Starting phenix.real_space_refine on Wed Mar 4 06:16:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lx3_30004/03_2026/6lx3_30004.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lx3_30004/03_2026/6lx3_30004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lx3_30004/03_2026/6lx3_30004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lx3_30004/03_2026/6lx3_30004.map" model { file = "/net/cci-nas-00/data/ceres_data/6lx3_30004/03_2026/6lx3_30004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lx3_30004/03_2026/6lx3_30004.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 62 5.16 5 C 7264 2.51 5 N 1981 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11503 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain breaks: 3 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1570 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 15, 'TRANS': 190} Chain breaks: 3 Chain: "C" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1613 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 17, 'TRANS': 191} Chain breaks: 4 Chain: "D" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1697 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 17, 'TRANS': 205} Chain breaks: 1 Chain: "J" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Chain: "P" Number of atoms: 3964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3964 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 485} Chain breaks: 5 Time building chain proxies: 2.79, per 1000 atoms: 0.24 Number of scatterers: 11503 At special positions: 0 Unit cell: (148.212, 104.328, 158.976, 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 62 16.00 O 2196 8.00 N 1981 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS J 68 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 323 " distance=2.03 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 369 " - pdb=" SG CYS D 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS P 38 " - pdb=" SG CYS P 46 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS P 478 " - pdb=" SG CYS P 485 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 624.6 milliseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 36 sheets defined 9.1% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.797A pdb=" N LEU A 361 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 362 " --> pdb=" O LEU A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 362' Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.517A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.722A pdb=" N TRP B 315 " --> pdb=" O CYS B 311 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 311 through 316' Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.663A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.828A pdb=" N LYS C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 Processing helix chain 'D' and resid 311 through 318 removed outlier: 4.205A pdb=" N TRP D 315 " --> pdb=" O CYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 421 through 427 removed outlier: 3.571A pdb=" N GLY D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.741A pdb=" N SER P 87 " --> pdb=" O GLN P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 197 removed outlier: 3.508A pdb=" N ALA P 197 " --> pdb=" O LEU P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 removed outlier: 3.778A pdb=" N VAL P 245 " --> pdb=" O GLY P 242 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA P 246 " --> pdb=" O PRO P 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 242 through 246' Processing helix chain 'P' and resid 414 through 418 removed outlier: 3.842A pdb=" N ASP P 417 " --> pdb=" O THR P 414 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA P 418 " --> pdb=" O SER P 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 414 through 418' Processing helix chain 'P' and resid 467 through 471 removed outlier: 3.561A pdb=" N PHE P 470 " --> pdb=" O PRO P 467 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER P 471 " --> pdb=" O CYS P 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 467 through 471' Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.284A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 396 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.284A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA6, first strand: chain 'A' and resid 463 through 465 removed outlier: 6.798A pdb=" N VAL A 463 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.707A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.707A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 246 through 249 removed outlier: 3.735A pdb=" N THR C 265 " --> pdb=" O HIS C 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AB5, first strand: chain 'C' and resid 348 through 352 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 388 through 389 Processing sheet with id=AB8, first strand: chain 'C' and resid 457 through 458 removed outlier: 5.793A pdb=" N HIS C 457 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 460 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS D 457 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE J 37 " --> pdb=" O HIS D 457 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 459 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 461 through 463 removed outlier: 7.273A pdb=" N VAL J 41 " --> pdb=" O SER D 461 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 463 " --> pdb=" O VAL J 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 245 through 248 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: 5.346A 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: 5.346A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (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: 6.652A pdb=" N VAL P 10 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER P 110 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER P 12 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG P 89 " --> pdb=" O GLN P 40 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS P 35 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER P 51 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP P 37 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 18 through 23 Processing sheet with id=AD1, first strand: chain 'P' and resid 121 through 125 removed outlier: 6.627A pdb=" N TYR P 122 " --> pdb=" O GLN P 218 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU P 220 " --> pdb=" O TYR P 122 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL P 124 " --> pdb=" O LEU P 220 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN P 199 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN P 150 " --> pdb=" O GLN P 199 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 129 through 133 Processing sheet with id=AD3, first strand: chain 'P' and resid 225 through 230 removed outlier: 6.168A pdb=" N GLU P 225 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE P 327 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL P 227 " --> pdb=" O PHE P 327 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASN P 329 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU P 229 " --> pdb=" O ASN P 329 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG P 304 " --> pdb=" O GLN P 255 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU P 252 " --> pdb=" O VAL P 265 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL P 265 " --> pdb=" O LEU P 252 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 235 through 240 removed outlier: 3.940A 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 removed outlier: 6.527A pdb=" N VAL P 341 " --> pdb=" O LYS P 438 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE P 440 " --> pdb=" O VAL P 341 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY P 343 " --> pdb=" O ILE P 440 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR P 433 " --> pdb=" O CYS P 423 " (cutoff:3.500A) 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 366 removed outlier: 3.637A pdb=" N VAL P 381 " --> pdb=" O TRP P 366 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 460 through 462 Processing sheet with id=AD9, first strand: chain 'P' and resid 486 through 487 removed outlier: 4.000A pdb=" N GLN P 486 " --> pdb=" O LYS P 479 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS P 479 " --> pdb=" O GLN P 486 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU P 536 " --> pdb=" O VAL P 528 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN P 530 " --> pdb=" O TYR P 534 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR P 534 " --> pdb=" O GLN P 530 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.26 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: 3331 1.33 - 1.46: 2961 1.46 - 1.59: 5392 1.59 - 1.71: 0 1.71 - 1.84: 71 Bond restraints: 11755 Sorted by residual: bond pdb=" C ARG P 278 " pdb=" N ILE P 279 " ideal model delta sigma weight residual 1.327 1.293 0.034 9.50e-03 1.11e+04 1.25e+01 bond pdb=" C PHE B 345 " pdb=" N ARG B 346 " ideal model delta sigma weight residual 1.327 1.267 0.060 1.71e-02 3.42e+03 1.23e+01 bond pdb=" CB THR P 33 " pdb=" CG2 THR P 33 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.02e+01 bond pdb=" CG LEU A 367 " pdb=" CD2 LEU A 367 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CD LYS P 35 " pdb=" CE LYS P 35 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.72e+00 ... (remaining 11750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 15263 2.55 - 5.10: 627 5.10 - 7.66: 88 7.66 - 10.21: 13 10.21 - 12.76: 7 Bond angle restraints: 15998 Sorted by residual: angle pdb=" C LEU J 78 " pdb=" N ASP J 79 " pdb=" CA ASP J 79 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" N VAL P 158 " pdb=" CA VAL P 158 " pdb=" C VAL P 158 " ideal model delta sigma weight residual 111.62 107.63 3.99 7.90e-01 1.60e+00 2.55e+01 angle pdb=" C SER J 88 " pdb=" N ASN J 89 " pdb=" CA ASN J 89 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" CA ASP J 131 " pdb=" CB ASP J 131 " pdb=" CG ASP J 131 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" C CYS P 92 " pdb=" N GLY P 93 " pdb=" CA GLY P 93 " ideal model delta sigma weight residual 121.15 113.62 7.53 1.80e+00 3.09e-01 1.75e+01 ... (remaining 15993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6208 17.89 - 35.77: 744 35.77 - 53.66: 139 53.66 - 71.54: 26 71.54 - 89.43: 11 Dihedral angle restraints: 7128 sinusoidal: 2843 harmonic: 4285 Sorted by residual: dihedral pdb=" CB CYS P 253 " pdb=" SG CYS P 253 " pdb=" SG CYS P 261 " pdb=" CB CYS P 261 " ideal model delta sinusoidal sigma weight residual 93.00 12.34 80.66 1 1.00e+01 1.00e-02 8.04e+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 93.00 169.80 -76.80 1 1.00e+01 1.00e-02 7.41e+01 dihedral pdb=" CB CYS P 38 " pdb=" SG CYS P 38 " pdb=" SG CYS P 46 " pdb=" CB CYS P 46 " ideal model delta sinusoidal sigma weight residual 93.00 25.03 67.97 1 1.00e+01 1.00e-02 6.00e+01 ... (remaining 7125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1442 0.077 - 0.154: 337 0.154 - 0.230: 50 0.230 - 0.307: 13 0.307 - 0.384: 2 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CB VAL P 245 " pdb=" CA VAL P 245 " pdb=" CG1 VAL P 245 " pdb=" CG2 VAL P 245 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL P 76 " pdb=" CA VAL P 76 " pdb=" CG1 VAL P 76 " pdb=" CG2 VAL P 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 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 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1841 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 472 " 0.027 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR A 472 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 472 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 472 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 472 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 472 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 472 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 472 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 282 " 0.051 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 283 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " -0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO C 283 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.046 5.00e-02 4.00e+02 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2872 2.79 - 3.32: 8927 3.32 - 3.85: 18193 3.85 - 4.37: 20751 4.37 - 4.90: 38206 Nonbonded interactions: 88949 Sorted by model distance: nonbonded pdb=" O SER P 195 " pdb=" OG SER P 195 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU C 403 " pdb=" OG1 THR C 410 " model vdw 2.267 3.040 nonbonded pdb=" O THR P 429 " pdb=" OG1 THR P 429 " model vdw 2.268 3.040 nonbonded pdb=" O SER J 50 " pdb=" OG SER J 50 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR D 282 " pdb=" OG1 THR D 322 " model vdw 2.308 3.040 ... (remaining 88944 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 281 or resid 287 through 294 or resid 303 thro \ ugh 405 or resid 408 through 452 or resid 462)) selection = (chain 'B' and (resid 244 through 270 or resid 278 through 281 or resid 287 thro \ ugh 405 or resid 408 through 452 or resid 462)) selection = (chain 'C' and (resid 244 through 270 or resid 278 through 281 or resid 287 thro \ ugh 294 or resid 303 through 452 or resid 458)) selection = (chain 'D' and (resid 244 through 270 or resid 278 through 281 or resid 287 thro \ ugh 294 or resid 303 through 405 or resid 408 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.016 0.119 11777 Z= 0.626 Angle : 1.205 12.762 16042 Z= 0.634 Chirality : 0.069 0.384 1844 Planarity : 0.009 0.076 2043 Dihedral : 15.566 89.429 4286 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 1.40 % Allowed : 15.62 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.19), residues: 1444 helix: -4.54 (0.17), residues: 108 sheet: -1.45 (0.20), residues: 598 loop : -3.08 (0.18), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 57 TYR 0.058 0.004 TYR A 472 PHE 0.027 0.004 PHE D 374 TRP 0.041 0.004 TRP P 431 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd covalent geometry : bond 0.01555 (11755) covalent geometry : angle 1.20127 (15998) SS BOND : bond 0.00750 ( 22) SS BOND : angle 2.23735 ( 44) hydrogen bonds : bond 0.15886 ( 350) hydrogen bonds : angle 7.68735 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7489 (tpt90) REVERT: A 425 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7933 (mmtt) REVERT: B 433 MET cc_start: 0.7603 (ttm) cc_final: 0.7340 (ttp) REVERT: C 423 ASP cc_start: 0.8594 (t70) cc_final: 0.8162 (t0) REVERT: C 426 LYS cc_start: 0.8776 (pttt) cc_final: 0.8480 (pttp) REVERT: C 428 ASP cc_start: 0.8080 (m-30) cc_final: 0.7765 (m-30) REVERT: D 423 ASP cc_start: 0.8426 (t0) cc_final: 0.8171 (t0) REVERT: J 44 ASN cc_start: 0.8583 (t0) cc_final: 0.8171 (t0) REVERT: J 51 ASP cc_start: 0.8731 (t70) cc_final: 0.8505 (t0) REVERT: J 59 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.8111 (ttt90) REVERT: J 107 LYS cc_start: 0.8681 (tttm) cc_final: 0.8351 (ttmm) REVERT: P 173 ILE cc_start: 0.7701 (tt) cc_final: 0.7434 (tt) REVERT: P 191 GLN cc_start: 0.7555 (mt0) cc_final: 0.7090 (pt0) outliers start: 18 outliers final: 13 residues processed: 184 average time/residue: 0.1357 time to fit residues: 32.7796 Evaluate side-chains 161 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 516 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN C 362 ASN ** C 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 457 HIS J 45 ASN ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 GLN ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 412 GLN P 530 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.178285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138347 restraints weight = 13082.867| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.52 r_work: 0.3305 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11777 Z= 0.151 Angle : 0.651 11.981 16042 Z= 0.328 Chirality : 0.042 0.164 1844 Planarity : 0.006 0.054 2043 Dihedral : 6.363 41.062 1605 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.87 % Allowed : 18.34 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.20), residues: 1444 helix: -3.38 (0.29), residues: 111 sheet: -0.95 (0.20), residues: 600 loop : -2.52 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 336 TYR 0.010 0.001 TYR A 395 PHE 0.015 0.001 PHE P 406 TRP 0.014 0.001 TRP P 431 HIS 0.002 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00367 (11755) covalent geometry : angle 0.64987 (15998) SS BOND : bond 0.00355 ( 22) SS BOND : angle 0.95091 ( 44) hydrogen bonds : bond 0.03739 ( 350) hydrogen bonds : angle 5.45831 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8913 (tt0) cc_final: 0.8696 (tt0) REVERT: A 392 ARG cc_start: 0.8602 (ttp-170) cc_final: 0.7439 (tpt90) REVERT: A 425 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7879 (mmtt) REVERT: B 433 MET cc_start: 0.8176 (ttm) cc_final: 0.7904 (ttp) REVERT: C 423 ASP cc_start: 0.8733 (t70) cc_final: 0.8132 (t0) REVERT: C 426 LYS cc_start: 0.8641 (pttt) cc_final: 0.8187 (pttp) REVERT: C 428 ASP cc_start: 0.8352 (m-30) cc_final: 0.7807 (m-30) REVERT: D 362 ASN cc_start: 0.7577 (t0) cc_final: 0.7314 (t0) REVERT: D 423 ASP cc_start: 0.8440 (t0) cc_final: 0.8185 (t0) REVERT: J 44 ASN cc_start: 0.8796 (t0) cc_final: 0.8496 (t0) REVERT: J 51 ASP cc_start: 0.8671 (t70) cc_final: 0.8379 (t0) REVERT: J 59 ARG cc_start: 0.8650 (mtp-110) cc_final: 0.8370 (ttt90) REVERT: J 107 LYS cc_start: 0.8764 (tttm) cc_final: 0.8265 (ttmm) REVERT: P 72 ASN cc_start: 0.7079 (m-40) cc_final: 0.6839 (m-40) REVERT: P 199 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: P 359 GLU cc_start: 0.7157 (pp20) cc_final: 0.6110 (pp20) REVERT: P 366 TRP cc_start: 0.9325 (OUTLIER) cc_final: 0.8785 (t60) REVERT: P 367 CYS cc_start: 0.6926 (t) cc_final: 0.6581 (t) REVERT: P 376 ARG cc_start: 0.7379 (mtt90) cc_final: 0.7148 (mmp-170) outliers start: 37 outliers final: 22 residues processed: 195 average time/residue: 0.1211 time to fit residues: 32.0188 Evaluate side-chains 169 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 199 GLN Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 109 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN ** C 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 GLN ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.177994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138336 restraints weight = 13175.426| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.59 r_work: 0.3282 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11777 Z= 0.161 Angle : 0.628 11.341 16042 Z= 0.313 Chirality : 0.042 0.154 1844 Planarity : 0.005 0.046 2043 Dihedral : 5.928 41.842 1599 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.57 % Allowed : 19.35 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.21), residues: 1444 helix: -2.41 (0.38), residues: 112 sheet: -0.67 (0.21), residues: 598 loop : -2.21 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 336 TYR 0.011 0.001 TYR P 148 PHE 0.014 0.001 PHE P 406 TRP 0.015 0.001 TRP P 431 HIS 0.002 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00401 (11755) covalent geometry : angle 0.62660 (15998) SS BOND : bond 0.00377 ( 22) SS BOND : angle 1.05774 ( 44) hydrogen bonds : bond 0.03505 ( 350) hydrogen bonds : angle 5.07841 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8916 (tt0) cc_final: 0.8694 (tt0) REVERT: A 392 ARG cc_start: 0.8616 (ttp-170) cc_final: 0.7438 (tpt90) REVERT: A 425 LYS cc_start: 0.8185 (mmtm) cc_final: 0.7900 (mmtt) REVERT: C 423 ASP cc_start: 0.8681 (t70) cc_final: 0.8039 (t0) REVERT: C 426 LYS cc_start: 0.8614 (pttt) cc_final: 0.8096 (pttp) REVERT: C 428 ASP cc_start: 0.8378 (m-30) cc_final: 0.7662 (m-30) REVERT: D 423 ASP cc_start: 0.8426 (t0) cc_final: 0.8060 (t0) REVERT: J 44 ASN cc_start: 0.8793 (t0) cc_final: 0.8509 (t0) REVERT: J 51 ASP cc_start: 0.8763 (t70) cc_final: 0.8500 (t0) REVERT: J 59 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.8406 (ttt90) REVERT: J 107 LYS cc_start: 0.8788 (tttm) cc_final: 0.8258 (ttmm) REVERT: P 40 GLN cc_start: 0.8281 (tp40) cc_final: 0.7991 (tt0) REVERT: P 72 ASN cc_start: 0.7038 (m-40) cc_final: 0.6802 (m-40) REVERT: P 108 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6486 (mm-30) REVERT: P 359 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6233 (pp20) REVERT: P 366 TRP cc_start: 0.9313 (OUTLIER) cc_final: 0.8648 (t60) REVERT: P 376 ARG cc_start: 0.7349 (mtt90) cc_final: 0.7089 (mmp-170) REVERT: P 536 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7159 (tm-30) outliers start: 46 outliers final: 33 residues processed: 198 average time/residue: 0.1166 time to fit residues: 31.6157 Evaluate side-chains 182 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 359 GLU Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 452 VAL Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 81 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 0.0170 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.179841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139926 restraints weight = 13070.100| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.59 r_work: 0.3305 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11777 Z= 0.131 Angle : 0.595 11.798 16042 Z= 0.295 Chirality : 0.041 0.154 1844 Planarity : 0.005 0.045 2043 Dihedral : 5.573 41.343 1597 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.34 % Allowed : 20.98 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.21), residues: 1444 helix: -1.93 (0.42), residues: 112 sheet: -0.39 (0.21), residues: 594 loop : -2.01 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 401 TYR 0.009 0.001 TYR A 395 PHE 0.016 0.001 PHE B 443 TRP 0.013 0.001 TRP P 431 HIS 0.002 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00328 (11755) covalent geometry : angle 0.59312 (15998) SS BOND : bond 0.00314 ( 22) SS BOND : angle 1.12047 ( 44) hydrogen bonds : bond 0.03206 ( 350) hydrogen bonds : angle 4.75411 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8917 (tt0) cc_final: 0.8692 (tt0) REVERT: A 392 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.7441 (tpt90) REVERT: A 425 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7897 (mmtt) REVERT: B 458 VAL cc_start: 0.7770 (t) cc_final: 0.7399 (p) REVERT: C 423 ASP cc_start: 0.8656 (t70) cc_final: 0.8054 (t0) REVERT: C 426 LYS cc_start: 0.8544 (pttt) cc_final: 0.8050 (pttp) REVERT: C 428 ASP cc_start: 0.8345 (m-30) cc_final: 0.7587 (m-30) REVERT: D 423 ASP cc_start: 0.8329 (t0) cc_final: 0.8044 (t0) REVERT: J 44 ASN cc_start: 0.8877 (t0) cc_final: 0.8515 (t0) REVERT: J 51 ASP cc_start: 0.8787 (t70) cc_final: 0.8503 (t0) REVERT: J 59 ARG cc_start: 0.8635 (mtp-110) cc_final: 0.8407 (ttt90) REVERT: J 107 LYS cc_start: 0.8841 (tttm) cc_final: 0.8292 (ttmm) REVERT: P 72 ASN cc_start: 0.7007 (m-40) cc_final: 0.6772 (m-40) REVERT: P 108 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6559 (mm-30) REVERT: P 359 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6294 (pp20) REVERT: P 366 TRP cc_start: 0.9315 (OUTLIER) cc_final: 0.8700 (t60) REVERT: P 367 CYS cc_start: 0.7015 (t) cc_final: 0.6683 (t) REVERT: P 376 ARG cc_start: 0.7251 (mtt90) cc_final: 0.6998 (mmp-170) REVERT: P 536 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7161 (tm-30) outliers start: 43 outliers final: 28 residues processed: 189 average time/residue: 0.1237 time to fit residues: 31.7555 Evaluate side-chains 180 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 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 C residue 313 GLU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 359 GLU Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 132 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 191 GLN ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.176885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136857 restraints weight = 13045.716| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.58 r_work: 0.3235 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11777 Z= 0.214 Angle : 0.652 11.405 16042 Z= 0.323 Chirality : 0.043 0.152 1844 Planarity : 0.005 0.047 2043 Dihedral : 5.734 42.376 1596 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.04 % Allowed : 21.06 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.22), residues: 1444 helix: -1.72 (0.44), residues: 112 sheet: -0.36 (0.21), residues: 597 loop : -1.90 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 57 TYR 0.011 0.002 TYR D 395 PHE 0.019 0.002 PHE B 443 TRP 0.016 0.001 TRP P 431 HIS 0.004 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00535 (11755) covalent geometry : angle 0.65004 (15998) SS BOND : bond 0.00358 ( 22) SS BOND : angle 1.22450 ( 44) hydrogen bonds : bond 0.03536 ( 350) hydrogen bonds : angle 4.86335 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8898 (tt0) cc_final: 0.8685 (tt0) REVERT: A 392 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.7416 (tpt90) REVERT: A 425 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7833 (mmtt) REVERT: C 423 ASP cc_start: 0.8595 (t70) cc_final: 0.7916 (t0) REVERT: C 426 LYS cc_start: 0.8586 (pttt) cc_final: 0.8057 (pttp) REVERT: C 428 ASP cc_start: 0.8379 (m-30) cc_final: 0.7627 (m-30) REVERT: D 291 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: D 423 ASP cc_start: 0.8417 (t0) cc_final: 0.8163 (t0) REVERT: J 44 ASN cc_start: 0.8869 (t0) cc_final: 0.8514 (t0) REVERT: J 51 ASP cc_start: 0.8698 (t70) cc_final: 0.8406 (t0) REVERT: J 59 ARG cc_start: 0.8616 (mtp-110) cc_final: 0.8379 (ttt90) REVERT: J 107 LYS cc_start: 0.8842 (tttm) cc_final: 0.8269 (ttmm) REVERT: P 72 ASN cc_start: 0.7012 (m-40) cc_final: 0.6798 (m-40) REVERT: P 108 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6556 (mm-30) REVERT: P 304 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8095 (ttt-90) REVERT: P 359 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6307 (pp20) REVERT: P 366 TRP cc_start: 0.9313 (OUTLIER) cc_final: 0.8763 (t60) REVERT: P 376 ARG cc_start: 0.7345 (mtt90) cc_final: 0.7088 (mmp-170) REVERT: P 536 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7227 (tm-30) outliers start: 52 outliers final: 39 residues processed: 194 average time/residue: 0.1186 time to fit residues: 31.0351 Evaluate side-chains 190 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 247 ASN Chi-restraints excluded: chain P residue 359 GLU Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 443 GLU Chi-restraints excluded: chain P residue 452 VAL Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 516 VAL Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 127 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 191 GLN ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.179478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139558 restraints weight = 13078.000| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.61 r_work: 0.3291 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11777 Z= 0.142 Angle : 0.594 11.771 16042 Z= 0.293 Chirality : 0.041 0.150 1844 Planarity : 0.005 0.045 2043 Dihedral : 5.501 43.004 1596 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.04 % Allowed : 21.83 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1444 helix: -1.49 (0.45), residues: 112 sheet: -0.28 (0.21), residues: 606 loop : -1.77 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 357 TYR 0.009 0.001 TYR A 395 PHE 0.017 0.001 PHE B 443 TRP 0.013 0.001 TRP P 431 HIS 0.002 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00356 (11755) covalent geometry : angle 0.59213 (15998) SS BOND : bond 0.00252 ( 22) SS BOND : angle 0.97310 ( 44) hydrogen bonds : bond 0.03159 ( 350) hydrogen bonds : angle 4.60698 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8916 (tt0) cc_final: 0.8661 (tt0) REVERT: A 392 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.7449 (tpt90) REVERT: A 425 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7887 (mmtt) REVERT: B 458 VAL cc_start: 0.8006 (t) cc_final: 0.7477 (p) REVERT: C 366 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.7963 (p) REVERT: C 423 ASP cc_start: 0.8608 (t70) cc_final: 0.8028 (t0) REVERT: C 426 LYS cc_start: 0.8579 (pttt) cc_final: 0.8051 (pttp) REVERT: C 428 ASP cc_start: 0.8349 (m-30) cc_final: 0.7611 (m-30) REVERT: D 291 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6639 (mp10) REVERT: D 423 ASP cc_start: 0.8344 (t0) cc_final: 0.8010 (t0) REVERT: J 44 ASN cc_start: 0.8860 (t0) cc_final: 0.8522 (t0) REVERT: J 51 ASP cc_start: 0.8718 (t70) cc_final: 0.8450 (t0) REVERT: J 59 ARG cc_start: 0.8642 (mtp-110) cc_final: 0.8415 (ttt90) REVERT: J 107 LYS cc_start: 0.8848 (tttm) cc_final: 0.8331 (ttmm) REVERT: P 108 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6586 (mm-30) REVERT: P 217 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7114 (mp) REVERT: P 265 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8719 (t) REVERT: P 304 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8176 (ttt-90) REVERT: P 359 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6389 (pp20) REVERT: P 366 TRP cc_start: 0.9305 (OUTLIER) cc_final: 0.8721 (t60) REVERT: P 367 CYS cc_start: 0.7022 (t) cc_final: 0.6651 (t) REVERT: P 376 ARG cc_start: 0.7286 (mtt90) cc_final: 0.6978 (mmp-170) REVERT: P 536 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7190 (tm-30) outliers start: 52 outliers final: 38 residues processed: 196 average time/residue: 0.1225 time to fit residues: 32.6488 Evaluate side-chains 191 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 247 ASN Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 359 GLU Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 452 VAL Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 70 optimal weight: 0.0870 chunk 123 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.180513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140385 restraints weight = 13065.360| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.55 r_work: 0.3317 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11777 Z= 0.118 Angle : 0.571 11.610 16042 Z= 0.281 Chirality : 0.041 0.148 1844 Planarity : 0.004 0.044 2043 Dihedral : 5.282 43.380 1596 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.27 % Allowed : 21.45 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.22), residues: 1444 helix: -1.25 (0.46), residues: 112 sheet: -0.07 (0.22), residues: 603 loop : -1.67 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 357 TYR 0.009 0.001 TYR P 148 PHE 0.017 0.001 PHE B 443 TRP 0.012 0.001 TRP P 431 HIS 0.002 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00295 (11755) covalent geometry : angle 0.56983 (15998) SS BOND : bond 0.00263 ( 22) SS BOND : angle 0.87008 ( 44) hydrogen bonds : bond 0.02968 ( 350) hydrogen bonds : angle 4.40646 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8896 (tt0) cc_final: 0.8675 (tt0) REVERT: A 392 ARG cc_start: 0.8580 (ttp-170) cc_final: 0.7441 (tpt90) REVERT: A 425 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7912 (mmtt) REVERT: B 458 VAL cc_start: 0.7969 (t) cc_final: 0.7464 (p) REVERT: C 423 ASP cc_start: 0.8548 (t70) cc_final: 0.7992 (t0) REVERT: C 426 LYS cc_start: 0.8554 (pttt) cc_final: 0.8015 (pttp) REVERT: C 428 ASP cc_start: 0.8336 (m-30) cc_final: 0.7523 (m-30) REVERT: D 423 ASP cc_start: 0.8260 (t0) cc_final: 0.8021 (t0) REVERT: J 44 ASN cc_start: 0.8860 (t0) cc_final: 0.8559 (t0) REVERT: J 59 ARG cc_start: 0.8668 (mtp-110) cc_final: 0.8432 (ttt90) REVERT: J 107 LYS cc_start: 0.8832 (tttm) cc_final: 0.8295 (ttmm) REVERT: P 108 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6622 (mm-30) REVERT: P 217 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7152 (mp) REVERT: P 265 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8699 (t) REVERT: P 304 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8209 (ttt-90) REVERT: P 359 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6448 (pp20) REVERT: P 366 TRP cc_start: 0.9277 (OUTLIER) cc_final: 0.8722 (t60) REVERT: P 367 CYS cc_start: 0.7016 (t) cc_final: 0.6629 (t) REVERT: P 376 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6832 (mmp-170) REVERT: P 443 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: P 536 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7189 (tm-30) outliers start: 55 outliers final: 40 residues processed: 190 average time/residue: 0.1190 time to fit residues: 30.8389 Evaluate side-chains 184 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 247 ASN Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 359 GLU Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 443 GLU Chi-restraints excluded: chain P residue 452 VAL Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142766 restraints weight = 12939.249| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.43 r_work: 0.3247 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11777 Z= 0.114 Angle : 0.571 11.736 16042 Z= 0.280 Chirality : 0.040 0.146 1844 Planarity : 0.004 0.044 2043 Dihedral : 5.207 44.151 1596 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.89 % Allowed : 21.83 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.22), residues: 1444 helix: -1.06 (0.47), residues: 112 sheet: 0.03 (0.22), residues: 601 loop : -1.59 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 357 TYR 0.008 0.001 TYR J 103 PHE 0.017 0.001 PHE B 443 TRP 0.012 0.001 TRP P 366 HIS 0.003 0.001 HIS P 465 Details of bonding type rmsd covalent geometry : bond 0.00286 (11755) covalent geometry : angle 0.57001 (15998) SS BOND : bond 0.00234 ( 22) SS BOND : angle 0.92981 ( 44) hydrogen bonds : bond 0.02914 ( 350) hydrogen bonds : angle 4.32756 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8878 (tt0) cc_final: 0.8644 (tt0) REVERT: A 392 ARG cc_start: 0.8561 (ttp-170) cc_final: 0.7383 (tpt90) REVERT: A 425 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7815 (mmtt) REVERT: B 458 VAL cc_start: 0.7913 (t) cc_final: 0.7384 (p) REVERT: C 423 ASP cc_start: 0.8445 (t70) cc_final: 0.7798 (t0) REVERT: C 426 LYS cc_start: 0.8468 (pttt) cc_final: 0.7887 (pttp) REVERT: C 428 ASP cc_start: 0.8312 (m-30) cc_final: 0.7416 (m-30) REVERT: C 451 LEU cc_start: 0.7979 (mt) cc_final: 0.7667 (pt) REVERT: D 423 ASP cc_start: 0.8161 (t0) cc_final: 0.7874 (t0) REVERT: J 38 ARG cc_start: 0.8296 (ttp-170) cc_final: 0.7954 (ttp-170) REVERT: J 44 ASN cc_start: 0.8812 (t0) cc_final: 0.8501 (t0) REVERT: J 59 ARG cc_start: 0.8628 (mtp-110) cc_final: 0.8380 (ttt90) REVERT: J 107 LYS cc_start: 0.8766 (tttm) cc_final: 0.8172 (ttmm) REVERT: P 108 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6526 (mm-30) REVERT: P 191 GLN cc_start: 0.7444 (mt0) cc_final: 0.6702 (tt0) REVERT: P 217 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7040 (mp) REVERT: P 265 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (t) REVERT: P 304 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8086 (ttt-90) REVERT: P 359 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6371 (pp20) REVERT: P 366 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.8716 (t60) REVERT: P 367 CYS cc_start: 0.7054 (t) cc_final: 0.6631 (t) REVERT: P 376 ARG cc_start: 0.6984 (mtt90) cc_final: 0.6546 (mmm160) REVERT: P 443 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: P 536 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7078 (tm-30) outliers start: 50 outliers final: 38 residues processed: 185 average time/residue: 0.1255 time to fit residues: 31.2885 Evaluate side-chains 184 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 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 C residue 271 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 247 ASN Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 359 GLU Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 443 GLU Chi-restraints excluded: chain P residue 452 VAL Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 117 optimal weight: 0.0010 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.181889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144081 restraints weight = 12841.173| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.37 r_work: 0.3338 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11777 Z= 0.113 Angle : 0.568 11.663 16042 Z= 0.278 Chirality : 0.040 0.146 1844 Planarity : 0.004 0.043 2043 Dihedral : 5.103 45.175 1595 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.96 % Allowed : 21.68 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.22), residues: 1444 helix: -1.00 (0.47), residues: 113 sheet: 0.09 (0.22), residues: 611 loop : -1.50 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 357 TYR 0.008 0.001 TYR J 103 PHE 0.017 0.001 PHE B 443 TRP 0.012 0.001 TRP P 431 HIS 0.002 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00285 (11755) covalent geometry : angle 0.56666 (15998) SS BOND : bond 0.00220 ( 22) SS BOND : angle 0.88678 ( 44) hydrogen bonds : bond 0.02871 ( 350) hydrogen bonds : angle 4.25413 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8903 (tt0) cc_final: 0.8677 (tt0) REVERT: A 425 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7889 (mmtt) REVERT: B 458 VAL cc_start: 0.7997 (t) cc_final: 0.7461 (p) REVERT: C 366 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.7794 (p) REVERT: C 423 ASP cc_start: 0.8491 (t70) cc_final: 0.7908 (t0) REVERT: C 426 LYS cc_start: 0.8541 (pttt) cc_final: 0.8001 (pttp) REVERT: C 428 ASP cc_start: 0.8297 (m-30) cc_final: 0.7445 (m-30) REVERT: C 451 LEU cc_start: 0.8060 (mt) cc_final: 0.7789 (pt) REVERT: D 423 ASP cc_start: 0.8169 (t0) cc_final: 0.7900 (t0) REVERT: J 38 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8095 (ttp-170) REVERT: J 44 ASN cc_start: 0.8823 (t0) cc_final: 0.8541 (t0) REVERT: J 59 ARG cc_start: 0.8659 (mtp-110) cc_final: 0.8439 (ttt90) REVERT: J 107 LYS cc_start: 0.8822 (tttm) cc_final: 0.8291 (ttmm) REVERT: P 108 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6632 (mm-30) REVERT: P 191 GLN cc_start: 0.7431 (mt0) cc_final: 0.6769 (tt0) REVERT: P 217 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7142 (mp) REVERT: P 265 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8680 (t) REVERT: P 304 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.8199 (ttt-90) REVERT: P 359 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6474 (pp20) REVERT: P 366 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8675 (t60) REVERT: P 376 ARG cc_start: 0.6945 (mtt90) cc_final: 0.6625 (mmm160) REVERT: P 443 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: P 536 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7216 (tm-30) outliers start: 51 outliers final: 38 residues processed: 184 average time/residue: 0.1251 time to fit residues: 31.2907 Evaluate side-chains 184 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 247 ASN Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 359 GLU Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 443 GLU Chi-restraints excluded: chain P residue 452 VAL Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 3 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.181683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141619 restraints weight = 13107.629| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.64 r_work: 0.3349 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11777 Z= 0.118 Angle : 0.572 11.730 16042 Z= 0.280 Chirality : 0.040 0.149 1844 Planarity : 0.005 0.069 2043 Dihedral : 5.103 45.755 1595 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.57 % Allowed : 22.30 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1444 helix: -0.89 (0.47), residues: 112 sheet: 0.12 (0.22), residues: 609 loop : -1.46 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 357 TYR 0.008 0.001 TYR J 103 PHE 0.018 0.001 PHE B 443 TRP 0.012 0.001 TRP P 431 HIS 0.002 0.001 HIS D 436 Details of bonding type rmsd covalent geometry : bond 0.00296 (11755) covalent geometry : angle 0.57044 (15998) SS BOND : bond 0.00216 ( 22) SS BOND : angle 0.88114 ( 44) hydrogen bonds : bond 0.02909 ( 350) hydrogen bonds : angle 4.22977 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8924 (tt0) cc_final: 0.8692 (tt0) REVERT: A 425 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7941 (mmtt) REVERT: B 458 VAL cc_start: 0.7973 (t) cc_final: 0.7427 (p) REVERT: C 366 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.7740 (p) REVERT: C 423 ASP cc_start: 0.8484 (t70) cc_final: 0.7900 (t0) REVERT: C 426 LYS cc_start: 0.8561 (pttt) cc_final: 0.8038 (pttp) REVERT: C 428 ASP cc_start: 0.8283 (m-30) cc_final: 0.7421 (m-30) REVERT: C 451 LEU cc_start: 0.8119 (mt) cc_final: 0.7870 (pt) REVERT: D 423 ASP cc_start: 0.8176 (t0) cc_final: 0.7960 (t0) REVERT: J 38 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.8086 (ttp-170) REVERT: J 44 ASN cc_start: 0.8798 (t0) cc_final: 0.8511 (t0) REVERT: J 59 ARG cc_start: 0.8684 (mtp-110) cc_final: 0.8471 (ttt90) REVERT: J 107 LYS cc_start: 0.8852 (tttm) cc_final: 0.8344 (ttmm) REVERT: P 108 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6665 (mm-30) REVERT: P 191 GLN cc_start: 0.7452 (mt0) cc_final: 0.6788 (tt0) REVERT: P 217 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7182 (mp) REVERT: P 265 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8689 (t) REVERT: P 304 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8237 (ttt-90) REVERT: P 359 GLU cc_start: 0.7528 (pp20) cc_final: 0.6476 (pp20) REVERT: P 366 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8670 (t60) REVERT: P 376 ARG cc_start: 0.6977 (mtt90) cc_final: 0.6657 (mmm160) REVERT: P 443 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: P 536 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7280 (tm-30) outliers start: 46 outliers final: 39 residues processed: 178 average time/residue: 0.1226 time to fit residues: 29.7627 Evaluate side-chains 182 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 247 ASN Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 443 GLU Chi-restraints excluded: chain P residue 452 VAL Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 75 optimal weight: 0.0470 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.181655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143719 restraints weight = 12922.087| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.41 r_work: 0.3347 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11777 Z= 0.125 Angle : 0.575 11.669 16042 Z= 0.281 Chirality : 0.041 0.147 1844 Planarity : 0.004 0.042 2043 Dihedral : 5.117 46.663 1595 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.73 % Allowed : 22.07 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.22), residues: 1444 helix: -0.85 (0.47), residues: 113 sheet: 0.13 (0.22), residues: 609 loop : -1.43 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 357 TYR 0.007 0.001 TYR J 103 PHE 0.018 0.001 PHE B 443 TRP 0.013 0.001 TRP P 431 HIS 0.002 0.001 HIS D 436 Details of bonding type rmsd covalent geometry : bond 0.00314 (11755) covalent geometry : angle 0.57372 (15998) SS BOND : bond 0.00224 ( 22) SS BOND : angle 0.90043 ( 44) hydrogen bonds : bond 0.02951 ( 350) hydrogen bonds : angle 4.23460 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.96 seconds wall clock time: 61 minutes 5.74 seconds (3665.74 seconds total)