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= 0.163 Angle : 0.626 10.138 17142 Z= 0.312 Chirality : 0.043 0.205 1962 Planarity : 0.005 0.066 2195 Dihedral : 5.381 53.946 1720 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.65 % Allowed : 23.13 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1565 helix: -0.88 (0.47), residues: 119 sheet: -0.33 (0.22), residues: 615 loop : -1.91 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 366 HIS 0.005 0.001 HIS P 465 PHE 0.019 0.001 PHE D 279 TYR 0.012 0.002 TYR D 327 ARG 0.008 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 372) hydrogen bonds : angle 4.85330 ( 1092) SS BOND : bond 0.00336 ( 23) SS BOND : angle 1.19356 ( 46) covalent geometry : bond 0.00403 (12565) covalent geometry : angle 0.62411 (17096) *********************** 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 212 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 464 MET cc_start: 0.8671 (mmm) cc_final: 0.8379 (mmm) REVERT: B 265 THR cc_start: 0.6885 (OUTLIER) cc_final: 0.6550 (p) REVERT: B 308 LEU cc_start: 0.6079 (tt) cc_final: 0.5840 (tt) REVERT: B 392 ARG cc_start: 0.8238 (ptp-170) cc_final: 0.7325 (tpt90) REVERT: C 357 GLU cc_start: 0.7709 (mp0) cc_final: 0.7064 (tt0) REVERT: C 433 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7715 (ptt) REVERT: J 20 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7430 (ptm160) REVERT: J 29 ASN cc_start: 0.7226 (p0) cc_final: 0.6993 (p0) REVERT: J 38 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8474 (ttp-170) REVERT: J 70 LYS cc_start: 0.8135 (mttp) cc_final: 0.7306 (mmmt) REVERT: P 536 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7096 (tm-30) outliers start: 64 outliers final: 54 residues processed: 196 average time/residue: 0.3068 time to fit residues: 82.8872 Evaluate side-chains 206 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 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 282 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 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 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 378 ASP 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.198587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.163478 restraints weight = 14352.756| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.04 r_work: 0.3754 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2690 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= 0.115 Angle : 0.593 9.905 17142 Z= 0.296 Chirality : 0.042 0.180 1962 Planarity : 0.004 0.065 2195 Dihedral : 5.192 56.134 1720 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.22 % Allowed : 23.78 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.21), residues: 1565 helix: -0.88 (0.47), residues: 124 sheet: -0.22 (0.22), residues: 618 loop : -1.81 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 366 HIS 0.004 0.000 HIS D 436 PHE 0.018 0.001 PHE D 279 TYR 0.010 0.001 TYR D 327 ARG 0.007 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 372) hydrogen bonds : angle 4.73142 ( 1092) SS BOND : bond 0.00284 ( 23) SS BOND : angle 1.09700 ( 46) covalent geometry : bond 0.00283 (12565) covalent geometry : angle 0.59123 (17096) ********************** 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 209 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7968 (mp) REVERT: B 265 THR cc_start: 0.6877 (OUTLIER) cc_final: 0.6537 (p) REVERT: B 308 LEU cc_start: 0.6020 (tt) cc_final: 0.5805 (tt) REVERT: B 392 ARG cc_start: 0.8167 (ptp-170) cc_final: 0.7257 (tpt90) REVERT: C 357 GLU cc_start: 0.7646 (mp0) cc_final: 0.7052 (tt0) REVERT: C 433 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7734 (ptt) REVERT: D 377 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7631 (tptt) REVERT: J 20 ARG cc_start: 0.7712 (ttp-170) cc_final: 0.7424 (ptm160) REVERT: J 29 ASN cc_start: 0.7211 (p0) cc_final: 0.6986 (p0) REVERT: J 38 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8324 (tmm-80) REVERT: J 103 TYR cc_start: 0.8942 (m-80) cc_final: 0.8692 (m-80) REVERT: P 262 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: P 536 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: S 262 LYS cc_start: 0.7218 (ttmt) cc_final: 0.6517 (mtmt) outliers start: 58 outliers final: 50 residues processed: 193 average time/residue: 0.3102 time to fit residues: 81.1237 Evaluate side-chains 204 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 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 282 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 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 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 378 ASP 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 99 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.195429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159974 restraints weight = 14424.963| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.14 r_work: 0.3739 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2560 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= 0.169 Angle : 0.635 10.088 17142 Z= 0.316 Chirality : 0.043 0.205 1962 Planarity : 0.005 0.068 2195 Dihedral : 5.419 59.028 1720 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 4.44 % Allowed : 23.64 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.21), residues: 1565 helix: -0.69 (0.48), residues: 119 sheet: -0.26 (0.22), residues: 619 loop : -1.84 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 366 HIS 0.005 0.001 HIS P 465 PHE 0.019 0.001 PHE D 279 TYR 0.012 0.002 TYR D 327 ARG 0.007 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 372) hydrogen bonds : angle 4.84634 ( 1092) SS BOND : bond 0.00355 ( 23) SS BOND : angle 1.23033 ( 46) covalent geometry : bond 0.00416 (12565) covalent geometry : angle 0.63226 (17096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7979.30 seconds wall clock time: 138 minutes 51.11 seconds (8331.11 seconds total)