Starting phenix.real_space_refine on Tue Jul 29 15:34:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lx3_30004/07_2025/6lx3_30004.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lx3_30004/07_2025/6lx3_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_30004/07_2025/6lx3_30004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lx3_30004/07_2025/6lx3_30004.map" model { file = "/net/cci-nas-00/data/ceres_data/6lx3_30004/07_2025/6lx3_30004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lx3_30004/07_2025/6lx3_30004.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.62, per 1000 atoms: 1.01 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: 5.02 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.11 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: 5.47 Time building geometry restraints manager: 4.04 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: 70.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.040 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (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 TRP 0.041 0.004 TRP P 431 HIS 0.010 0.002 HIS D 350 PHE 0.027 0.004 PHE D 374 TYR 0.058 0.004 TYR A 472 ARG 0.021 0.001 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.15886 ( 350) hydrogen bonds : angle 7.68735 ( 1032) SS BOND : bond 0.00750 ( 22) SS BOND : angle 2.23735 ( 44) covalent geometry : bond 0.01555 (11755) covalent geometry : angle 1.20127 (15998) *********************** 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 : 2.456 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: 0.8081 (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: 0.3697 time to fit residues: 90.9958 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 : 2.273 ------------------------------------------------------------------------------- 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 122 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3971 r_free = 0.3971 target = 0.178960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139105 restraints weight = 13068.267| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.53 r_work: 0.3241 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1211 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= 0.134 Angle : 0.639 11.966 16042 Z= 0.321 Chirality : 0.042 0.166 1844 Planarity : 0.006 0.054 2043 Dihedral : 6.304 40.656 1605 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.72 % Allowed : 18.18 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.20), residues: 1444 helix: -3.35 (0.30), residues: 111 sheet: -0.92 (0.20), residues: 597 loop : -2.53 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 431 HIS 0.002 0.001 HIS D 457 PHE 0.015 0.001 PHE P 406 TYR 0.010 0.001 TYR J 103 ARG 0.007 0.000 ARG P 336 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 350) hydrogen bonds : angle 5.40947 ( 1032) SS BOND : bond 0.00309 ( 22) SS BOND : angle 0.91984 ( 44) covalent geometry : bond 0.00328 (11755) covalent geometry : angle 0.63768 (15998) *********************** 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 199 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8905 (tt0) cc_final: 0.8678 (tt0) REVERT: A 392 ARG cc_start: 0.8601 (ttp-170) cc_final: 0.7376 (tpt90) REVERT: A 425 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7775 (mmtt) REVERT: B 433 MET cc_start: 0.8154 (ttm) cc_final: 0.7861 (ttp) REVERT: C 423 ASP cc_start: 0.8655 (t70) cc_final: 0.8014 (t0) REVERT: C 426 LYS cc_start: 0.8570 (pttt) cc_final: 0.8080 (pttp) REVERT: C 428 ASP cc_start: 0.8345 (m-30) cc_final: 0.7744 (m-30) REVERT: D 362 ASN cc_start: 0.7423 (t0) cc_final: 0.7176 (t0) REVERT: D 423 ASP cc_start: 0.8412 (t0) cc_final: 0.8137 (t0) REVERT: J 44 ASN cc_start: 0.8750 (t0) cc_final: 0.8468 (t0) REVERT: J 51 ASP cc_start: 0.8579 (t70) cc_final: 0.8238 (t0) REVERT: J 59 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.8300 (ttt90) REVERT: J 107 LYS cc_start: 0.8703 (tttm) cc_final: 0.8143 (ttmm) REVERT: P 72 ASN cc_start: 0.6946 (m-40) cc_final: 0.6713 (m-40) REVERT: P 172 ARG cc_start: 0.6989 (mtm180) cc_final: 0.6427 (mtm180) REVERT: P 199 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: P 359 GLU cc_start: 0.7024 (pp20) cc_final: 0.5995 (pp20) REVERT: P 366 TRP cc_start: 0.9332 (OUTLIER) cc_final: 0.8781 (t60) REVERT: P 367 CYS cc_start: 0.6981 (t) cc_final: 0.6616 (t) REVERT: P 376 ARG cc_start: 0.7320 (mtt90) cc_final: 0.7023 (mmp-170) outliers start: 35 outliers final: 21 residues processed: 194 average time/residue: 0.2792 time to fit residues: 73.4131 Evaluate side-chains 169 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 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 129 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 16 ASN ** 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 = 0.3950 r_free = 0.3950 target = 0.176881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136778 restraints weight = 13130.797| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.50 r_work: 0.3206 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11777 Z= 0.192 Angle : 0.651 11.266 16042 Z= 0.324 Chirality : 0.043 0.156 1844 Planarity : 0.005 0.047 2043 Dihedral : 5.939 42.196 1597 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.65 % Allowed : 19.11 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.21), residues: 1444 helix: -2.40 (0.38), residues: 112 sheet: -0.71 (0.21), residues: 597 loop : -2.22 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 431 HIS 0.003 0.001 HIS D 457 PHE 0.015 0.001 PHE P 406 TYR 0.011 0.002 TYR P 148 ARG 0.008 0.000 ARG P 336 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 350) hydrogen bonds : angle 5.14907 ( 1032) SS BOND : bond 0.00332 ( 22) SS BOND : angle 1.08361 ( 44) covalent geometry : bond 0.00480 (11755) covalent geometry : angle 0.64980 (15998) *********************** 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: 47 poor density : 157 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8886 (tt0) cc_final: 0.8656 (tt0) REVERT: A 392 ARG cc_start: 0.8594 (ttp-170) cc_final: 0.7391 (tpt90) REVERT: A 425 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7812 (mmtt) REVERT: B 413 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8287 (p) REVERT: B 433 MET cc_start: 0.8107 (ttm) cc_final: 0.7756 (ttp) REVERT: C 423 ASP cc_start: 0.8631 (t70) cc_final: 0.7939 (t0) REVERT: C 426 LYS cc_start: 0.8596 (pttt) cc_final: 0.8050 (pttp) REVERT: C 428 ASP cc_start: 0.8369 (m-30) cc_final: 0.7643 (m-30) REVERT: D 362 ASN cc_start: 0.7540 (t0) cc_final: 0.7304 (t0) REVERT: D 423 ASP cc_start: 0.8423 (t0) cc_final: 0.8038 (t0) REVERT: J 44 ASN cc_start: 0.8778 (t0) cc_final: 0.8455 (t0) REVERT: J 51 ASP cc_start: 0.8700 (t70) cc_final: 0.8421 (t0) REVERT: J 59 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.8362 (ttt90) REVERT: J 107 LYS cc_start: 0.8737 (tttm) cc_final: 0.8171 (ttmm) REVERT: P 40 GLN cc_start: 0.8244 (tp40) cc_final: 0.7925 (tt0) REVERT: P 72 ASN cc_start: 0.6999 (m-40) cc_final: 0.6752 (m-40) REVERT: P 108 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6392 (mm-30) REVERT: P 359 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6168 (pp20) REVERT: P 366 TRP cc_start: 0.9310 (OUTLIER) cc_final: 0.8739 (t60) REVERT: P 376 ARG cc_start: 0.7350 (mtt90) cc_final: 0.7038 (mmp-170) REVERT: P 536 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7059 (tm-30) outliers start: 47 outliers final: 32 residues processed: 197 average time/residue: 0.2877 time to fit residues: 77.2806 Evaluate side-chains 183 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 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 413 VAL 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 18 THR Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 113 VAL 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 460 LEU 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 45 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 25 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.179506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139766 restraints weight = 12985.918| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.59 r_work: 0.3316 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1625 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= 0.132 Angle : 0.592 11.865 16042 Z= 0.293 Chirality : 0.041 0.155 1844 Planarity : 0.005 0.045 2043 Dihedral : 5.582 41.470 1597 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.19 % Allowed : 20.98 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.21), residues: 1444 helix: -1.88 (0.42), residues: 112 sheet: -0.45 (0.21), residues: 600 loop : -2.01 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 431 HIS 0.002 0.001 HIS D 436 PHE 0.014 0.001 PHE P 406 TYR 0.009 0.001 TYR A 395 ARG 0.006 0.000 ARG D 401 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 350) hydrogen bonds : angle 4.74564 ( 1032) SS BOND : bond 0.00270 ( 22) SS BOND : angle 1.11729 ( 44) covalent geometry : bond 0.00329 (11755) covalent geometry : angle 0.59035 (15998) *********************** 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 203 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8930 (tt0) cc_final: 0.8710 (tt0) REVERT: A 392 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.7441 (tpt90) REVERT: A 425 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7891 (mmtt) REVERT: B 433 MET cc_start: 0.8102 (ttm) cc_final: 0.7775 (ttp) REVERT: B 458 VAL cc_start: 0.7803 (t) cc_final: 0.7437 (p) REVERT: C 423 ASP cc_start: 0.8668 (t70) cc_final: 0.8073 (t0) REVERT: C 426 LYS cc_start: 0.8554 (pttt) cc_final: 0.8060 (pttp) REVERT: C 428 ASP cc_start: 0.8365 (m-30) cc_final: 0.7644 (m-30) REVERT: D 423 ASP cc_start: 0.8373 (t0) cc_final: 0.8138 (t0) REVERT: J 44 ASN cc_start: 0.8845 (t0) cc_final: 0.8525 (t0) REVERT: J 51 ASP cc_start: 0.8763 (t70) cc_final: 0.8470 (t0) REVERT: J 59 ARG cc_start: 0.8633 (mtp-110) cc_final: 0.8410 (ttt90) REVERT: J 107 LYS cc_start: 0.8841 (tttm) cc_final: 0.8294 (ttmm) REVERT: P 108 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6576 (mm-30) REVERT: P 304 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8188 (ttt-90) REVERT: P 359 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6298 (pp20) REVERT: P 366 TRP cc_start: 0.9311 (OUTLIER) cc_final: 0.8713 (t60) REVERT: P 367 CYS cc_start: 0.6982 (t) cc_final: 0.6616 (t) REVERT: P 376 ARG cc_start: 0.7254 (mtt90) cc_final: 0.7005 (mmp-170) REVERT: P 536 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7148 (tm-30) outliers start: 41 outliers final: 26 residues processed: 194 average time/residue: 0.3124 time to fit residues: 81.5130 Evaluate side-chains 180 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 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 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 536 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 64 optimal weight: 0.0070 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 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 = 0.3993 r_free = 0.3993 target = 0.181028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141061 restraints weight = 12949.133| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.62 r_work: 0.3318 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1869 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= 0.115 Angle : 0.571 11.452 16042 Z= 0.282 Chirality : 0.041 0.149 1844 Planarity : 0.004 0.045 2043 Dihedral : 5.302 41.261 1596 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.42 % Allowed : 21.29 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.22), residues: 1444 helix: -1.51 (0.45), residues: 112 sheet: -0.26 (0.22), residues: 598 loop : -1.77 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 431 HIS 0.002 0.000 HIS D 436 PHE 0.013 0.001 PHE P 406 TYR 0.008 0.001 TYR A 395 ARG 0.006 0.000 ARG D 401 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 350) hydrogen bonds : angle 4.51827 ( 1032) SS BOND : bond 0.00252 ( 22) SS BOND : angle 0.89714 ( 44) covalent geometry : bond 0.00286 (11755) covalent geometry : angle 0.56999 (15998) *********************** 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 198 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8898 (tt0) cc_final: 0.8644 (tt0) REVERT: A 392 ARG cc_start: 0.8605 (ttp-170) cc_final: 0.7442 (tpt90) REVERT: A 425 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7872 (mmtt) REVERT: B 433 MET cc_start: 0.8081 (ttm) cc_final: 0.7748 (ttp) REVERT: B 458 VAL cc_start: 0.7819 (t) cc_final: 0.7431 (p) REVERT: C 423 ASP cc_start: 0.8573 (t70) cc_final: 0.7993 (t0) REVERT: C 426 LYS cc_start: 0.8505 (pttt) cc_final: 0.7971 (pttp) REVERT: C 428 ASP cc_start: 0.8287 (m-30) cc_final: 0.7494 (m-30) REVERT: D 423 ASP cc_start: 0.8298 (t0) cc_final: 0.7950 (t0) REVERT: J 44 ASN cc_start: 0.8897 (t0) cc_final: 0.8546 (t0) REVERT: J 59 ARG cc_start: 0.8629 (mtp-110) cc_final: 0.8402 (ttt90) REVERT: J 107 LYS cc_start: 0.8820 (tttm) cc_final: 0.8243 (ttmm) REVERT: P 108 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6576 (mm-30) REVERT: P 304 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8191 (ttt-90) REVERT: P 359 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6336 (pp20) REVERT: P 366 TRP cc_start: 0.9296 (OUTLIER) cc_final: 0.8736 (t60) REVERT: P 367 CYS cc_start: 0.6975 (t) cc_final: 0.6595 (t) REVERT: P 376 ARG cc_start: 0.7060 (mtt90) cc_final: 0.6789 (mmp-170) REVERT: P 536 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7174 (tm-30) outliers start: 44 outliers final: 32 residues processed: 189 average time/residue: 0.4062 time to fit residues: 105.1488 Evaluate side-chains 178 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 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 B residue 443 PHE 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** D 291 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 = 0.3972 r_free = 0.3972 target = 0.178995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138952 restraints weight = 13169.798| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.63 r_work: 0.3258 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1804 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= 0.170 Angle : 0.611 11.683 16042 Z= 0.301 Chirality : 0.042 0.148 1844 Planarity : 0.005 0.044 2043 Dihedral : 5.441 42.512 1596 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.27 % Allowed : 20.98 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.22), residues: 1444 helix: -1.42 (0.45), residues: 112 sheet: -0.18 (0.22), residues: 600 loop : -1.75 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 431 HIS 0.003 0.001 HIS D 457 PHE 0.014 0.001 PHE P 406 TYR 0.009 0.001 TYR D 395 ARG 0.007 0.000 ARG P 357 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 350) hydrogen bonds : angle 4.59893 ( 1032) SS BOND : bond 0.00285 ( 22) SS BOND : angle 1.03532 ( 44) covalent geometry : bond 0.00426 (11755) covalent geometry : angle 0.60951 (15998) *********************** 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 203 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8869 (tt0) cc_final: 0.8640 (tt0) REVERT: A 392 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.7443 (tpt90) REVERT: A 425 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7845 (mmtt) REVERT: B 433 MET cc_start: 0.8090 (ttm) cc_final: 0.7768 (ttp) REVERT: B 458 VAL cc_start: 0.7769 (t) cc_final: 0.7308 (p) REVERT: C 423 ASP cc_start: 0.8560 (t70) cc_final: 0.7952 (t0) REVERT: C 426 LYS cc_start: 0.8547 (pttt) cc_final: 0.7999 (pttp) REVERT: C 428 ASP cc_start: 0.8333 (m-30) cc_final: 0.7553 (m-30) REVERT: D 423 ASP cc_start: 0.8274 (t0) cc_final: 0.8022 (t0) REVERT: J 44 ASN cc_start: 0.8869 (t0) cc_final: 0.8539 (t0) REVERT: J 59 ARG cc_start: 0.8638 (mtp-110) cc_final: 0.8391 (ttt90) REVERT: J 107 LYS cc_start: 0.8803 (tttm) cc_final: 0.8243 (ttmm) REVERT: P 108 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6538 (mm-30) REVERT: P 217 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7093 (mp) REVERT: P 304 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8148 (ttt-90) REVERT: P 359 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6327 (pp20) REVERT: P 366 TRP cc_start: 0.9310 (OUTLIER) cc_final: 0.8640 (t60) REVERT: P 376 ARG cc_start: 0.7261 (mtt90) cc_final: 0.6954 (mmp-170) REVERT: P 443 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: P 536 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7166 (tm-30) outliers start: 55 outliers final: 42 residues processed: 189 average time/residue: 0.3012 time to fit residues: 76.3069 Evaluate side-chains 187 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 416 ILE Chi-restraints excluded: chain B residue 443 PHE 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 C residue 451 LEU 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 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 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 460 LEU Chi-restraints excluded: chain P residue 516 VAL 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 23 optimal weight: 5.9990 chunk 85 optimal weight: 0.0370 chunk 115 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS D 291 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.180202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140445 restraints weight = 13178.892| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.63 r_work: 0.3300 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1953 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= 0.126 Angle : 0.580 11.620 16042 Z= 0.285 Chirality : 0.041 0.148 1844 Planarity : 0.004 0.043 2043 Dihedral : 5.311 42.969 1596 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.73 % Allowed : 21.60 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1444 helix: -1.23 (0.46), residues: 112 sheet: -0.09 (0.22), residues: 603 loop : -1.66 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 431 HIS 0.002 0.001 HIS D 436 PHE 0.013 0.001 PHE P 406 TYR 0.010 0.001 TYR P 148 ARG 0.007 0.000 ARG P 357 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 350) hydrogen bonds : angle 4.45154 ( 1032) SS BOND : bond 0.00237 ( 22) SS BOND : angle 0.92700 ( 44) covalent geometry : bond 0.00315 (11755) covalent geometry : angle 0.57926 (15998) *********************** 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 196 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8898 (tt0) cc_final: 0.8689 (tt0) REVERT: A 392 ARG cc_start: 0.8628 (ttp-170) cc_final: 0.7467 (tpt90) REVERT: A 425 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7897 (mmtt) REVERT: B 433 MET cc_start: 0.8110 (ttm) cc_final: 0.7800 (ttp) REVERT: B 458 VAL cc_start: 0.7812 (t) cc_final: 0.7352 (p) REVERT: C 423 ASP cc_start: 0.8570 (t70) cc_final: 0.8002 (t0) REVERT: C 426 LYS cc_start: 0.8546 (pttt) cc_final: 0.8006 (pttp) REVERT: C 428 ASP cc_start: 0.8351 (m-30) cc_final: 0.7540 (m-30) REVERT: D 423 ASP cc_start: 0.8258 (t0) cc_final: 0.7974 (t0) REVERT: J 38 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8054 (ttp-170) REVERT: J 44 ASN cc_start: 0.8892 (t0) cc_final: 0.8547 (t0) REVERT: J 59 ARG cc_start: 0.8671 (mtp-110) cc_final: 0.8447 (ttt90) REVERT: J 107 LYS cc_start: 0.8831 (tttm) cc_final: 0.8294 (ttmm) REVERT: P 108 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6612 (mm-30) REVERT: P 217 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7171 (mp) REVERT: P 304 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8198 (ttt-90) REVERT: P 359 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6398 (pp20) REVERT: P 366 TRP cc_start: 0.9296 (OUTLIER) cc_final: 0.8646 (t60) REVERT: P 367 CYS cc_start: 0.7040 (t) cc_final: 0.6653 (t) REVERT: P 376 ARG cc_start: 0.7211 (mtt90) cc_final: 0.6976 (mmp-170) REVERT: P 443 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: P 536 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7154 (tm-30) outliers start: 48 outliers final: 38 residues processed: 186 average time/residue: 0.3178 time to fit residues: 80.6164 Evaluate side-chains 184 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 B residue 443 PHE Chi-restraints excluded: chain C residue 271 LEU 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 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 217 LEU 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 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 89 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 ASN ** C 436 HIS ** 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 = 0.3953 r_free = 0.3953 target = 0.176874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137201 restraints weight = 13102.677| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.62 r_work: 0.3218 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11777 Z= 0.233 Angle : 0.660 11.584 16042 Z= 0.326 Chirality : 0.043 0.148 1844 Planarity : 0.005 0.043 2043 Dihedral : 5.667 45.849 1596 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.20 % Allowed : 21.21 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1444 helix: -1.33 (0.46), residues: 112 sheet: -0.15 (0.22), residues: 600 loop : -1.70 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 431 HIS 0.004 0.001 HIS D 457 PHE 0.015 0.002 PHE P 406 TYR 0.012 0.002 TYR B 395 ARG 0.008 0.001 ARG P 357 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 350) hydrogen bonds : angle 4.72226 ( 1032) SS BOND : bond 0.00357 ( 22) SS BOND : angle 1.25251 ( 44) covalent geometry : bond 0.00582 (11755) covalent geometry : angle 0.65768 (15998) *********************** 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 200 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8892 (tt0) cc_final: 0.8670 (tt0) REVERT: A 392 ARG cc_start: 0.8589 (ttp-170) cc_final: 0.7422 (tpt90) REVERT: A 425 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7775 (mmtt) REVERT: B 433 MET cc_start: 0.8143 (ttm) cc_final: 0.7839 (ttp) REVERT: C 423 ASP cc_start: 0.8573 (t70) cc_final: 0.7949 (t0) REVERT: C 426 LYS cc_start: 0.8606 (pttt) cc_final: 0.8042 (pttp) REVERT: C 428 ASP cc_start: 0.8427 (m-30) cc_final: 0.7622 (m-30) REVERT: D 423 ASP cc_start: 0.8349 (t0) cc_final: 0.8094 (t0) REVERT: J 44 ASN cc_start: 0.8861 (t0) cc_final: 0.8542 (t0) REVERT: J 59 ARG cc_start: 0.8657 (mtp-110) cc_final: 0.8413 (ttt90) REVERT: J 107 LYS cc_start: 0.8801 (tttm) cc_final: 0.8234 (ttmm) REVERT: P 108 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6540 (mm-30) REVERT: P 217 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7121 (mp) REVERT: P 304 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8123 (ttt-90) REVERT: P 359 GLU cc_start: 0.7469 (pp20) cc_final: 0.6406 (pp20) REVERT: P 366 TRP cc_start: 0.9310 (OUTLIER) cc_final: 0.8675 (t60) REVERT: P 376 ARG cc_start: 0.7410 (mtt90) cc_final: 0.7093 (mmp-170) REVERT: P 443 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: P 536 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7242 (tm-30) outliers start: 54 outliers final: 44 residues processed: 188 average time/residue: 0.2789 time to fit residues: 71.0106 Evaluate side-chains 188 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 B residue 443 PHE 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 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 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 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 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 460 LEU Chi-restraints excluded: chain P residue 516 VAL 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 96 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.180931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143163 restraints weight = 13086.831| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.61 r_work: 0.3329 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2077 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= 0.113 Angle : 0.569 11.762 16042 Z= 0.280 Chirality : 0.041 0.148 1844 Planarity : 0.004 0.043 2043 Dihedral : 5.293 44.447 1596 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.04 % Allowed : 21.52 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.22), residues: 1444 helix: -1.08 (0.47), residues: 112 sheet: 0.02 (0.22), residues: 605 loop : -1.55 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 431 HIS 0.001 0.000 HIS J 63 PHE 0.013 0.001 PHE P 406 TYR 0.007 0.001 TYR A 395 ARG 0.008 0.000 ARG P 357 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 350) hydrogen bonds : angle 4.36675 ( 1032) SS BOND : bond 0.00215 ( 22) SS BOND : angle 0.81596 ( 44) covalent geometry : bond 0.00284 (11755) covalent geometry : angle 0.56780 (15998) *********************** 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 198 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8904 (tt0) cc_final: 0.8675 (tt0) REVERT: A 392 ARG cc_start: 0.8597 (ttp-170) cc_final: 0.7442 (tpt90) REVERT: A 425 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7899 (mmtt) REVERT: B 433 MET cc_start: 0.8090 (ttm) cc_final: 0.7796 (ttp) REVERT: B 458 VAL cc_start: 0.7888 (t) cc_final: 0.7487 (p) REVERT: C 423 ASP cc_start: 0.8561 (t70) cc_final: 0.7993 (t0) REVERT: C 426 LYS cc_start: 0.8566 (pttt) cc_final: 0.8014 (pttp) REVERT: C 428 ASP cc_start: 0.8353 (m-30) cc_final: 0.7499 (m-30) REVERT: C 451 LEU cc_start: 0.8059 (mt) cc_final: 0.7749 (pt) REVERT: D 423 ASP cc_start: 0.8233 (t0) cc_final: 0.7993 (t0) REVERT: J 38 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.8104 (ttp-170) REVERT: J 44 ASN cc_start: 0.8771 (t0) cc_final: 0.8478 (t0) REVERT: J 59 ARG cc_start: 0.8672 (mtp-110) cc_final: 0.8440 (ttt90) REVERT: J 107 LYS cc_start: 0.8822 (tttm) cc_final: 0.8279 (ttmm) REVERT: P 108 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6617 (mm-30) REVERT: P 191 GLN cc_start: 0.7512 (mt0) cc_final: 0.6834 (tt0) REVERT: P 217 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7163 (mp) REVERT: P 304 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8213 (ttt-90) REVERT: P 359 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6484 (pp20) REVERT: P 366 TRP cc_start: 0.9288 (OUTLIER) cc_final: 0.8621 (t60) REVERT: P 367 CYS cc_start: 0.6969 (t) cc_final: 0.6589 (t) REVERT: P 443 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: P 536 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7119 (tm-30) outliers start: 52 outliers final: 40 residues processed: 186 average time/residue: 0.2973 time to fit residues: 74.5204 Evaluate side-chains 186 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 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 B residue 443 PHE Chi-restraints excluded: chain B residue 464 MET 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 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 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 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 453 THR Chi-restraints excluded: chain P residue 516 VAL 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: 0.8980 chunk 41 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 87 optimal weight: 0.0270 chunk 99 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.181012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140891 restraints weight = 12993.439| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.52 r_work: 0.3332 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2146 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= 0.122 Angle : 0.584 11.695 16042 Z= 0.286 Chirality : 0.041 0.150 1844 Planarity : 0.005 0.072 2043 Dihedral : 5.235 45.701 1596 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.73 % Allowed : 22.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1444 helix: -0.93 (0.48), residues: 112 sheet: 0.08 (0.22), residues: 603 loop : -1.48 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 431 HIS 0.002 0.001 HIS D 436 PHE 0.013 0.001 PHE P 406 TYR 0.008 0.001 TYR J 103 ARG 0.012 0.000 ARG P 357 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 350) hydrogen bonds : angle 4.32401 ( 1032) SS BOND : bond 0.00215 ( 22) SS BOND : angle 0.93089 ( 44) covalent geometry : bond 0.00308 (11755) covalent geometry : angle 0.58293 (15998) ********************** 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 189 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8935 (tt0) cc_final: 0.8707 (tt0) REVERT: A 392 ARG cc_start: 0.8593 (ttp-170) cc_final: 0.7481 (tpt90) REVERT: A 425 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7966 (mmtt) REVERT: B 377 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8353 (ttpp) REVERT: B 433 MET cc_start: 0.8107 (ttm) cc_final: 0.7814 (ttp) REVERT: B 458 VAL cc_start: 0.7867 (t) cc_final: 0.7474 (p) REVERT: C 366 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.7933 (p) REVERT: C 423 ASP cc_start: 0.8566 (t70) cc_final: 0.8012 (t0) REVERT: C 426 LYS cc_start: 0.8571 (pttt) cc_final: 0.8049 (pttp) REVERT: C 428 ASP cc_start: 0.8336 (m-30) cc_final: 0.7484 (m-30) REVERT: C 451 LEU cc_start: 0.8130 (mt) cc_final: 0.7840 (pt) REVERT: D 423 ASP cc_start: 0.8239 (t0) cc_final: 0.7986 (t0) REVERT: J 44 ASN cc_start: 0.8846 (t0) cc_final: 0.8550 (t0) REVERT: J 59 ARG cc_start: 0.8692 (mtp-110) cc_final: 0.8484 (ttt90) REVERT: J 107 LYS cc_start: 0.8848 (tttm) cc_final: 0.8338 (ttmm) REVERT: P 108 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6652 (mm-30) REVERT: P 191 GLN cc_start: 0.7567 (mt0) cc_final: 0.6915 (tt0) REVERT: P 217 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7196 (mp) REVERT: P 304 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8251 (ttt-90) REVERT: P 359 GLU cc_start: 0.7579 (pp20) cc_final: 0.6522 (pp20) REVERT: P 366 TRP cc_start: 0.9292 (OUTLIER) cc_final: 0.8649 (t60) REVERT: P 367 CYS cc_start: 0.7030 (t) cc_final: 0.6645 (t) REVERT: P 443 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: P 536 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7280 (tm-30) outliers start: 48 outliers final: 42 residues processed: 180 average time/residue: 0.2789 time to fit residues: 68.5029 Evaluate side-chains 187 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 B residue 443 PHE Chi-restraints excluded: chain B residue 464 MET 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 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 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 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 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 516 VAL 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 139 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.181135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141293 restraints weight = 13040.050| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.49 r_work: 0.3340 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2204 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= 0.121 Angle : 0.577 11.709 16042 Z= 0.283 Chirality : 0.041 0.145 1844 Planarity : 0.004 0.043 2043 Dihedral : 5.195 46.186 1596 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.73 % Allowed : 21.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1444 helix: -0.84 (0.48), residues: 112 sheet: 0.13 (0.22), residues: 605 loop : -1.42 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 431 HIS 0.002 0.001 HIS D 436 PHE 0.013 0.001 PHE P 406 TYR 0.007 0.001 TYR A 395 ARG 0.010 0.000 ARG P 357 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 350) hydrogen bonds : angle 4.28810 ( 1032) SS BOND : bond 0.00218 ( 22) SS BOND : angle 0.91937 ( 44) covalent geometry : bond 0.00306 (11755) covalent geometry : angle 0.57599 (15998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8748.13 seconds wall clock time: 153 minutes 20.97 seconds (9200.97 seconds total)