Starting phenix.real_space_refine on Wed Jan 22 03:12:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jka_61549/01_2025/9jka_61549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jka_61549/01_2025/9jka_61549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jka_61549/01_2025/9jka_61549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jka_61549/01_2025/9jka_61549.map" model { file = "/net/cci-nas-00/data/ceres_data/9jka_61549/01_2025/9jka_61549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jka_61549/01_2025/9jka_61549.cif" } resolution = 2.5 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= 0.015 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 60 5.16 5 C 11706 2.51 5 N 3084 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17820 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2970 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.66, per 1000 atoms: 0.43 Number of scatterers: 17820 At special positions: 0 Unit cell: (99.51, 89.88, 219.35, 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 60 16.00 O 2970 8.00 N 3084 7.00 C 11706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 145 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.2 seconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4212 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 62.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 109 through 134 Proline residue: A 123 - end of helix Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 142 through 168 removed outlier: 4.048A pdb=" N GLU A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 204 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS A 509 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 134 Proline residue: B 123 - end of helix Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 168 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 204 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 336 Processing helix chain 'B' and resid 339 through 368 removed outlier: 3.598A pdb=" N TYR B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 416 through 430 Processing helix chain 'B' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 456 through 459 Processing helix chain 'B' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS B 509 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 Proline residue: C 123 - end of helix Proline residue: C 130 - end of helix Processing helix chain 'C' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 204 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA C 396 " --> pdb=" O GLN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 416 through 430 Processing helix chain 'C' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR C 441 " --> pdb=" O PHE C 437 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 456 through 459 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS C 509 " --> pdb=" O PRO C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 134 Proline residue: D 123 - end of helix Proline residue: D 130 - end of helix Processing helix chain 'D' and resid 142 through 168 removed outlier: 4.048A pdb=" N GLU D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 204 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 336 Processing helix chain 'D' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA D 396 " --> pdb=" O GLN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 416 through 430 Processing helix chain 'D' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 456 through 459 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS D 509 " --> pdb=" O PRO D 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 134 Proline residue: E 123 - end of helix Proline residue: E 130 - end of helix Processing helix chain 'E' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 168 " --> pdb=" O TRP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 204 Processing helix chain 'E' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 Processing helix chain 'E' and resid 339 through 368 removed outlier: 3.598A pdb=" N TYR E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA E 396 " --> pdb=" O GLN E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 409 Processing helix chain 'E' and resid 416 through 430 Processing helix chain 'E' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR E 441 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 456 through 459 Processing helix chain 'E' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS E 509 " --> pdb=" O PRO E 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 134 Proline residue: F 123 - end of helix Proline residue: F 130 - end of helix Processing helix chain 'F' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 168 " --> pdb=" O TRP F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 204 Processing helix chain 'F' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 336 Processing helix chain 'F' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 396 removed outlier: 4.116A pdb=" N ALA F 396 " --> pdb=" O GLN F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 409 Processing helix chain 'F' and resid 416 through 430 Processing helix chain 'F' and resid 433 through 443 removed outlier: 4.951A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR F 441 " --> pdb=" O PHE F 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA F 443 " --> pdb=" O GLU F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 450 Processing helix chain 'F' and resid 456 through 459 Processing helix chain 'F' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS F 509 " --> pdb=" O PRO F 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.920A pdb=" N TRP A 460 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.586A pdb=" N LYS A 371 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 173 through 174 removed outlier: 6.487A pdb=" N PHE A 497 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS A 498 " --> pdb=" O TRP C 460 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU C 462 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER A 500 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 512 removed outlier: 3.595A pdb=" N LYS B 371 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.755A pdb=" N TRP B 460 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AA7, first strand: chain 'D' and resid 173 through 174 removed outlier: 3.678A pdb=" N TRP D 460 " --> pdb=" O LYS E 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 371 through 372 Processing sheet with id=AA9, first strand: chain 'F' and resid 173 through 174 removed outlier: 6.627A pdb=" N PHE D 497 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS D 498 " --> pdb=" O TRP F 460 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU F 462 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER D 500 " --> pdb=" O LEU F 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 511 through 512 removed outlier: 3.511A pdb=" N LYS E 371 " --> pdb=" O VAL D 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.869A pdb=" N TRP E 460 " --> pdb=" O LYS F 498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 511 through 512 1086 hydrogen bonds defined for protein. 3159 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: 6.65 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5102 1.34 - 1.45: 3097 1.45 - 1.57: 9969 1.57 - 1.69: 0 1.69 - 1.80: 102 Bond restraints: 18270 Sorted by residual: bond pdb=" CA THR C 122 " pdb=" C THR C 122 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.26e-02 6.30e+03 1.84e+00 bond pdb=" CA THR D 122 " pdb=" C THR D 122 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.26e-02 6.30e+03 1.82e+00 bond pdb=" CA THR B 122 " pdb=" C THR B 122 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.26e-02 6.30e+03 1.80e+00 bond pdb=" CB TRP E 274 " pdb=" CG TRP E 274 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.78e+00 bond pdb=" CA THR E 122 " pdb=" C THR E 122 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.26e-02 6.30e+03 1.77e+00 ... (remaining 18265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 23116 1.56 - 3.11: 1299 3.11 - 4.67: 249 4.67 - 6.23: 62 6.23 - 7.78: 36 Bond angle restraints: 24762 Sorted by residual: angle pdb=" CA PRO F 130 " pdb=" C PRO F 130 " pdb=" N PRO F 131 " ideal model delta sigma weight residual 117.93 122.37 -4.44 1.20e+00 6.94e-01 1.37e+01 angle pdb=" CA PRO C 130 " pdb=" C PRO C 130 " pdb=" N PRO C 131 " ideal model delta sigma weight residual 117.93 122.37 -4.44 1.20e+00 6.94e-01 1.37e+01 angle pdb=" CA PRO E 130 " pdb=" C PRO E 130 " pdb=" N PRO E 131 " ideal model delta sigma weight residual 117.93 122.37 -4.44 1.20e+00 6.94e-01 1.37e+01 angle pdb=" CA PRO B 130 " pdb=" C PRO B 130 " pdb=" N PRO B 131 " ideal model delta sigma weight residual 117.93 122.34 -4.41 1.20e+00 6.94e-01 1.35e+01 angle pdb=" CA PRO A 130 " pdb=" C PRO A 130 " pdb=" N PRO A 131 " ideal model delta sigma weight residual 117.93 122.34 -4.41 1.20e+00 6.94e-01 1.35e+01 ... (remaining 24757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.59: 9820 10.59 - 21.18: 899 21.18 - 31.77: 142 31.77 - 42.36: 48 42.36 - 52.94: 8 Dihedral angle restraints: 10917 sinusoidal: 4461 harmonic: 6456 Sorted by residual: dihedral pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " pdb=" SG CYS A 145 " pdb=" CB CYS A 145 " ideal model delta sinusoidal sigma weight residual -86.00 -138.94 52.94 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CA PRO F 467 " pdb=" C PRO F 467 " pdb=" N VAL F 468 " pdb=" CA VAL F 468 " ideal model delta harmonic sigma weight residual -180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PRO A 467 " pdb=" C PRO A 467 " pdb=" N VAL A 468 " pdb=" CA VAL A 468 " ideal model delta harmonic sigma weight residual -180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 10914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1563 0.034 - 0.068: 729 0.068 - 0.102: 329 0.102 - 0.136: 133 0.136 - 0.170: 54 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA LEU F 129 " pdb=" N LEU F 129 " pdb=" C LEU F 129 " pdb=" CB LEU F 129 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA LEU E 129 " pdb=" N LEU E 129 " pdb=" C LEU E 129 " pdb=" CB LEU E 129 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA LEU B 129 " pdb=" N LEU B 129 " pdb=" C LEU B 129 " pdb=" CB LEU B 129 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 2805 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 260 " 0.014 2.00e-02 2.50e+03 2.20e-02 8.50e+00 pdb=" CG PHE B 260 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 260 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 260 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 260 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 260 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 260 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 260 " -0.014 2.00e-02 2.50e+03 2.19e-02 8.39e+00 pdb=" CG PHE D 260 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE D 260 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE D 260 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 260 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE D 260 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE D 260 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 260 " -0.014 2.00e-02 2.50e+03 2.19e-02 8.36e+00 pdb=" CG PHE F 260 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE F 260 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE F 260 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 260 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE F 260 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE F 260 " 0.002 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 103 2.60 - 3.18: 14126 3.18 - 3.75: 28546 3.75 - 4.33: 39935 4.33 - 4.90: 66861 Nonbonded interactions: 149571 Sorted by model distance: nonbonded pdb=" SG CYS F 141 " pdb=" SG CYS F 145 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 141 " pdb=" SG CYS C 145 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 141 " pdb=" SG CYS B 145 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 141 " pdb=" SG CYS E 145 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 141 " pdb=" SG CYS D 145 " model vdw 2.030 3.760 ... (remaining 149566 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.220 Process input model: 38.390 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.007 0.061 18270 Z= 0.430 Angle : 0.902 7.783 24762 Z= 0.501 Chirality : 0.052 0.170 2808 Planarity : 0.007 0.053 3072 Dihedral : 8.501 52.931 6702 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.23 (0.15), residues: 2136 helix: -1.44 (0.12), residues: 1200 sheet: 1.47 (0.38), residues: 168 loop : -2.01 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 164 HIS 0.012 0.002 HIS E 423 PHE 0.045 0.006 PHE B 260 TYR 0.020 0.003 TYR D 279 ARG 0.012 0.001 ARG E 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8567 (tp) cc_final: 0.8272 (tm) REVERT: A 217 GLN cc_start: 0.7433 (mt0) cc_final: 0.7162 (mt0) REVERT: A 222 LEU cc_start: 0.7935 (tp) cc_final: 0.7684 (tp) REVERT: A 344 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 350 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6844 (ttm110) REVERT: A 418 GLU cc_start: 0.7634 (tp30) cc_final: 0.7292 (tp30) REVERT: A 422 GLN cc_start: 0.7628 (mt0) cc_final: 0.7003 (mt0) REVERT: B 135 ARG cc_start: 0.7199 (ttt180) cc_final: 0.6944 (tpt-90) REVERT: B 341 TYR cc_start: 0.8206 (t80) cc_final: 0.7774 (t80) REVERT: B 350 ARG cc_start: 0.7348 (ttm110) cc_final: 0.7093 (ttm110) REVERT: B 385 MET cc_start: 0.8593 (ttp) cc_final: 0.8149 (ttp) REVERT: B 403 GLN cc_start: 0.7952 (tt0) cc_final: 0.7748 (tt0) REVERT: B 418 GLU cc_start: 0.7989 (tp30) cc_final: 0.7607 (tp30) REVERT: B 422 GLN cc_start: 0.7766 (mt0) cc_final: 0.7464 (mm110) REVERT: B 435 LYS cc_start: 0.7679 (ttmp) cc_final: 0.7282 (tptp) REVERT: C 172 LYS cc_start: 0.8251 (pttp) cc_final: 0.7510 (mtpp) REVERT: C 344 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 385 MET cc_start: 0.8820 (ttp) cc_final: 0.8539 (ttp) REVERT: C 404 LYS cc_start: 0.8378 (mttm) cc_final: 0.8106 (mttm) REVERT: C 418 GLU cc_start: 0.7942 (tp30) cc_final: 0.7430 (tp30) REVERT: C 422 GLN cc_start: 0.7615 (mt0) cc_final: 0.7255 (mt0) REVERT: C 513 MET cc_start: 0.7389 (tpp) cc_final: 0.7088 (tpp) REVERT: D 213 GLN cc_start: 0.7984 (tt0) cc_final: 0.7593 (tm-30) REVERT: D 217 GLN cc_start: 0.7458 (mt0) cc_final: 0.7225 (mt0) REVERT: D 341 TYR cc_start: 0.7997 (t80) cc_final: 0.7623 (t80) REVERT: D 344 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7275 (mt-10) REVERT: D 347 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7494 (mt-10) REVERT: D 349 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 350 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6867 (ttm110) REVERT: D 385 MET cc_start: 0.8741 (ttp) cc_final: 0.8512 (ttp) REVERT: D 418 GLU cc_start: 0.7816 (tp30) cc_final: 0.7598 (tp30) REVERT: D 422 GLN cc_start: 0.7701 (mt0) cc_final: 0.7182 (mm-40) REVERT: D 435 LYS cc_start: 0.7833 (ttmp) cc_final: 0.7425 (tptp) REVERT: E 117 LEU cc_start: 0.8819 (tp) cc_final: 0.8616 (tm) REVERT: E 120 PHE cc_start: 0.7504 (t80) cc_final: 0.7018 (m-80) REVERT: E 170 ARG cc_start: 0.7369 (mtt180) cc_final: 0.7155 (mmp80) REVERT: E 172 LYS cc_start: 0.8306 (pttp) cc_final: 0.7542 (mtpp) REVERT: E 341 TYR cc_start: 0.8426 (t80) cc_final: 0.8029 (t80) REVERT: E 344 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 350 ARG cc_start: 0.7181 (ttm110) cc_final: 0.6852 (ttm110) REVERT: E 404 LYS cc_start: 0.8502 (mttm) cc_final: 0.8300 (mtmm) REVERT: E 418 GLU cc_start: 0.7950 (tp30) cc_final: 0.7457 (tp30) REVERT: E 435 LYS cc_start: 0.7614 (ttmp) cc_final: 0.7298 (tptp) REVERT: F 120 PHE cc_start: 0.7384 (t80) cc_final: 0.7172 (m-80) REVERT: F 172 LYS cc_start: 0.8230 (pttp) cc_final: 0.7474 (mtpp) REVERT: F 344 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7397 (mt-10) REVERT: F 385 MET cc_start: 0.8804 (ttp) cc_final: 0.8544 (ttp) REVERT: F 404 LYS cc_start: 0.8380 (mttm) cc_final: 0.8110 (mttm) REVERT: F 418 GLU cc_start: 0.7944 (tp30) cc_final: 0.7412 (tp30) REVERT: F 422 GLN cc_start: 0.7624 (mt0) cc_final: 0.7251 (mt0) REVERT: F 513 MET cc_start: 0.7402 (tpp) cc_final: 0.7199 (tpp) outliers start: 0 outliers final: 1 residues processed: 489 average time/residue: 1.8432 time to fit residues: 976.0583 Evaluate side-chains 301 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 282 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 411 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN B 411 GLN B 449 GLN C 412 GLN C 415 HIS C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN D 451 HIS E 411 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 GLN F 415 HIS F 449 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100401 restraints weight = 21326.037| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.05 r_work: 0.3094 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18270 Z= 0.244 Angle : 0.560 7.105 24762 Z= 0.293 Chirality : 0.040 0.144 2808 Planarity : 0.005 0.044 3072 Dihedral : 4.477 49.431 2420 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.69 % Allowed : 11.55 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.17), residues: 2136 helix: 1.06 (0.14), residues: 1212 sheet: 1.75 (0.39), residues: 168 loop : -1.23 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 164 HIS 0.005 0.001 HIS E 423 PHE 0.027 0.003 PHE B 149 TYR 0.011 0.002 TYR C 280 ARG 0.005 0.001 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 324 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.5404 (mmp-170) REVERT: A 182 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7114 (ttp80) REVERT: A 217 GLN cc_start: 0.7493 (mt0) cc_final: 0.7212 (mt0) REVERT: A 344 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 350 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7008 (ttm110) REVERT: A 364 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7974 (mt-10) REVERT: A 418 GLU cc_start: 0.8593 (tp30) cc_final: 0.8213 (tp30) REVERT: A 422 GLN cc_start: 0.8168 (mt0) cc_final: 0.7741 (mt0) REVERT: B 172 LYS cc_start: 0.8371 (pttt) cc_final: 0.8159 (pttm) REVERT: B 182 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7012 (ttm170) REVERT: B 341 TYR cc_start: 0.8598 (t80) cc_final: 0.8185 (t80) REVERT: B 350 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7299 (ttm110) REVERT: B 418 GLU cc_start: 0.8779 (tp30) cc_final: 0.8244 (tp30) REVERT: B 422 GLN cc_start: 0.8326 (mt0) cc_final: 0.8019 (mt0) REVERT: B 435 LYS cc_start: 0.8280 (ttmp) cc_final: 0.7576 (tptt) REVERT: C 172 LYS cc_start: 0.8445 (pttp) cc_final: 0.7521 (mtpt) REVERT: C 190 PHE cc_start: 0.8149 (t80) cc_final: 0.7870 (t80) REVERT: C 344 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 364 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: C 418 GLU cc_start: 0.8779 (tp30) cc_final: 0.8150 (tp30) REVERT: C 422 GLN cc_start: 0.8140 (mt0) cc_final: 0.7782 (mt0) REVERT: C 456 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7514 (mt) REVERT: C 459 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: C 513 MET cc_start: 0.7588 (tpp) cc_final: 0.7129 (tpp) REVERT: D 120 PHE cc_start: 0.6752 (m-80) cc_final: 0.6265 (t80) REVERT: D 344 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7902 (mt-10) REVERT: D 347 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7780 (mt-10) REVERT: D 350 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7197 (ttm110) REVERT: D 364 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7790 (mt-10) REVERT: D 418 GLU cc_start: 0.8653 (tp30) cc_final: 0.8305 (tp30) REVERT: D 459 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: E 120 PHE cc_start: 0.7502 (t80) cc_final: 0.6924 (m-80) REVERT: E 170 ARG cc_start: 0.7871 (mtt180) cc_final: 0.6924 (mmp80) REVERT: E 195 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8091 (p) REVERT: E 217 GLN cc_start: 0.7854 (mt0) cc_final: 0.7614 (mt0) REVERT: E 341 TYR cc_start: 0.8667 (t80) cc_final: 0.8241 (t80) REVERT: E 344 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7903 (mt-10) REVERT: E 350 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7264 (ttm110) REVERT: E 412 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7604 (mp10) REVERT: E 418 GLU cc_start: 0.8653 (tp30) cc_final: 0.8191 (tp30) REVERT: F 120 PHE cc_start: 0.7381 (t80) cc_final: 0.7083 (m-80) REVERT: F 172 LYS cc_start: 0.8449 (pttp) cc_final: 0.7460 (mtpp) REVERT: F 190 PHE cc_start: 0.8154 (t80) cc_final: 0.7861 (t80) REVERT: F 344 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7807 (mt-10) REVERT: F 364 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: F 418 GLU cc_start: 0.8777 (tp30) cc_final: 0.8153 (tp30) REVERT: F 422 GLN cc_start: 0.8151 (mt0) cc_final: 0.7794 (mt0) REVERT: F 456 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7515 (mt) REVERT: F 459 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7544 (mt0) REVERT: F 513 MET cc_start: 0.7270 (tpp) cc_final: 0.6880 (tpp) outliers start: 51 outliers final: 8 residues processed: 348 average time/residue: 1.6345 time to fit residues: 622.4112 Evaluate side-chains 301 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 284 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 459 GLN Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 459 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS E 412 GLN E 449 GLN F 449 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098613 restraints weight = 21176.618| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.05 r_work: 0.3065 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18270 Z= 0.233 Angle : 0.551 8.817 24762 Z= 0.278 Chirality : 0.039 0.137 2808 Planarity : 0.004 0.038 3072 Dihedral : 4.155 14.480 2418 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.06 % Allowed : 13.24 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.18), residues: 2136 helix: 1.99 (0.14), residues: 1212 sheet: 1.92 (0.40), residues: 168 loop : -0.82 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 134 HIS 0.004 0.001 HIS B 281 PHE 0.024 0.002 PHE B 149 TYR 0.013 0.002 TYR A 341 ARG 0.005 0.001 ARG B 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 295 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: A 170 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.5646 (mmp-170) REVERT: A 182 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7175 (ttp80) REVERT: A 217 GLN cc_start: 0.7549 (mt0) cc_final: 0.7235 (mt0) REVERT: A 344 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 350 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7073 (ttm110) REVERT: A 364 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7831 (mt-10) REVERT: A 402 MET cc_start: 0.9068 (tpt) cc_final: 0.8865 (tpp) REVERT: A 418 GLU cc_start: 0.8688 (tp30) cc_final: 0.8359 (tp30) REVERT: B 182 ARG cc_start: 0.7855 (ttm170) cc_final: 0.6998 (ttm170) REVERT: B 213 GLN cc_start: 0.7851 (tt0) cc_final: 0.7650 (tm-30) REVERT: B 341 TYR cc_start: 0.8647 (t80) cc_final: 0.8286 (t80) REVERT: B 350 ARG cc_start: 0.7783 (ttm110) cc_final: 0.7433 (ttm110) REVERT: B 418 GLU cc_start: 0.8773 (tp30) cc_final: 0.8206 (tp30) REVERT: B 422 GLN cc_start: 0.8286 (mt0) cc_final: 0.7950 (mt0) REVERT: C 172 LYS cc_start: 0.8491 (pttp) cc_final: 0.7517 (mtpt) REVERT: C 344 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7817 (mt-10) REVERT: C 364 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: C 418 GLU cc_start: 0.8787 (tp30) cc_final: 0.8200 (tp30) REVERT: C 422 GLN cc_start: 0.8148 (mt0) cc_final: 0.7811 (mt0) REVERT: C 513 MET cc_start: 0.7594 (tpp) cc_final: 0.7108 (tpp) REVERT: D 170 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5949 (mmp-170) REVERT: D 344 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7943 (mt-10) REVERT: D 350 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7200 (ttm110) REVERT: D 364 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7787 (mt-10) REVERT: D 402 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8845 (tpp) REVERT: D 418 GLU cc_start: 0.8729 (tp30) cc_final: 0.8376 (tp30) REVERT: E 120 PHE cc_start: 0.7663 (t80) cc_final: 0.7097 (m-80) REVERT: E 170 ARG cc_start: 0.7928 (mtt180) cc_final: 0.6982 (mmp80) REVERT: E 186 MET cc_start: 0.8312 (mmt) cc_final: 0.7713 (mtp) REVERT: E 195 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (p) REVERT: E 217 GLN cc_start: 0.7632 (mt0) cc_final: 0.7378 (mm-40) REVERT: E 344 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7897 (mt-10) REVERT: E 350 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7322 (ttm110) REVERT: E 418 GLU cc_start: 0.8605 (tp30) cc_final: 0.8159 (tp30) REVERT: F 120 PHE cc_start: 0.7387 (t80) cc_final: 0.7059 (m-80) REVERT: F 172 LYS cc_start: 0.8446 (pttp) cc_final: 0.7479 (mtpp) REVERT: F 344 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7807 (mt-10) REVERT: F 364 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: F 418 GLU cc_start: 0.8782 (tp30) cc_final: 0.8199 (tp30) REVERT: F 422 GLN cc_start: 0.8140 (mt0) cc_final: 0.7803 (mt0) REVERT: F 513 MET cc_start: 0.7251 (tpp) cc_final: 0.6726 (tpp) outliers start: 58 outliers final: 12 residues processed: 318 average time/residue: 1.5919 time to fit residues: 556.0207 Evaluate side-chains 294 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 275 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 412 GLN Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 215 optimal weight: 0.0770 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS F 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.098903 restraints weight = 21211.054| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.05 r_work: 0.3070 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18270 Z= 0.202 Angle : 0.520 8.205 24762 Z= 0.263 Chirality : 0.039 0.145 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.996 13.687 2418 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.69 % Allowed : 14.66 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.18), residues: 2136 helix: 2.27 (0.15), residues: 1248 sheet: 1.45 (0.40), residues: 180 loop : -0.53 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.003 0.001 HIS E 423 PHE 0.026 0.002 PHE B 149 TYR 0.011 0.001 TYR E 414 ARG 0.004 0.000 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.5872 (mmp-170) REVERT: A 182 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7157 (ttp80) REVERT: A 217 GLN cc_start: 0.7629 (mt0) cc_final: 0.7350 (mt0) REVERT: A 344 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7946 (mt-10) REVERT: A 350 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7103 (ttm110) REVERT: A 364 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7768 (mt-10) REVERT: A 418 GLU cc_start: 0.8753 (tp30) cc_final: 0.8400 (tp30) REVERT: B 117 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8284 (tm) REVERT: B 172 LYS cc_start: 0.8178 (pttt) cc_final: 0.7930 (pttt) REVERT: B 182 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7003 (ttm170) REVERT: B 186 MET cc_start: 0.8324 (mmt) cc_final: 0.7686 (mtp) REVERT: B 213 GLN cc_start: 0.7817 (tt0) cc_final: 0.7516 (tm-30) REVERT: B 341 TYR cc_start: 0.8656 (t80) cc_final: 0.8299 (t80) REVERT: B 350 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7288 (ttm110) REVERT: B 371 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8372 (ttpp) REVERT: B 418 GLU cc_start: 0.8731 (tp30) cc_final: 0.8127 (tp30) REVERT: B 422 GLN cc_start: 0.8274 (mt0) cc_final: 0.7946 (mt0) REVERT: C 172 LYS cc_start: 0.8485 (pttp) cc_final: 0.7509 (mtpt) REVERT: C 186 MET cc_start: 0.8303 (mmt) cc_final: 0.7553 (mtp) REVERT: C 344 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7834 (mt-10) REVERT: C 364 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: C 371 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8206 (ptmm) REVERT: C 418 GLU cc_start: 0.8801 (tp30) cc_final: 0.8227 (tp30) REVERT: C 422 GLN cc_start: 0.8153 (mt0) cc_final: 0.7723 (mt0) REVERT: C 513 MET cc_start: 0.7549 (tpp) cc_final: 0.7061 (tpp) REVERT: D 344 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7942 (mt-10) REVERT: D 350 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7141 (ttm110) REVERT: D 364 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7749 (mt-10) REVERT: D 418 GLU cc_start: 0.8716 (tp30) cc_final: 0.8413 (tp30) REVERT: E 120 PHE cc_start: 0.7670 (t80) cc_final: 0.7073 (m-80) REVERT: E 170 ARG cc_start: 0.7928 (mtt180) cc_final: 0.6968 (mmp80) REVERT: E 172 LYS cc_start: 0.8324 (pttt) cc_final: 0.8116 (pttt) REVERT: E 186 MET cc_start: 0.8287 (mmt) cc_final: 0.7734 (mtp) REVERT: E 195 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.8102 (p) REVERT: E 344 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7904 (mt-10) REVERT: E 350 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7318 (ttm110) REVERT: E 364 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: E 418 GLU cc_start: 0.8628 (tp30) cc_final: 0.8157 (tp30) REVERT: F 120 PHE cc_start: 0.7428 (t80) cc_final: 0.7055 (m-80) REVERT: F 172 LYS cc_start: 0.8443 (pttp) cc_final: 0.7544 (mtpt) REVERT: F 344 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7815 (mt-10) REVERT: F 364 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: F 371 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8213 (ptmm) REVERT: F 418 GLU cc_start: 0.8794 (tp30) cc_final: 0.8199 (tp30) REVERT: F 422 GLN cc_start: 0.8149 (mt0) cc_final: 0.7701 (mt0) REVERT: F 513 MET cc_start: 0.7276 (tpp) cc_final: 0.6755 (tpp) outliers start: 51 outliers final: 17 residues processed: 305 average time/residue: 1.6138 time to fit residues: 541.4163 Evaluate side-chains 290 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098045 restraints weight = 21287.549| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.05 r_work: 0.3057 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18270 Z= 0.214 Angle : 0.518 6.548 24762 Z= 0.263 Chirality : 0.039 0.133 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.966 13.491 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.11 % Allowed : 16.19 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.18), residues: 2136 helix: 2.42 (0.14), residues: 1248 sheet: 1.45 (0.40), residues: 180 loop : -0.36 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 134 HIS 0.003 0.001 HIS E 423 PHE 0.028 0.002 PHE B 149 TYR 0.013 0.001 TYR F 280 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5886 (mmp-170) REVERT: A 217 GLN cc_start: 0.7544 (mt0) cc_final: 0.7245 (mt0) REVERT: A 344 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7959 (mt-10) REVERT: A 350 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7087 (ttm110) REVERT: A 364 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7777 (mt-10) REVERT: A 418 GLU cc_start: 0.8784 (tp30) cc_final: 0.8411 (tp30) REVERT: B 172 LYS cc_start: 0.8322 (pttt) cc_final: 0.8092 (pttt) REVERT: B 186 MET cc_start: 0.8302 (mmt) cc_final: 0.7759 (mtp) REVERT: B 350 ARG cc_start: 0.7621 (ttm110) cc_final: 0.7260 (ttm110) REVERT: B 371 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8280 (ttpp) REVERT: B 418 GLU cc_start: 0.8732 (tp30) cc_final: 0.8164 (tp30) REVERT: B 422 GLN cc_start: 0.8261 (mt0) cc_final: 0.7931 (mt0) REVERT: C 172 LYS cc_start: 0.8493 (pttp) cc_final: 0.7519 (mtpt) REVERT: C 186 MET cc_start: 0.8272 (mmt) cc_final: 0.7553 (mtp) REVERT: C 344 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 364 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: C 371 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8279 (ptmm) REVERT: C 418 GLU cc_start: 0.8790 (tp30) cc_final: 0.8208 (tp30) REVERT: C 422 GLN cc_start: 0.8141 (mt0) cc_final: 0.7704 (mt0) REVERT: C 513 MET cc_start: 0.7597 (tpp) cc_final: 0.7101 (tpp) REVERT: D 170 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5929 (mmp-170) REVERT: D 344 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7955 (mt-10) REVERT: D 350 ARG cc_start: 0.7604 (ttm110) cc_final: 0.7187 (ttm110) REVERT: D 364 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7769 (mt-10) REVERT: D 418 GLU cc_start: 0.8741 (tp30) cc_final: 0.8436 (tp30) REVERT: E 120 PHE cc_start: 0.7616 (t80) cc_final: 0.7022 (m-80) REVERT: E 170 ARG cc_start: 0.7961 (mtt180) cc_final: 0.6965 (mmp80) REVERT: E 172 LYS cc_start: 0.8351 (pttt) cc_final: 0.8135 (pttt) REVERT: E 186 MET cc_start: 0.8284 (mmt) cc_final: 0.7743 (mtp) REVERT: E 195 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.8099 (p) REVERT: E 341 TYR cc_start: 0.8595 (t80) cc_final: 0.8218 (t80) REVERT: E 344 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7932 (mt-10) REVERT: E 350 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7306 (ttm110) REVERT: E 364 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: E 418 GLU cc_start: 0.8637 (tp30) cc_final: 0.8163 (tp30) REVERT: F 120 PHE cc_start: 0.7404 (t80) cc_final: 0.7053 (m-80) REVERT: F 172 LYS cc_start: 0.8443 (pttp) cc_final: 0.7549 (mtpt) REVERT: F 186 MET cc_start: 0.8296 (mmt) cc_final: 0.7575 (mtp) REVERT: F 344 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7858 (mt-10) REVERT: F 364 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: F 418 GLU cc_start: 0.8784 (tp30) cc_final: 0.8201 (tp30) REVERT: F 422 GLN cc_start: 0.8138 (mt0) cc_final: 0.7702 (mt0) REVERT: F 513 MET cc_start: 0.7406 (tpp) cc_final: 0.6882 (tpp) outliers start: 40 outliers final: 18 residues processed: 295 average time/residue: 1.5431 time to fit residues: 501.4503 Evaluate side-chains 286 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 111 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097625 restraints weight = 21212.991| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.05 r_work: 0.3054 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18270 Z= 0.219 Angle : 0.530 9.369 24762 Z= 0.265 Chirality : 0.039 0.133 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.956 13.667 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.00 % Allowed : 17.46 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.18), residues: 2136 helix: 2.45 (0.14), residues: 1248 sheet: 1.44 (0.39), residues: 180 loop : -0.26 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 134 HIS 0.003 0.001 HIS C 423 PHE 0.030 0.002 PHE B 149 TYR 0.013 0.002 TYR A 280 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8295 (m-80) cc_final: 0.7652 (m-80) REVERT: A 170 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.5906 (mmp-170) REVERT: A 210 ARG cc_start: 0.6932 (mpp80) cc_final: 0.6690 (mpt-90) REVERT: A 217 GLN cc_start: 0.7530 (mt0) cc_final: 0.7271 (mt0) REVERT: A 344 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7959 (mt-10) REVERT: A 350 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7100 (ttm110) REVERT: A 364 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7773 (mt-10) REVERT: A 418 GLU cc_start: 0.8773 (tp30) cc_final: 0.8426 (tp30) REVERT: B 172 LYS cc_start: 0.8323 (pttt) cc_final: 0.8068 (pttt) REVERT: B 186 MET cc_start: 0.8325 (mmt) cc_final: 0.7772 (mtp) REVERT: B 350 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7256 (ttm110) REVERT: B 371 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8294 (ttpp) REVERT: B 418 GLU cc_start: 0.8746 (tp30) cc_final: 0.8181 (tp30) REVERT: B 422 GLN cc_start: 0.8257 (mt0) cc_final: 0.7928 (mt0) REVERT: C 172 LYS cc_start: 0.8435 (pttp) cc_final: 0.7502 (mtpt) REVERT: C 186 MET cc_start: 0.8267 (mmt) cc_final: 0.7565 (mtp) REVERT: C 243 GLN cc_start: 0.8973 (tt0) cc_final: 0.8618 (tt0) REVERT: C 344 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 364 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: C 418 GLU cc_start: 0.8729 (tp30) cc_final: 0.8192 (tp30) REVERT: C 422 GLN cc_start: 0.8131 (mt0) cc_final: 0.7727 (mt0) REVERT: C 513 MET cc_start: 0.7634 (tpp) cc_final: 0.7140 (tpp) REVERT: D 170 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5904 (mmp-170) REVERT: D 344 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 350 ARG cc_start: 0.7607 (ttm110) cc_final: 0.7186 (ttm110) REVERT: D 364 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7760 (mt-10) REVERT: D 371 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8262 (mtmm) REVERT: D 418 GLU cc_start: 0.8803 (tp30) cc_final: 0.8467 (tp30) REVERT: E 120 PHE cc_start: 0.7591 (t80) cc_final: 0.6998 (m-80) REVERT: E 170 ARG cc_start: 0.7952 (mtt180) cc_final: 0.6958 (mmp80) REVERT: E 172 LYS cc_start: 0.8356 (pttt) cc_final: 0.8129 (pttt) REVERT: E 186 MET cc_start: 0.8315 (mmt) cc_final: 0.7758 (mtp) REVERT: E 195 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.8104 (p) REVERT: E 341 TYR cc_start: 0.8575 (t80) cc_final: 0.8262 (t80) REVERT: E 344 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7902 (mt-10) REVERT: E 350 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7366 (ttm110) REVERT: E 364 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: E 418 GLU cc_start: 0.8647 (tp30) cc_final: 0.8180 (tp30) REVERT: F 120 PHE cc_start: 0.7576 (t80) cc_final: 0.7124 (m-80) REVERT: F 172 LYS cc_start: 0.8440 (pttp) cc_final: 0.7549 (mtpt) REVERT: F 186 MET cc_start: 0.8287 (mmt) cc_final: 0.7580 (mtp) REVERT: F 243 GLN cc_start: 0.8985 (tt0) cc_final: 0.8633 (tt0) REVERT: F 344 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7848 (mt-10) REVERT: F 364 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: F 371 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8343 (ptmm) REVERT: F 418 GLU cc_start: 0.8729 (tp30) cc_final: 0.8190 (tp30) REVERT: F 422 GLN cc_start: 0.8124 (mt0) cc_final: 0.7720 (mt0) REVERT: F 513 MET cc_start: 0.7442 (tpp) cc_final: 0.6855 (tpp) outliers start: 38 outliers final: 17 residues processed: 292 average time/residue: 1.5517 time to fit residues: 499.2027 Evaluate side-chains 293 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 195 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 42 optimal weight: 0.0070 chunk 120 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 135 optimal weight: 0.0870 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099585 restraints weight = 21112.511| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.05 r_work: 0.3080 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18270 Z= 0.171 Angle : 0.498 7.568 24762 Z= 0.252 Chirality : 0.038 0.131 2808 Planarity : 0.004 0.036 3072 Dihedral : 3.811 13.566 2418 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.85 % Allowed : 17.83 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.18), residues: 2136 helix: 2.59 (0.14), residues: 1248 sheet: 1.40 (0.39), residues: 180 loop : -0.17 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 274 HIS 0.002 0.001 HIS E 230 PHE 0.030 0.002 PHE B 149 TYR 0.010 0.001 TYR F 280 ARG 0.005 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 295 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.5941 (mmp-170) REVERT: A 217 GLN cc_start: 0.7637 (mt0) cc_final: 0.7411 (mt0) REVERT: A 344 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 350 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7138 (ttm110) REVERT: A 364 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7751 (mt-10) REVERT: A 402 MET cc_start: 0.9033 (tpt) cc_final: 0.8803 (tpp) REVERT: A 418 GLU cc_start: 0.8775 (tp30) cc_final: 0.8313 (tp30) REVERT: A 422 GLN cc_start: 0.8146 (mt0) cc_final: 0.7691 (mt0) REVERT: B 172 LYS cc_start: 0.8324 (pttt) cc_final: 0.8092 (pttt) REVERT: B 186 MET cc_start: 0.8403 (mmt) cc_final: 0.7809 (mtp) REVERT: B 341 TYR cc_start: 0.8609 (t80) cc_final: 0.8238 (t80) REVERT: B 350 ARG cc_start: 0.7662 (ttm110) cc_final: 0.7259 (ttm110) REVERT: B 371 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8291 (ttpp) REVERT: B 418 GLU cc_start: 0.8776 (tp30) cc_final: 0.8211 (tp30) REVERT: B 422 GLN cc_start: 0.8264 (mt0) cc_final: 0.7939 (mt0) REVERT: C 172 LYS cc_start: 0.8419 (pttp) cc_final: 0.7483 (mtpt) REVERT: C 186 MET cc_start: 0.8284 (mmt) cc_final: 0.7563 (mtp) REVERT: C 243 GLN cc_start: 0.8952 (tt0) cc_final: 0.8598 (tt0) REVERT: C 344 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 364 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: C 371 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8246 (ptmm) REVERT: C 418 GLU cc_start: 0.8740 (tp30) cc_final: 0.8128 (tp30) REVERT: C 422 GLN cc_start: 0.8114 (mt0) cc_final: 0.7677 (mt0) REVERT: C 513 MET cc_start: 0.7637 (tpp) cc_final: 0.7171 (tpp) REVERT: D 170 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5883 (mmp-170) REVERT: D 344 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7983 (mt-10) REVERT: D 350 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7206 (ttm110) REVERT: D 364 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7728 (mt-10) REVERT: D 371 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8375 (mtmm) REVERT: D 418 GLU cc_start: 0.8771 (tp30) cc_final: 0.8450 (tp30) REVERT: E 120 PHE cc_start: 0.7526 (t80) cc_final: 0.6951 (m-80) REVERT: E 170 ARG cc_start: 0.7943 (mtt180) cc_final: 0.6925 (mmp80) REVERT: E 172 LYS cc_start: 0.8344 (pttt) cc_final: 0.8133 (pttt) REVERT: E 186 MET cc_start: 0.8296 (mmt) cc_final: 0.7750 (mtp) REVERT: E 195 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.8087 (p) REVERT: E 213 GLN cc_start: 0.7780 (tt0) cc_final: 0.7553 (tm-30) REVERT: E 341 TYR cc_start: 0.8584 (t80) cc_final: 0.8250 (t80) REVERT: E 344 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7829 (mt-10) REVERT: E 350 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7359 (ttm110) REVERT: E 418 GLU cc_start: 0.8663 (tp30) cc_final: 0.8219 (tp30) REVERT: F 120 PHE cc_start: 0.7541 (t80) cc_final: 0.7100 (m-80) REVERT: F 172 LYS cc_start: 0.8443 (pttp) cc_final: 0.7553 (mtpt) REVERT: F 186 MET cc_start: 0.8272 (mmt) cc_final: 0.7604 (mtp) REVERT: F 243 GLN cc_start: 0.8964 (tt0) cc_final: 0.8609 (tt0) REVERT: F 344 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7862 (mt-10) REVERT: F 364 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: F 371 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8304 (ptmm) REVERT: F 418 GLU cc_start: 0.8750 (tp30) cc_final: 0.8145 (tp30) REVERT: F 422 GLN cc_start: 0.8113 (mt0) cc_final: 0.7678 (mt0) REVERT: F 513 MET cc_start: 0.7419 (tpp) cc_final: 0.6843 (tpp) outliers start: 35 outliers final: 16 residues processed: 307 average time/residue: 1.5092 time to fit residues: 511.6651 Evaluate side-chains 300 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 279 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 164 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 206 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN D 243 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097088 restraints weight = 21130.142| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.03 r_work: 0.3042 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18270 Z= 0.241 Angle : 0.540 9.028 24762 Z= 0.270 Chirality : 0.040 0.132 2808 Planarity : 0.004 0.038 3072 Dihedral : 3.971 14.771 2418 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.85 % Allowed : 18.30 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.31 (0.18), residues: 2136 helix: 2.45 (0.14), residues: 1248 sheet: 1.43 (0.40), residues: 180 loop : -0.12 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 134 HIS 0.003 0.001 HIS D 281 PHE 0.032 0.002 PHE E 149 TYR 0.015 0.002 TYR A 280 ARG 0.006 0.001 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8281 (m-80) cc_final: 0.7693 (m-80) REVERT: A 170 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6047 (mmp-170) REVERT: A 217 GLN cc_start: 0.7621 (mt0) cc_final: 0.7387 (mt0) REVERT: A 344 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 350 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7167 (ttm110) REVERT: A 418 GLU cc_start: 0.8791 (tp30) cc_final: 0.8437 (tp30) REVERT: B 172 LYS cc_start: 0.8282 (pttt) cc_final: 0.8052 (pttt) REVERT: B 186 MET cc_start: 0.8411 (mmt) cc_final: 0.7773 (mtp) REVERT: B 350 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7304 (ttm110) REVERT: B 371 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8303 (ttpp) REVERT: B 412 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7777 (mp10) REVERT: B 418 GLU cc_start: 0.8750 (tp30) cc_final: 0.8193 (tp30) REVERT: B 422 GLN cc_start: 0.8268 (mt0) cc_final: 0.7890 (mt0) REVERT: C 172 LYS cc_start: 0.8428 (pttp) cc_final: 0.7452 (mtpp) REVERT: C 186 MET cc_start: 0.8256 (mmt) cc_final: 0.7572 (mtp) REVERT: C 243 GLN cc_start: 0.8962 (tt0) cc_final: 0.8580 (tt0) REVERT: C 344 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 364 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: C 371 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8273 (ptmm) REVERT: C 418 GLU cc_start: 0.8724 (tp30) cc_final: 0.8187 (tp30) REVERT: C 422 GLN cc_start: 0.8144 (mt0) cc_final: 0.7741 (mt0) REVERT: C 459 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: C 513 MET cc_start: 0.7682 (tpp) cc_final: 0.7209 (tpp) REVERT: D 170 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.5910 (mmp-170) REVERT: D 344 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7980 (mt-10) REVERT: D 350 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7179 (ttm110) REVERT: D 364 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7727 (mt-10) REVERT: D 371 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8323 (mtmm) REVERT: D 418 GLU cc_start: 0.8804 (tp30) cc_final: 0.8463 (tp30) REVERT: E 120 PHE cc_start: 0.7581 (t80) cc_final: 0.6981 (m-80) REVERT: E 170 ARG cc_start: 0.7991 (mtt180) cc_final: 0.6962 (mmp80) REVERT: E 172 LYS cc_start: 0.8360 (pttt) cc_final: 0.8118 (pttt) REVERT: E 186 MET cc_start: 0.8314 (mmt) cc_final: 0.7782 (mtp) REVERT: E 195 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.8104 (p) REVERT: E 213 GLN cc_start: 0.7762 (tt0) cc_final: 0.7538 (tm-30) REVERT: E 344 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7858 (mt-10) REVERT: E 350 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7329 (ttm110) REVERT: F 120 PHE cc_start: 0.7608 (t80) cc_final: 0.7083 (m-80) REVERT: F 172 LYS cc_start: 0.8442 (pttp) cc_final: 0.7427 (mtpp) REVERT: F 186 MET cc_start: 0.8275 (mmt) cc_final: 0.7607 (mtp) REVERT: F 243 GLN cc_start: 0.8981 (tt0) cc_final: 0.8601 (tt0) REVERT: F 344 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7857 (mt-10) REVERT: F 364 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: F 371 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8276 (ptmm) REVERT: F 418 GLU cc_start: 0.8742 (tp30) cc_final: 0.8211 (tp30) REVERT: F 422 GLN cc_start: 0.8148 (mt0) cc_final: 0.7748 (mt0) REVERT: F 513 MET cc_start: 0.7450 (tpp) cc_final: 0.6859 (tpp) outliers start: 35 outliers final: 16 residues processed: 283 average time/residue: 1.5856 time to fit residues: 496.3423 Evaluate side-chains 287 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097710 restraints weight = 21266.679| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.03 r_work: 0.3052 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18270 Z= 0.219 Angle : 0.528 8.473 24762 Z= 0.266 Chirality : 0.039 0.162 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.931 15.068 2418 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.74 % Allowed : 18.62 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.37 (0.18), residues: 2136 helix: 2.49 (0.14), residues: 1248 sheet: 1.38 (0.39), residues: 180 loop : -0.06 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 134 HIS 0.003 0.001 HIS A 281 PHE 0.035 0.002 PHE E 149 TYR 0.014 0.002 TYR A 280 ARG 0.006 0.000 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8282 (m-80) cc_final: 0.7683 (m-80) REVERT: A 170 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.5940 (mmp-170) REVERT: A 217 GLN cc_start: 0.7672 (mt0) cc_final: 0.7452 (mt0) REVERT: A 344 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 350 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7157 (ttm110) REVERT: A 418 GLU cc_start: 0.8794 (tp30) cc_final: 0.8440 (tp30) REVERT: B 172 LYS cc_start: 0.8282 (pttt) cc_final: 0.8053 (pttt) REVERT: B 186 MET cc_start: 0.8406 (mmt) cc_final: 0.7775 (mtp) REVERT: B 350 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7302 (ttm110) REVERT: B 371 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8357 (ttpp) REVERT: B 412 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7768 (mp10) REVERT: B 418 GLU cc_start: 0.8733 (tp30) cc_final: 0.8175 (tp30) REVERT: B 422 GLN cc_start: 0.8255 (mt0) cc_final: 0.7883 (mt0) REVERT: C 172 LYS cc_start: 0.8429 (pttp) cc_final: 0.7457 (mtpp) REVERT: C 186 MET cc_start: 0.8253 (mmt) cc_final: 0.7560 (mtp) REVERT: C 243 GLN cc_start: 0.8965 (tt0) cc_final: 0.8578 (tt0) REVERT: C 344 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7875 (mt-10) REVERT: C 364 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 371 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8212 (ptmm) REVERT: C 418 GLU cc_start: 0.8732 (tp30) cc_final: 0.8196 (tp30) REVERT: C 422 GLN cc_start: 0.8138 (mt0) cc_final: 0.7740 (mt0) REVERT: C 459 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: C 513 MET cc_start: 0.7658 (tpp) cc_final: 0.7125 (tpp) REVERT: D 170 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5914 (mmp-170) REVERT: D 344 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7978 (mt-10) REVERT: D 350 ARG cc_start: 0.7587 (ttm110) cc_final: 0.7166 (ttm110) REVERT: D 364 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7728 (mt-10) REVERT: D 371 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8333 (mtmm) REVERT: D 418 GLU cc_start: 0.8792 (tp30) cc_final: 0.8452 (tp30) REVERT: E 120 PHE cc_start: 0.7593 (t80) cc_final: 0.6934 (m-80) REVERT: E 170 ARG cc_start: 0.7991 (mtt180) cc_final: 0.6966 (mmp80) REVERT: E 172 LYS cc_start: 0.8356 (pttt) cc_final: 0.8123 (pttt) REVERT: E 186 MET cc_start: 0.8314 (mmt) cc_final: 0.7773 (mtp) REVERT: E 195 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.8081 (p) REVERT: E 213 GLN cc_start: 0.7773 (tt0) cc_final: 0.7555 (tm-30) REVERT: E 341 TYR cc_start: 0.8580 (t80) cc_final: 0.8283 (t80) REVERT: E 344 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7807 (mt-10) REVERT: E 350 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7341 (ttm110) REVERT: F 120 PHE cc_start: 0.7612 (t80) cc_final: 0.7084 (m-80) REVERT: F 172 LYS cc_start: 0.8441 (pttp) cc_final: 0.7430 (mtpp) REVERT: F 186 MET cc_start: 0.8247 (mmt) cc_final: 0.7588 (mtp) REVERT: F 243 GLN cc_start: 0.8985 (tt0) cc_final: 0.8603 (tt0) REVERT: F 344 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7872 (mt-10) REVERT: F 364 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: F 371 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8253 (ptmm) REVERT: F 418 GLU cc_start: 0.8727 (tp30) cc_final: 0.8196 (tp30) REVERT: F 422 GLN cc_start: 0.8134 (mt0) cc_final: 0.7734 (mt0) REVERT: F 513 MET cc_start: 0.7439 (tpp) cc_final: 0.6848 (tpp) outliers start: 33 outliers final: 19 residues processed: 285 average time/residue: 1.5525 time to fit residues: 488.4197 Evaluate side-chains 292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.135708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097780 restraints weight = 21234.108| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.04 r_work: 0.3054 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18270 Z= 0.213 Angle : 0.530 8.875 24762 Z= 0.266 Chirality : 0.039 0.131 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.915 15.338 2418 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.69 % Allowed : 18.99 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2136 helix: 2.51 (0.14), residues: 1248 sheet: 1.33 (0.39), residues: 180 loop : -0.03 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 134 HIS 0.003 0.001 HIS A 281 PHE 0.035 0.002 PHE B 149 TYR 0.014 0.002 TYR A 280 ARG 0.006 0.000 ARG C 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.5857 (mmt180) REVERT: A 217 GLN cc_start: 0.7650 (mt0) cc_final: 0.7409 (mt0) REVERT: A 344 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7966 (mt-10) REVERT: A 350 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7180 (ttm110) REVERT: A 402 MET cc_start: 0.9075 (tpt) cc_final: 0.8863 (tpp) REVERT: A 418 GLU cc_start: 0.8802 (tp30) cc_final: 0.8307 (tp30) REVERT: A 422 GLN cc_start: 0.8186 (mt0) cc_final: 0.7710 (mt0) REVERT: B 172 LYS cc_start: 0.8285 (pttt) cc_final: 0.8054 (pttt) REVERT: B 186 MET cc_start: 0.8401 (mmt) cc_final: 0.7776 (mtp) REVERT: B 341 TYR cc_start: 0.8643 (t80) cc_final: 0.8287 (t80) REVERT: B 350 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7311 (ttm110) REVERT: B 371 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8342 (ttpp) REVERT: B 412 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7785 (mp10) REVERT: B 418 GLU cc_start: 0.8740 (tp30) cc_final: 0.8185 (tp30) REVERT: B 422 GLN cc_start: 0.8242 (mt0) cc_final: 0.7877 (mt0) REVERT: C 172 LYS cc_start: 0.8424 (pttp) cc_final: 0.7507 (mtpt) REVERT: C 186 MET cc_start: 0.8249 (mmt) cc_final: 0.7555 (mtp) REVERT: C 243 GLN cc_start: 0.8962 (tt0) cc_final: 0.8573 (tt0) REVERT: C 344 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7876 (mt-10) REVERT: C 364 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: C 371 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8191 (ptmm) REVERT: C 418 GLU cc_start: 0.8730 (tp30) cc_final: 0.8199 (tp30) REVERT: C 422 GLN cc_start: 0.8133 (mt0) cc_final: 0.7743 (mt0) REVERT: C 459 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: C 513 MET cc_start: 0.7614 (tpp) cc_final: 0.7079 (tpp) REVERT: D 170 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5902 (mmt180) REVERT: D 344 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7986 (mt-10) REVERT: D 350 ARG cc_start: 0.7597 (ttm110) cc_final: 0.7165 (ttm110) REVERT: D 364 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7736 (mt-10) REVERT: D 371 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8350 (mtmm) REVERT: D 418 GLU cc_start: 0.8794 (tp30) cc_final: 0.8451 (tp30) REVERT: E 120 PHE cc_start: 0.7620 (t80) cc_final: 0.7000 (m-80) REVERT: E 170 ARG cc_start: 0.7966 (mtt180) cc_final: 0.6955 (mmp80) REVERT: E 172 LYS cc_start: 0.8355 (pttt) cc_final: 0.8124 (pttt) REVERT: E 186 MET cc_start: 0.8312 (mmt) cc_final: 0.7775 (mtp) REVERT: E 195 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.8052 (p) REVERT: E 213 GLN cc_start: 0.7812 (tt0) cc_final: 0.7605 (tm-30) REVERT: E 341 TYR cc_start: 0.8577 (t80) cc_final: 0.8281 (t80) REVERT: E 344 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7869 (mt-10) REVERT: E 350 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7320 (ttm110) REVERT: E 418 GLU cc_start: 0.8659 (tp30) cc_final: 0.8256 (tp30) REVERT: F 120 PHE cc_start: 0.7735 (t80) cc_final: 0.7144 (m-80) REVERT: F 172 LYS cc_start: 0.8437 (pttp) cc_final: 0.7425 (mtpp) REVERT: F 186 MET cc_start: 0.8247 (mmt) cc_final: 0.7587 (mtp) REVERT: F 243 GLN cc_start: 0.8981 (tt0) cc_final: 0.8616 (tt0) REVERT: F 344 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7867 (mt-10) REVERT: F 364 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: F 371 LYS cc_start: 0.8731 (ttpp) cc_final: 0.8251 (ptmm) REVERT: F 418 GLU cc_start: 0.8729 (tp30) cc_final: 0.8203 (tp30) REVERT: F 422 GLN cc_start: 0.8134 (mt0) cc_final: 0.7742 (mt0) REVERT: F 513 MET cc_start: 0.7435 (tpp) cc_final: 0.6847 (tpp) outliers start: 32 outliers final: 19 residues processed: 283 average time/residue: 1.5500 time to fit residues: 483.8323 Evaluate side-chains 291 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 266 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 203 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN E 451 HIS ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097935 restraints weight = 21216.018| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.03 r_work: 0.3057 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18270 Z= 0.210 Angle : 0.533 9.331 24762 Z= 0.266 Chirality : 0.039 0.131 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.913 15.671 2418 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.64 % Allowed : 19.15 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.18), residues: 2136 helix: 2.52 (0.14), residues: 1248 sheet: 1.32 (0.39), residues: 180 loop : 0.01 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 134 HIS 0.003 0.001 HIS A 281 PHE 0.034 0.002 PHE B 149 TYR 0.014 0.001 TYR A 280 ARG 0.006 0.000 ARG C 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16032.94 seconds wall clock time: 282 minutes 31.13 seconds (16951.13 seconds total)