Starting phenix.real_space_refine on Wed Jan 22 02:39:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk7_61546/01_2025/9jk7_61546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk7_61546/01_2025/9jk7_61546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jk7_61546/01_2025/9jk7_61546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk7_61546/01_2025/9jk7_61546.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk7_61546/01_2025/9jk7_61546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk7_61546/01_2025/9jk7_61546.cif" } resolution = 2.9 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= 0.037 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 12 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: 7.26, per 1000 atoms: 0.41 Number of scatterers: 17820 At special positions: 0 Unit cell: (97.37, 88.81, 217.21, 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: 4.45 Conformation dependent library (CDL) restraints added in 2.4 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: 78 helices and 6 sheets defined 61.6% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 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: 4.313A pdb=" N GLU A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.748A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 4.740A 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 369 Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.081A 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: 4.917A pdb=" N ARG A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.249A 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 451 through 455 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: 4.313A pdb=" N GLU B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.749A pdb=" N VAL B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 removed outlier: 4.740A 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 369 Processing helix chain 'B' and resid 386 through 396 removed outlier: 4.081A 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: 4.917A pdb=" N ARG B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 4.249A 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 451 through 455 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: 4.313A pdb=" N GLU C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.749A pdb=" N VAL C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 283 removed outlier: 4.740A 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 369 Processing helix chain 'C' and resid 386 through 396 removed outlier: 4.081A 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: 4.918A pdb=" N ARG C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR C 441 " --> pdb=" O PHE C 437 " (cutoff:3.500A) removed outlier: 4.249A 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 451 through 455 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: 4.314A pdb=" N GLU D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.748A pdb=" N VAL D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 283 removed outlier: 4.741A 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 369 Processing helix chain 'D' and resid 386 through 396 removed outlier: 4.081A 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: 4.917A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 4.249A 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 451 through 455 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: 4.314A pdb=" N GLU E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.748A pdb=" N VAL E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 4.740A 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 369 Processing helix chain 'E' and resid 386 through 396 removed outlier: 4.081A 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: 4.917A pdb=" N ARG E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR E 441 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 4.249A 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 451 through 455 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: 4.314A pdb=" N GLU F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.702A 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: 3.748A pdb=" N VAL F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 removed outlier: 4.740A 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 369 Processing helix chain 'F' and resid 386 through 396 removed outlier: 4.081A 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: 4.917A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR F 441 " --> pdb=" O PHE F 437 " (cutoff:3.500A) removed outlier: 4.249A 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 451 through 455 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.724A pdb=" N TRP A 460 " --> pdb=" O LYS B 498 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 464 " --> pdb=" O GLU B 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 173 through 174 removed outlier: 6.739A pdb=" N PHE A 497 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS A 498 " --> pdb=" O TRP C 460 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU C 462 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER A 500 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER C 464 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A 502 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.638A pdb=" N TRP B 460 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 464 " --> pdb=" O GLU C 502 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 173 through 174 removed outlier: 3.646A pdb=" N TRP D 460 " --> pdb=" O LYS E 498 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 464 " --> pdb=" O GLU E 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 173 through 174 removed outlier: 6.742A pdb=" N PHE D 497 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS D 498 " --> pdb=" O TRP F 460 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU F 462 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER D 500 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER F 464 " --> pdb=" O SER D 500 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU D 502 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.565A pdb=" N TRP E 460 " --> pdb=" O LYS F 498 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 464 " --> pdb=" O GLU F 502 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 5.12 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: 5579 1.34 - 1.46: 2735 1.46 - 1.57: 9854 1.57 - 1.69: 0 1.69 - 1.80: 102 Bond restraints: 18270 Sorted by residual: bond pdb=" CA TYR B 450 " pdb=" C TYR B 450 " ideal model delta sigma weight residual 1.528 1.508 0.020 1.28e-02 6.10e+03 2.56e+00 bond pdb=" CA TYR A 450 " pdb=" C TYR A 450 " ideal model delta sigma weight residual 1.528 1.508 0.020 1.28e-02 6.10e+03 2.47e+00 bond pdb=" CA TYR F 450 " pdb=" C TYR F 450 " ideal model delta sigma weight residual 1.528 1.509 0.020 1.28e-02 6.10e+03 2.38e+00 bond pdb=" CA TYR C 450 " pdb=" C TYR C 450 " ideal model delta sigma weight residual 1.528 1.509 0.020 1.28e-02 6.10e+03 2.35e+00 bond pdb=" CA TYR D 450 " pdb=" C TYR D 450 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.28e-02 6.10e+03 2.28e+00 ... (remaining 18265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 23763 1.46 - 2.92: 823 2.92 - 4.38: 122 4.38 - 5.84: 42 5.84 - 7.30: 12 Bond angle restraints: 24762 Sorted by residual: angle pdb=" N TYR B 450 " pdb=" CA TYR B 450 " pdb=" C TYR B 450 " ideal model delta sigma weight residual 109.86 117.16 -7.30 1.55e+00 4.16e-01 2.22e+01 angle pdb=" N TYR C 450 " pdb=" CA TYR C 450 " pdb=" C TYR C 450 " ideal model delta sigma weight residual 109.86 117.15 -7.29 1.55e+00 4.16e-01 2.21e+01 angle pdb=" N TYR A 450 " pdb=" CA TYR A 450 " pdb=" C TYR A 450 " ideal model delta sigma weight residual 109.86 117.15 -7.29 1.55e+00 4.16e-01 2.21e+01 angle pdb=" N TYR F 450 " pdb=" CA TYR F 450 " pdb=" C TYR F 450 " ideal model delta sigma weight residual 109.86 117.15 -7.29 1.55e+00 4.16e-01 2.21e+01 angle pdb=" N TYR D 450 " pdb=" CA TYR D 450 " pdb=" C TYR D 450 " ideal model delta sigma weight residual 109.86 117.14 -7.28 1.55e+00 4.16e-01 2.21e+01 ... (remaining 24757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.50: 10098 10.50 - 20.99: 667 20.99 - 31.49: 110 31.49 - 41.99: 35 41.99 - 52.49: 7 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 -138.49 52.49 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA MET F 513 " pdb=" C MET F 513 " pdb=" N ARG F 514 " pdb=" CA ARG F 514 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA MET E 513 " pdb=" C MET E 513 " pdb=" N ARG E 514 " pdb=" CA ARG E 514 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 10914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2333 0.059 - 0.119: 432 0.119 - 0.178: 37 0.178 - 0.237: 0 0.237 - 0.296: 6 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA TYR A 450 " pdb=" N TYR A 450 " pdb=" C TYR A 450 " pdb=" CB TYR A 450 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR F 450 " pdb=" N TYR F 450 " pdb=" C TYR F 450 " pdb=" CB TYR F 450 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA TYR D 450 " pdb=" N TYR D 450 " pdb=" C TYR D 450 " pdb=" CB TYR D 450 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2805 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 260 " -0.011 2.00e-02 2.50e+03 1.82e-02 5.81e+00 pdb=" CG PHE B 260 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 260 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 260 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 260 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 260 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 260 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 260 " 0.011 2.00e-02 2.50e+03 1.82e-02 5.77e+00 pdb=" CG PHE C 260 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C 260 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE C 260 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 260 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 260 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 260 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 260 " 0.011 2.00e-02 2.50e+03 1.80e-02 5.70e+00 pdb=" CG PHE E 260 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE E 260 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE E 260 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 260 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE E 260 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE E 260 " 0.000 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 150 2.60 - 3.18: 15418 3.18 - 3.75: 29073 3.75 - 4.33: 40672 4.33 - 4.90: 67908 Nonbonded interactions: 153221 Sorted by model distance: nonbonded pdb=" SG CYS D 141 " pdb=" SG CYS D 145 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 141 " pdb=" SG CYS B 145 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 141 " pdb=" SG CYS C 145 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS F 141 " pdb=" SG CYS F 145 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS E 141 " pdb=" SG CYS E 145 " model vdw 2.026 3.760 ... (remaining 153216 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: 0.14 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: 6.060 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.350 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.005 0.036 18270 Z= 0.304 Angle : 0.669 7.303 24762 Z= 0.375 Chirality : 0.046 0.296 2808 Planarity : 0.004 0.045 3072 Dihedral : 7.686 45.725 6702 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.76 (0.17), residues: 2136 helix: 0.13 (0.14), residues: 1242 sheet: 0.11 (0.38), residues: 186 loop : -1.71 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 164 HIS 0.008 0.001 HIS F 423 PHE 0.037 0.004 PHE B 260 TYR 0.022 0.002 TYR A 450 ARG 0.006 0.001 ARG E 334 *********************** 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 444 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7389 (tp) cc_final: 0.7136 (mp) REVERT: A 120 PHE cc_start: 0.7245 (t80) cc_final: 0.5751 (m-80) REVERT: A 149 PHE cc_start: 0.7864 (m-80) cc_final: 0.7448 (m-10) REVERT: A 243 GLN cc_start: 0.7922 (tt0) cc_final: 0.7596 (tt0) REVERT: A 278 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8437 (mmtp) REVERT: A 290 LEU cc_start: 0.8455 (mt) cc_final: 0.8188 (mp) REVERT: A 385 MET cc_start: 0.8132 (ttp) cc_final: 0.7842 (ttm) REVERT: A 404 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7846 (mmtt) REVERT: A 452 LYS cc_start: 0.8202 (mttt) cc_final: 0.7169 (mppt) REVERT: A 513 MET cc_start: 0.6483 (mmp) cc_final: 0.5387 (mmt) REVERT: B 149 PHE cc_start: 0.7948 (m-80) cc_final: 0.7659 (m-80) REVERT: B 186 MET cc_start: 0.7212 (mtt) cc_final: 0.6931 (mtp) REVERT: B 208 ARG cc_start: 0.6196 (mtt-85) cc_final: 0.5793 (mtt180) REVERT: B 245 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7761 (mp10) REVERT: B 371 LYS cc_start: 0.7719 (tttt) cc_final: 0.7436 (ttpt) REVERT: B 404 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7907 (mmtt) REVERT: B 452 LYS cc_start: 0.8263 (mttt) cc_final: 0.7361 (mppt) REVERT: B 473 LYS cc_start: 0.7651 (pttp) cc_final: 0.7288 (pttm) REVERT: B 481 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7549 (mttt) REVERT: C 118 LEU cc_start: 0.7538 (tp) cc_final: 0.7233 (mp) REVERT: C 120 PHE cc_start: 0.7076 (t80) cc_final: 0.5422 (m-80) REVERT: C 186 MET cc_start: 0.7146 (mtt) cc_final: 0.6864 (mtp) REVERT: C 217 GLN cc_start: 0.7219 (mt0) cc_final: 0.6708 (mt0) REVERT: C 273 VAL cc_start: 0.8479 (t) cc_final: 0.8262 (m) REVERT: C 353 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.7038 (mtm-85) REVERT: C 371 LYS cc_start: 0.7808 (tttt) cc_final: 0.7577 (ttpt) REVERT: C 404 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7770 (mmtt) REVERT: C 452 LYS cc_start: 0.8271 (mttt) cc_final: 0.7411 (mppt) REVERT: C 473 LYS cc_start: 0.7784 (pttp) cc_final: 0.7311 (pttm) REVERT: C 513 MET cc_start: 0.6503 (mmp) cc_final: 0.5106 (mmt) REVERT: D 118 LEU cc_start: 0.7451 (tp) cc_final: 0.7124 (mp) REVERT: D 120 PHE cc_start: 0.7188 (t80) cc_final: 0.5728 (m-80) REVERT: D 149 PHE cc_start: 0.7815 (m-80) cc_final: 0.7433 (m-10) REVERT: D 290 LEU cc_start: 0.8458 (mt) cc_final: 0.8207 (mp) REVERT: D 385 MET cc_start: 0.8145 (ttp) cc_final: 0.7852 (ttm) REVERT: D 404 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7878 (mmtt) REVERT: D 452 LYS cc_start: 0.8246 (mttt) cc_final: 0.7277 (mppt) REVERT: D 513 MET cc_start: 0.6455 (mmp) cc_final: 0.5435 (mmt) REVERT: E 120 PHE cc_start: 0.7153 (t80) cc_final: 0.5675 (m-80) REVERT: E 186 MET cc_start: 0.7216 (mtt) cc_final: 0.6910 (mtp) REVERT: E 217 GLN cc_start: 0.7182 (mt0) cc_final: 0.6667 (mt0) REVERT: E 290 LEU cc_start: 0.8429 (mt) cc_final: 0.8100 (mt) REVERT: E 371 LYS cc_start: 0.7749 (tttt) cc_final: 0.7459 (ttpt) REVERT: E 404 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7936 (mmtt) REVERT: E 452 LYS cc_start: 0.8256 (mttt) cc_final: 0.7280 (mppt) REVERT: E 473 LYS cc_start: 0.7926 (pttp) cc_final: 0.7528 (pttm) REVERT: E 513 MET cc_start: 0.6547 (mmp) cc_final: 0.5215 (mmp) REVERT: F 118 LEU cc_start: 0.7470 (tp) cc_final: 0.7209 (mp) REVERT: F 120 PHE cc_start: 0.7272 (t80) cc_final: 0.5553 (m-10) REVERT: F 186 MET cc_start: 0.7134 (mtt) cc_final: 0.6904 (mtp) REVERT: F 217 GLN cc_start: 0.7215 (mt0) cc_final: 0.6701 (mt0) REVERT: F 278 LYS cc_start: 0.8565 (mmtp) cc_final: 0.8348 (mmmt) REVERT: F 353 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7050 (mtm-85) REVERT: F 404 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7744 (mmtt) REVERT: F 452 LYS cc_start: 0.8254 (mttt) cc_final: 0.7349 (mppt) REVERT: F 473 LYS cc_start: 0.7909 (pttp) cc_final: 0.7450 (pttm) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 1.6371 time to fit residues: 796.7794 Evaluate side-chains 281 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 196 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 339 ASN A 403 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN B 217 GLN B 403 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 243 GLN D 339 ASN D 403 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.164454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.129160 restraints weight = 19298.490| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.59 r_work: 0.3276 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18270 Z= 0.247 Angle : 0.592 7.594 24762 Z= 0.298 Chirality : 0.043 0.185 2808 Planarity : 0.004 0.039 3072 Dihedral : 4.389 19.075 2418 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.90 % Allowed : 9.76 % Favored : 88.34 % 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: 0.86 (0.18), residues: 2136 helix: 1.50 (0.14), residues: 1248 sheet: 0.34 (0.39), residues: 186 loop : -1.04 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 164 HIS 0.006 0.001 HIS A 423 PHE 0.020 0.003 PHE C 260 TYR 0.015 0.002 TYR B 342 ARG 0.005 0.000 ARG F 372 *********************** 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 358 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 322 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7522 (tp) cc_final: 0.7143 (mp) REVERT: A 120 PHE cc_start: 0.7168 (t80) cc_final: 0.5476 (m-80) REVERT: A 158 ILE cc_start: 0.8564 (mt) cc_final: 0.8332 (mm) REVERT: A 170 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.5896 (mmt-90) REVERT: A 243 GLN cc_start: 0.8197 (tt0) cc_final: 0.7407 (tt0) REVERT: A 245 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.6806 (mp10) REVERT: A 333 ARG cc_start: 0.6925 (mtm180) cc_final: 0.6381 (tpm170) REVERT: A 385 MET cc_start: 0.8248 (ttp) cc_final: 0.7739 (ttm) REVERT: A 404 LYS cc_start: 0.8524 (mtpp) cc_final: 0.7929 (mmtt) REVERT: A 452 LYS cc_start: 0.7744 (mttt) cc_final: 0.6409 (mppt) REVERT: A 513 MET cc_start: 0.7256 (mmp) cc_final: 0.6500 (mmp) REVERT: B 120 PHE cc_start: 0.6807 (t80) cc_final: 0.5139 (m-80) REVERT: B 149 PHE cc_start: 0.7900 (m-80) cc_final: 0.7631 (m-80) REVERT: B 177 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7599 (mtp180) REVERT: B 186 MET cc_start: 0.7985 (mtt) cc_final: 0.7621 (mtp) REVERT: B 290 LEU cc_start: 0.8451 (mt) cc_final: 0.8144 (mt) REVERT: B 341 TYR cc_start: 0.8610 (t80) cc_final: 0.8334 (t80) REVERT: B 404 LYS cc_start: 0.8521 (mtpp) cc_final: 0.7894 (mmtt) REVERT: B 473 LYS cc_start: 0.8036 (pttp) cc_final: 0.7461 (pttm) REVERT: C 120 PHE cc_start: 0.6965 (t80) cc_final: 0.5142 (m-80) REVERT: C 160 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8402 (mt) REVERT: C 186 MET cc_start: 0.8104 (mtt) cc_final: 0.7844 (mtp) REVERT: C 255 ASP cc_start: 0.8388 (p0) cc_final: 0.8164 (p0) REVERT: C 371 LYS cc_start: 0.7719 (tttt) cc_final: 0.7316 (ttpt) REVERT: C 398 MET cc_start: 0.8804 (ptm) cc_final: 0.8584 (ptm) REVERT: C 404 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7775 (mmtt) REVERT: C 417 MET cc_start: 0.7787 (tmm) cc_final: 0.7540 (tmm) REVERT: C 470 ASN cc_start: 0.8151 (m110) cc_final: 0.7932 (m110) REVERT: C 473 LYS cc_start: 0.8248 (pttp) cc_final: 0.7544 (pttm) REVERT: C 502 GLU cc_start: 0.7154 (tt0) cc_final: 0.6944 (tp30) REVERT: C 513 MET cc_start: 0.7221 (mmp) cc_final: 0.5725 (mmt) REVERT: D 118 LEU cc_start: 0.7607 (tp) cc_final: 0.7253 (mt) REVERT: D 120 PHE cc_start: 0.7108 (t80) cc_final: 0.5491 (m-80) REVERT: D 149 PHE cc_start: 0.7726 (m-80) cc_final: 0.7331 (m-10) REVERT: D 158 ILE cc_start: 0.8585 (mt) cc_final: 0.8328 (mm) REVERT: D 170 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.5983 (mmt-90) REVERT: D 290 LEU cc_start: 0.8501 (mt) cc_final: 0.8244 (mp) REVERT: D 333 ARG cc_start: 0.6884 (mtm180) cc_final: 0.6368 (tpm170) REVERT: D 385 MET cc_start: 0.8407 (ttp) cc_final: 0.7963 (ttm) REVERT: D 404 LYS cc_start: 0.8489 (mtpp) cc_final: 0.7939 (mmtt) REVERT: D 452 LYS cc_start: 0.7800 (mttt) cc_final: 0.6474 (mppt) REVERT: D 513 MET cc_start: 0.7213 (mmp) cc_final: 0.6094 (mmt) REVERT: E 120 PHE cc_start: 0.6970 (t80) cc_final: 0.5375 (m-80) REVERT: E 177 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7580 (mtp180) REVERT: E 186 MET cc_start: 0.7995 (mtt) cc_final: 0.7634 (mtp) REVERT: E 217 GLN cc_start: 0.7227 (mt0) cc_final: 0.6694 (mt0) REVERT: E 290 LEU cc_start: 0.8450 (mt) cc_final: 0.8071 (mt) REVERT: E 341 TYR cc_start: 0.8591 (t80) cc_final: 0.8382 (t80) REVERT: E 354 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8070 (mtmm) REVERT: E 403 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7457 (tm130) REVERT: E 404 LYS cc_start: 0.8560 (mtpp) cc_final: 0.7862 (mmtt) REVERT: E 473 LYS cc_start: 0.8176 (pttp) cc_final: 0.7548 (pttm) REVERT: E 502 GLU cc_start: 0.7529 (tt0) cc_final: 0.6978 (tp30) REVERT: E 513 MET cc_start: 0.6973 (mmp) cc_final: 0.5699 (mmt) REVERT: F 118 LEU cc_start: 0.7453 (tp) cc_final: 0.7052 (mp) REVERT: F 120 PHE cc_start: 0.7015 (t80) cc_final: 0.5231 (m-80) REVERT: F 186 MET cc_start: 0.8098 (mtt) cc_final: 0.7845 (mtp) REVERT: F 217 GLN cc_start: 0.7285 (mt0) cc_final: 0.6725 (mt0) REVERT: F 255 ASP cc_start: 0.8400 (p0) cc_final: 0.8160 (p0) REVERT: F 353 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7726 (mtm-85) REVERT: F 398 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8549 (ptm) REVERT: F 404 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7788 (mmtt) REVERT: F 416 THR cc_start: 0.8375 (p) cc_final: 0.8010 (t) REVERT: F 473 LYS cc_start: 0.8237 (pttp) cc_final: 0.7578 (pttm) REVERT: F 501 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7052 (tt0) outliers start: 36 outliers final: 11 residues processed: 339 average time/residue: 1.4959 time to fit residues: 560.4877 Evaluate side-chains 302 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 284 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 513 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 185 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 403 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN B 217 GLN B 243 GLN B 403 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN C 217 GLN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 403 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 403 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.162893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.127117 restraints weight = 19235.807| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.62 r_work: 0.3255 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18270 Z= 0.256 Angle : 0.574 6.906 24762 Z= 0.287 Chirality : 0.042 0.211 2808 Planarity : 0.004 0.042 3072 Dihedral : 4.262 18.063 2418 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.53 % Allowed : 11.45 % Favored : 86.02 % 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: 1.39 (0.18), residues: 2136 helix: 1.90 (0.15), residues: 1248 sheet: 0.49 (0.39), residues: 186 loop : -0.74 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 164 HIS 0.005 0.001 HIS D 423 PHE 0.022 0.002 PHE E 367 TYR 0.015 0.002 TYR D 450 ARG 0.005 0.000 ARG B 454 *********************** 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 342 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7591 (tp) cc_final: 0.7278 (mt) REVERT: A 120 PHE cc_start: 0.7123 (t80) cc_final: 0.5484 (m-80) REVERT: A 158 ILE cc_start: 0.8561 (mt) cc_final: 0.8273 (mm) REVERT: A 170 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6026 (mmt-90) REVERT: A 243 GLN cc_start: 0.8224 (tt0) cc_final: 0.7494 (tt0) REVERT: A 245 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.6933 (mp10) REVERT: A 333 ARG cc_start: 0.7018 (mtm180) cc_final: 0.6398 (tpm170) REVERT: A 385 MET cc_start: 0.8287 (ttp) cc_final: 0.7628 (ttm) REVERT: A 404 LYS cc_start: 0.8534 (mtpp) cc_final: 0.7974 (mmtt) REVERT: A 418 GLU cc_start: 0.7891 (tp30) cc_final: 0.7593 (tp30) REVERT: A 452 LYS cc_start: 0.7639 (mttt) cc_final: 0.6365 (mppt) REVERT: A 473 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7630 (pttm) REVERT: B 120 PHE cc_start: 0.6898 (t80) cc_final: 0.5190 (m-80) REVERT: B 149 PHE cc_start: 0.7892 (m-80) cc_final: 0.7608 (m-80) REVERT: B 177 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7548 (mtp180) REVERT: B 186 MET cc_start: 0.8127 (mtt) cc_final: 0.7743 (mtp) REVERT: B 341 TYR cc_start: 0.8665 (t80) cc_final: 0.8444 (t80) REVERT: B 365 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: B 388 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.6790 (ttt90) REVERT: B 404 LYS cc_start: 0.8559 (mtpp) cc_final: 0.7938 (mmtt) REVERT: B 473 LYS cc_start: 0.8094 (pttp) cc_final: 0.7553 (pttm) REVERT: C 120 PHE cc_start: 0.6875 (t80) cc_final: 0.5142 (m-80) REVERT: C 186 MET cc_start: 0.8152 (mtt) cc_final: 0.7932 (mtp) REVERT: C 217 GLN cc_start: 0.7312 (mt0) cc_final: 0.6717 (mt0) REVERT: C 245 GLN cc_start: 0.8573 (mm110) cc_final: 0.8368 (mm110) REVERT: C 371 LYS cc_start: 0.7810 (tttt) cc_final: 0.7363 (ttpt) REVERT: C 404 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7807 (mmtt) REVERT: C 417 MET cc_start: 0.7835 (tmm) cc_final: 0.7543 (tmm) REVERT: C 473 LYS cc_start: 0.8298 (pttp) cc_final: 0.7628 (pttm) REVERT: C 502 GLU cc_start: 0.7265 (tt0) cc_final: 0.6940 (tp30) REVERT: D 118 LEU cc_start: 0.7610 (tp) cc_final: 0.7244 (mt) REVERT: D 120 PHE cc_start: 0.7085 (t80) cc_final: 0.5463 (m-80) REVERT: D 158 ILE cc_start: 0.8580 (mt) cc_final: 0.8307 (mm) REVERT: D 170 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6049 (mmt-90) REVERT: D 245 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: D 290 LEU cc_start: 0.8615 (mt) cc_final: 0.8365 (mp) REVERT: D 333 ARG cc_start: 0.6977 (mtm180) cc_final: 0.6382 (tpm170) REVERT: D 385 MET cc_start: 0.8390 (ttp) cc_final: 0.7789 (ttm) REVERT: D 404 LYS cc_start: 0.8500 (mtpp) cc_final: 0.7980 (mmtt) REVERT: D 418 GLU cc_start: 0.7889 (tp30) cc_final: 0.7580 (tp30) REVERT: D 452 LYS cc_start: 0.7706 (mttt) cc_final: 0.6463 (mppt) REVERT: D 473 LYS cc_start: 0.8180 (ptmt) cc_final: 0.7606 (pttm) REVERT: D 513 MET cc_start: 0.7247 (mmp) cc_final: 0.6249 (mmt) REVERT: E 120 PHE cc_start: 0.6988 (t80) cc_final: 0.5412 (m-80) REVERT: E 177 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7617 (mtp180) REVERT: E 186 MET cc_start: 0.8101 (mtt) cc_final: 0.7720 (mtp) REVERT: E 217 GLN cc_start: 0.7275 (mt0) cc_final: 0.6761 (mt0) REVERT: E 290 LEU cc_start: 0.8491 (mt) cc_final: 0.8114 (mt) REVERT: E 341 TYR cc_start: 0.8585 (t80) cc_final: 0.8384 (t80) REVERT: E 365 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: E 371 LYS cc_start: 0.7908 (tttt) cc_final: 0.7397 (ttpt) REVERT: E 388 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6514 (ttt90) REVERT: E 404 LYS cc_start: 0.8552 (mtpp) cc_final: 0.7915 (mmtt) REVERT: E 473 LYS cc_start: 0.8206 (pttp) cc_final: 0.7624 (pttm) REVERT: E 502 GLU cc_start: 0.7494 (tt0) cc_final: 0.6976 (tp30) REVERT: F 120 PHE cc_start: 0.6885 (t80) cc_final: 0.5072 (m-80) REVERT: F 160 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8450 (mt) REVERT: F 177 ARG cc_start: 0.8237 (mtt180) cc_final: 0.7616 (mtp180) REVERT: F 186 MET cc_start: 0.8155 (mtt) cc_final: 0.7944 (mtp) REVERT: F 217 GLN cc_start: 0.7310 (mt0) cc_final: 0.6763 (mt0) REVERT: F 255 ASP cc_start: 0.8460 (p0) cc_final: 0.8259 (p0) REVERT: F 349 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7281 (tm-30) REVERT: F 388 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6712 (ttt90) REVERT: F 398 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8481 (ptm) REVERT: F 404 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7807 (mmtt) REVERT: F 422 GLN cc_start: 0.7672 (mt0) cc_final: 0.7109 (mm110) REVERT: F 473 LYS cc_start: 0.8223 (pttp) cc_final: 0.7558 (pttm) REVERT: F 501 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: F 502 GLU cc_start: 0.7248 (tt0) cc_final: 0.6916 (tp30) REVERT: F 513 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7239 (tpp) outliers start: 48 outliers final: 13 residues processed: 317 average time/residue: 1.5841 time to fit residues: 552.0713 Evaluate side-chains 305 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 388 ARG Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 513 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 215 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 403 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 243 GLN B 403 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 403 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 470 ASN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.177745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146357 restraints weight = 19789.062| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.49 r_work: 0.3523 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2367 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= 0.233 Angle : 0.551 6.920 24762 Z= 0.275 Chirality : 0.041 0.144 2808 Planarity : 0.004 0.044 3072 Dihedral : 4.134 17.385 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.22 % Allowed : 11.87 % Favored : 84.92 % 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: 1.73 (0.18), residues: 2136 helix: 2.16 (0.15), residues: 1248 sheet: 0.61 (0.40), residues: 186 loop : -0.57 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 274 HIS 0.005 0.001 HIS A 423 PHE 0.017 0.002 PHE E 367 TYR 0.013 0.002 TYR A 450 ARG 0.005 0.000 ARG C 350 *********************** 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 365 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 304 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7680 (tp) cc_final: 0.7342 (mt) REVERT: A 120 PHE cc_start: 0.7157 (t80) cc_final: 0.5580 (m-80) REVERT: A 158 ILE cc_start: 0.8649 (mt) cc_final: 0.8378 (mm) REVERT: A 170 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6195 (mmt-90) REVERT: A 196 TYR cc_start: 0.8161 (m-80) cc_final: 0.7520 (m-80) REVERT: A 243 GLN cc_start: 0.8223 (tt0) cc_final: 0.7521 (tt0) REVERT: A 245 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7029 (mp10) REVERT: A 333 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6471 (tpm170) REVERT: A 371 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7482 (ttpt) REVERT: A 385 MET cc_start: 0.8539 (ttp) cc_final: 0.8116 (ttm) REVERT: A 404 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8127 (mmtt) REVERT: A 418 GLU cc_start: 0.7812 (tp30) cc_final: 0.7580 (tp30) REVERT: A 452 LYS cc_start: 0.7681 (mttt) cc_final: 0.6556 (mppt) REVERT: A 473 LYS cc_start: 0.8317 (ptmt) cc_final: 0.7765 (pttm) REVERT: B 120 PHE cc_start: 0.6903 (t80) cc_final: 0.5205 (m-80) REVERT: B 158 ILE cc_start: 0.8757 (mt) cc_final: 0.8488 (mp) REVERT: B 177 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7637 (mtp180) REVERT: B 186 MET cc_start: 0.8199 (mtt) cc_final: 0.7877 (mtp) REVERT: B 365 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 388 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.6812 (ttt90) REVERT: B 398 MET cc_start: 0.8902 (ptm) cc_final: 0.8573 (ptm) REVERT: B 404 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8102 (mmtt) REVERT: B 473 LYS cc_start: 0.8236 (pttp) cc_final: 0.7679 (pttm) REVERT: C 120 PHE cc_start: 0.6892 (t80) cc_final: 0.5146 (m-80) REVERT: C 160 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8570 (mt) REVERT: C 177 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7585 (mtp180) REVERT: C 217 GLN cc_start: 0.7314 (mt0) cc_final: 0.6752 (mt0) REVERT: C 371 LYS cc_start: 0.7842 (tttt) cc_final: 0.7428 (ttpt) REVERT: C 404 LYS cc_start: 0.8417 (mtpp) cc_final: 0.7985 (mmtt) REVERT: C 417 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7588 (tmm) REVERT: C 473 LYS cc_start: 0.8370 (pttp) cc_final: 0.7767 (pttm) REVERT: C 502 GLU cc_start: 0.7284 (tt0) cc_final: 0.7007 (tp30) REVERT: D 118 LEU cc_start: 0.7726 (tp) cc_final: 0.7328 (mt) REVERT: D 120 PHE cc_start: 0.7133 (t80) cc_final: 0.5570 (m-80) REVERT: D 158 ILE cc_start: 0.8658 (mt) cc_final: 0.8378 (mm) REVERT: D 170 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6191 (mmt-90) REVERT: D 196 TYR cc_start: 0.7975 (m-80) cc_final: 0.7761 (m-80) REVERT: D 245 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: D 290 LEU cc_start: 0.8633 (mt) cc_final: 0.8361 (mp) REVERT: D 333 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6424 (tpm170) REVERT: D 349 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7576 (mp0) REVERT: D 371 LYS cc_start: 0.7757 (ttpt) cc_final: 0.7539 (ttpt) REVERT: D 385 MET cc_start: 0.8461 (ttp) cc_final: 0.7819 (ttm) REVERT: D 392 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8184 (tp40) REVERT: D 404 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8106 (mmtt) REVERT: D 418 GLU cc_start: 0.7853 (tp30) cc_final: 0.7629 (tp30) REVERT: D 452 LYS cc_start: 0.7692 (mttt) cc_final: 0.6562 (mppt) REVERT: D 473 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7781 (pttm) REVERT: D 513 MET cc_start: 0.6777 (mmp) cc_final: 0.5697 (mmt) REVERT: E 120 PHE cc_start: 0.6937 (t80) cc_final: 0.5366 (m-80) REVERT: E 177 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7632 (mtp180) REVERT: E 186 MET cc_start: 0.8183 (mtt) cc_final: 0.7865 (mtp) REVERT: E 217 GLN cc_start: 0.7357 (mt0) cc_final: 0.6860 (mt0) REVERT: E 282 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: E 290 LEU cc_start: 0.8496 (mt) cc_final: 0.8135 (mt) REVERT: E 365 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: E 371 LYS cc_start: 0.7838 (tttt) cc_final: 0.7353 (ttpt) REVERT: E 388 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6581 (ttt90) REVERT: E 404 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8064 (mmtt) REVERT: E 473 LYS cc_start: 0.8247 (pttp) cc_final: 0.7690 (pttm) REVERT: E 502 GLU cc_start: 0.7424 (tt0) cc_final: 0.7063 (tp30) REVERT: F 120 PHE cc_start: 0.6884 (t80) cc_final: 0.5138 (m-80) REVERT: F 160 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8575 (mt) REVERT: F 177 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7594 (mtp180) REVERT: F 217 GLN cc_start: 0.7348 (mt0) cc_final: 0.6816 (mt0) REVERT: F 349 GLU cc_start: 0.7264 (tm-30) cc_final: 0.7016 (tm-30) REVERT: F 371 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7558 (mtmt) REVERT: F 404 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8011 (mmtt) REVERT: F 473 LYS cc_start: 0.8339 (pttp) cc_final: 0.7786 (pttm) REVERT: F 502 GLU cc_start: 0.7289 (tt0) cc_final: 0.7052 (tp30) outliers start: 61 outliers final: 20 residues processed: 333 average time/residue: 1.5760 time to fit residues: 576.7287 Evaluate side-chains 321 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 289 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 185 optimal weight: 0.9980 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 217 GLN A 403 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 243 GLN B 403 GLN B 470 ASN C 403 GLN D 217 GLN D 245 GLN D 403 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 470 ASN F 403 GLN F 470 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.168809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134694 restraints weight = 20183.955| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.64 r_work: 0.3482 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18270 Z= 0.267 Angle : 0.565 7.095 24762 Z= 0.281 Chirality : 0.042 0.214 2808 Planarity : 0.004 0.046 3072 Dihedral : 4.163 17.371 2418 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.16 % Allowed : 12.24 % Favored : 84.60 % 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: 1.79 (0.18), residues: 2136 helix: 2.18 (0.14), residues: 1248 sheet: 0.68 (0.41), residues: 186 loop : -0.49 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 274 HIS 0.005 0.001 HIS D 423 PHE 0.018 0.002 PHE E 367 TYR 0.017 0.002 TYR D 280 ARG 0.005 0.000 ARG C 350 *********************** 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 353 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 2.006 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7668 (tp) cc_final: 0.7240 (mp) REVERT: A 120 PHE cc_start: 0.7248 (t80) cc_final: 0.5546 (m-80) REVERT: A 158 ILE cc_start: 0.8659 (mt) cc_final: 0.8371 (mm) REVERT: A 170 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6150 (mmt-90) REVERT: A 196 TYR cc_start: 0.8192 (m-80) cc_final: 0.7586 (m-80) REVERT: A 243 GLN cc_start: 0.8166 (tt0) cc_final: 0.7492 (tt0) REVERT: A 245 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7067 (mp10) REVERT: A 333 ARG cc_start: 0.7057 (mtm180) cc_final: 0.6417 (tpm170) REVERT: A 349 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7555 (mp0) REVERT: A 371 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7541 (ttmt) REVERT: A 385 MET cc_start: 0.8498 (ttp) cc_final: 0.7988 (ttm) REVERT: A 388 ARG cc_start: 0.8031 (tpt170) cc_final: 0.7687 (ttm-80) REVERT: A 404 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8127 (mmtt) REVERT: A 452 LYS cc_start: 0.7664 (mttt) cc_final: 0.6513 (mppt) REVERT: A 473 LYS cc_start: 0.8392 (ptmt) cc_final: 0.7822 (pttm) REVERT: B 120 PHE cc_start: 0.6901 (t80) cc_final: 0.5171 (m-80) REVERT: B 177 ARG cc_start: 0.8270 (mtt180) cc_final: 0.7656 (mtp180) REVERT: B 186 MET cc_start: 0.8244 (mtt) cc_final: 0.7906 (mtp) REVERT: B 217 GLN cc_start: 0.7229 (mt0) cc_final: 0.6746 (mt0) REVERT: B 341 TYR cc_start: 0.8783 (t80) cc_final: 0.8578 (t80) REVERT: B 365 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: B 388 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.6845 (ttt90) REVERT: B 404 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8061 (mmtt) REVERT: B 473 LYS cc_start: 0.8250 (pttp) cc_final: 0.7735 (pttm) REVERT: C 120 PHE cc_start: 0.6906 (t80) cc_final: 0.5117 (m-80) REVERT: C 160 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8595 (mt) REVERT: C 177 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7557 (mtp180) REVERT: C 217 GLN cc_start: 0.7330 (mt0) cc_final: 0.6773 (mt0) REVERT: C 371 LYS cc_start: 0.8063 (tttt) cc_final: 0.7647 (ttpt) REVERT: C 404 LYS cc_start: 0.8426 (mtpp) cc_final: 0.7983 (mmtt) REVERT: C 417 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7692 (tmm) REVERT: C 473 LYS cc_start: 0.8335 (pttp) cc_final: 0.7742 (pttm) REVERT: D 118 LEU cc_start: 0.7711 (tp) cc_final: 0.7253 (mp) REVERT: D 120 PHE cc_start: 0.7164 (t80) cc_final: 0.5537 (m-80) REVERT: D 158 ILE cc_start: 0.8677 (mt) cc_final: 0.8386 (mm) REVERT: D 170 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6149 (mmt-90) REVERT: D 196 TYR cc_start: 0.8077 (m-80) cc_final: 0.7706 (m-80) REVERT: D 290 LEU cc_start: 0.8616 (mt) cc_final: 0.8364 (mp) REVERT: D 333 ARG cc_start: 0.7068 (mtm180) cc_final: 0.6404 (tpm170) REVERT: D 371 LYS cc_start: 0.7810 (ttpt) cc_final: 0.7576 (ttmt) REVERT: D 385 MET cc_start: 0.8508 (ttp) cc_final: 0.8047 (ttm) REVERT: D 404 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8067 (mmtt) REVERT: D 452 LYS cc_start: 0.7665 (mttt) cc_final: 0.6497 (mppt) REVERT: D 473 LYS cc_start: 0.8321 (ptmt) cc_final: 0.7757 (pttm) REVERT: E 120 PHE cc_start: 0.6958 (t80) cc_final: 0.5393 (m-80) REVERT: E 177 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7672 (mtp180) REVERT: E 186 MET cc_start: 0.8229 (mtt) cc_final: 0.7892 (mtp) REVERT: E 217 GLN cc_start: 0.7327 (mt0) cc_final: 0.6813 (mt0) REVERT: E 371 LYS cc_start: 0.7868 (tttt) cc_final: 0.7401 (ttpt) REVERT: E 388 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6607 (ttt90) REVERT: E 404 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8035 (mmtt) REVERT: E 465 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: E 473 LYS cc_start: 0.8249 (pttp) cc_final: 0.7734 (pttm) REVERT: E 502 GLU cc_start: 0.7556 (tt0) cc_final: 0.7033 (tp30) REVERT: F 120 PHE cc_start: 0.6982 (t80) cc_final: 0.5143 (m-80) REVERT: F 160 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8595 (mt) REVERT: F 177 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7673 (mtp180) REVERT: F 217 GLN cc_start: 0.7365 (mt0) cc_final: 0.6825 (mt0) REVERT: F 349 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7103 (tm-30) REVERT: F 371 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7676 (mtmt) REVERT: F 404 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8018 (mmtt) REVERT: F 473 LYS cc_start: 0.8393 (pttp) cc_final: 0.7791 (pttm) REVERT: F 501 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7300 (tt0) outliers start: 60 outliers final: 22 residues processed: 326 average time/residue: 1.6372 time to fit residues: 584.1857 Evaluate side-chains 315 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 465 GLU Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 501 GLU 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: 0.5980 chunk 155 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 215 optimal weight: 0.0070 chunk 65 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 403 GLN B 403 GLN B 470 ASN C 245 GLN D 217 GLN D 403 GLN E 403 GLN F 470 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.171301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137175 restraints weight = 19725.619| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.55 r_work: 0.3410 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18270 Z= 0.173 Angle : 0.510 6.791 24762 Z= 0.256 Chirality : 0.039 0.148 2808 Planarity : 0.004 0.045 3072 Dihedral : 3.895 15.190 2418 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.48 % Allowed : 13.34 % Favored : 84.18 % 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: 2.14 (0.19), residues: 2136 helix: 2.47 (0.15), residues: 1248 sheet: 1.07 (0.41), residues: 180 loop : -0.44 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 274 HIS 0.003 0.001 HIS A 423 PHE 0.013 0.002 PHE C 149 TYR 0.011 0.001 TYR B 450 ARG 0.006 0.000 ARG C 350 *********************** 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 359 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 312 time to evaluate : 1.972 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7713 (tp) cc_final: 0.7365 (mt) REVERT: A 120 PHE cc_start: 0.7057 (t80) cc_final: 0.5466 (m-80) REVERT: A 158 ILE cc_start: 0.8641 (mt) cc_final: 0.8355 (mm) REVERT: A 170 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6125 (mmt-90) REVERT: A 196 TYR cc_start: 0.8155 (m-80) cc_final: 0.7634 (m-80) REVERT: A 243 GLN cc_start: 0.8093 (tt0) cc_final: 0.7454 (tt0) REVERT: A 245 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 333 ARG cc_start: 0.7137 (mtm180) cc_final: 0.6482 (tpm170) REVERT: A 385 MET cc_start: 0.8401 (ttp) cc_final: 0.7664 (ttm) REVERT: A 388 ARG cc_start: 0.8032 (tpt170) cc_final: 0.7731 (ttm-80) REVERT: A 404 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8031 (mmtt) REVERT: A 431 ASP cc_start: 0.8470 (m-30) cc_final: 0.8205 (m-30) REVERT: A 452 LYS cc_start: 0.7713 (mttt) cc_final: 0.6611 (mppt) REVERT: A 473 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7781 (pttm) REVERT: B 120 PHE cc_start: 0.6883 (t80) cc_final: 0.5173 (m-80) REVERT: B 177 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7540 (mtp180) REVERT: B 186 MET cc_start: 0.8152 (mtt) cc_final: 0.7868 (mtp) REVERT: B 217 GLN cc_start: 0.7215 (mt0) cc_final: 0.6753 (mt0) REVERT: B 339 ASN cc_start: 0.8163 (t0) cc_final: 0.7952 (t0) REVERT: B 341 TYR cc_start: 0.8695 (t80) cc_final: 0.8473 (t80) REVERT: B 388 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.6824 (ttt90) REVERT: B 398 MET cc_start: 0.8975 (ptm) cc_final: 0.8724 (ptm) REVERT: B 404 LYS cc_start: 0.8596 (mtpp) cc_final: 0.7992 (mmtt) REVERT: B 473 LYS cc_start: 0.8198 (pttp) cc_final: 0.7740 (pttm) REVERT: C 120 PHE cc_start: 0.6852 (t80) cc_final: 0.5199 (m-80) REVERT: C 160 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8556 (mt) REVERT: C 217 GLN cc_start: 0.7245 (mt0) cc_final: 0.6708 (mt0) REVERT: C 339 ASN cc_start: 0.8149 (t0) cc_final: 0.7942 (t160) REVERT: C 371 LYS cc_start: 0.7905 (tttt) cc_final: 0.7531 (ttpt) REVERT: C 404 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7862 (mmtt) REVERT: C 473 LYS cc_start: 0.8316 (pttp) cc_final: 0.7857 (pttm) REVERT: D 118 LEU cc_start: 0.7703 (tp) cc_final: 0.7313 (mt) REVERT: D 120 PHE cc_start: 0.7033 (t80) cc_final: 0.5448 (m-80) REVERT: D 158 ILE cc_start: 0.8635 (mt) cc_final: 0.8344 (mm) REVERT: D 170 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6104 (mmt-90) REVERT: D 196 TYR cc_start: 0.8078 (m-80) cc_final: 0.7841 (m-80) REVERT: D 217 GLN cc_start: 0.7555 (mt0) cc_final: 0.7094 (mt0) REVERT: D 290 LEU cc_start: 0.8515 (mt) cc_final: 0.8233 (mp) REVERT: D 333 ARG cc_start: 0.7190 (mtm180) cc_final: 0.6474 (tpm170) REVERT: D 385 MET cc_start: 0.8414 (ttp) cc_final: 0.7712 (ttm) REVERT: D 388 ARG cc_start: 0.8007 (tpt170) cc_final: 0.7724 (ttm-80) REVERT: D 404 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8044 (mmtt) REVERT: D 431 ASP cc_start: 0.8477 (m-30) cc_final: 0.8222 (m-30) REVERT: D 452 LYS cc_start: 0.7729 (mttt) cc_final: 0.6594 (mppt) REVERT: D 473 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7740 (pttm) REVERT: E 120 PHE cc_start: 0.6863 (t80) cc_final: 0.5317 (m-80) REVERT: E 186 MET cc_start: 0.8149 (mtt) cc_final: 0.7864 (mtp) REVERT: E 217 GLN cc_start: 0.7371 (mt0) cc_final: 0.6879 (mt0) REVERT: E 371 LYS cc_start: 0.7580 (tttt) cc_final: 0.7122 (ttpt) REVERT: E 388 ARG cc_start: 0.7850 (ttt90) cc_final: 0.6748 (ttt90) REVERT: E 403 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7528 (tm130) REVERT: E 404 LYS cc_start: 0.8596 (mtpp) cc_final: 0.7970 (mmtt) REVERT: E 465 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: E 473 LYS cc_start: 0.8176 (pttp) cc_final: 0.7705 (pttm) REVERT: E 502 GLU cc_start: 0.7312 (tt0) cc_final: 0.6960 (tp30) REVERT: F 120 PHE cc_start: 0.6913 (t80) cc_final: 0.5167 (m-80) REVERT: F 126 PHE cc_start: 0.8018 (m-10) cc_final: 0.7651 (m-10) REVERT: F 160 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8572 (mt) REVERT: F 217 GLN cc_start: 0.7320 (mt0) cc_final: 0.6806 (mt0) REVERT: F 349 GLU cc_start: 0.7307 (tm-30) cc_final: 0.7087 (tm-30) REVERT: F 371 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7633 (mtmt) REVERT: F 404 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7891 (mmtt) REVERT: F 473 LYS cc_start: 0.8252 (pttp) cc_final: 0.7809 (pttm) outliers start: 47 outliers final: 17 residues processed: 336 average time/residue: 1.4797 time to fit residues: 549.9980 Evaluate side-chains 326 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 465 GLU Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 195 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 106 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 135 optimal weight: 0.0370 chunk 125 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 156 optimal weight: 0.3980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 403 GLN B 403 GLN B 470 ASN C 403 GLN D 403 GLN E 403 GLN F 339 ASN F 470 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.171345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137306 restraints weight = 19752.719| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.54 r_work: 0.3409 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18270 Z= 0.179 Angle : 0.515 8.010 24762 Z= 0.258 Chirality : 0.040 0.153 2808 Planarity : 0.004 0.045 3072 Dihedral : 3.884 15.610 2418 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.90 % Allowed : 14.77 % Favored : 83.33 % 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: 2.24 (0.19), residues: 2136 helix: 2.54 (0.14), residues: 1248 sheet: 1.13 (0.42), residues: 180 loop : -0.38 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 274 HIS 0.003 0.001 HIS A 423 PHE 0.015 0.002 PHE F 149 TYR 0.011 0.001 TYR E 450 ARG 0.005 0.000 ARG F 350 *********************** 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 345 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 2.028 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7752 (tp) cc_final: 0.7353 (mt) REVERT: A 120 PHE cc_start: 0.7063 (t80) cc_final: 0.5477 (m-80) REVERT: A 158 ILE cc_start: 0.8639 (mt) cc_final: 0.8337 (mm) REVERT: A 196 TYR cc_start: 0.8245 (m-80) cc_final: 0.7780 (m-80) REVERT: A 243 GLN cc_start: 0.8032 (tt0) cc_final: 0.7399 (tt0) REVERT: A 245 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: A 333 ARG cc_start: 0.7176 (mtm180) cc_final: 0.6505 (tpm170) REVERT: A 404 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8015 (mmtt) REVERT: A 422 GLN cc_start: 0.7562 (mt0) cc_final: 0.7142 (mm110) REVERT: A 431 ASP cc_start: 0.8474 (m-30) cc_final: 0.8223 (m-30) REVERT: A 452 LYS cc_start: 0.7723 (mttt) cc_final: 0.6585 (mppt) REVERT: A 473 LYS cc_start: 0.8287 (ptmt) cc_final: 0.7764 (pttm) REVERT: B 120 PHE cc_start: 0.6878 (t80) cc_final: 0.5195 (m-80) REVERT: B 170 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6040 (mmt180) REVERT: B 177 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7540 (mtp180) REVERT: B 186 MET cc_start: 0.8168 (mtt) cc_final: 0.7822 (mtp) REVERT: B 217 GLN cc_start: 0.7198 (mt0) cc_final: 0.6733 (mt0) REVERT: B 341 TYR cc_start: 0.8655 (t80) cc_final: 0.8451 (t80) REVERT: B 388 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.6814 (ttt90) REVERT: B 398 MET cc_start: 0.8982 (ptm) cc_final: 0.8741 (ptm) REVERT: B 403 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7439 (tm130) REVERT: B 404 LYS cc_start: 0.8591 (mtpp) cc_final: 0.7977 (mmtt) REVERT: B 473 LYS cc_start: 0.8201 (pttp) cc_final: 0.7735 (pttm) REVERT: C 120 PHE cc_start: 0.6820 (t80) cc_final: 0.5207 (m-80) REVERT: C 160 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8561 (mt) REVERT: C 177 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7574 (mtp180) REVERT: C 217 GLN cc_start: 0.7242 (mt0) cc_final: 0.6714 (mt0) REVERT: C 371 LYS cc_start: 0.7898 (tttt) cc_final: 0.7548 (ttpt) REVERT: C 404 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7879 (mmtt) REVERT: C 473 LYS cc_start: 0.8264 (pttp) cc_final: 0.7800 (pttm) REVERT: D 118 LEU cc_start: 0.7705 (tp) cc_final: 0.7311 (mt) REVERT: D 120 PHE cc_start: 0.7033 (t80) cc_final: 0.5446 (m-80) REVERT: D 196 TYR cc_start: 0.8073 (m-80) cc_final: 0.7824 (m-80) REVERT: D 217 GLN cc_start: 0.7537 (mt0) cc_final: 0.7064 (mt0) REVERT: D 290 LEU cc_start: 0.8503 (mt) cc_final: 0.8207 (mp) REVERT: D 385 MET cc_start: 0.8388 (ttp) cc_final: 0.7659 (ttm) REVERT: D 398 MET cc_start: 0.9019 (ptm) cc_final: 0.8693 (ptt) REVERT: D 404 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8053 (mmtt) REVERT: D 422 GLN cc_start: 0.7565 (mt0) cc_final: 0.7143 (mm110) REVERT: D 431 ASP cc_start: 0.8472 (m-30) cc_final: 0.8227 (m-30) REVERT: D 452 LYS cc_start: 0.7746 (mttt) cc_final: 0.6582 (mppt) REVERT: D 473 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7750 (pttm) REVERT: E 120 PHE cc_start: 0.6860 (t80) cc_final: 0.5207 (m-80) REVERT: E 186 MET cc_start: 0.8153 (mtt) cc_final: 0.7798 (mtp) REVERT: E 217 GLN cc_start: 0.7483 (mt0) cc_final: 0.6998 (mt0) REVERT: E 371 LYS cc_start: 0.7594 (tttt) cc_final: 0.7167 (ttpt) REVERT: E 388 ARG cc_start: 0.7858 (ttt90) cc_final: 0.6770 (ttt90) REVERT: E 404 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8036 (mmtt) REVERT: E 473 LYS cc_start: 0.8179 (pttp) cc_final: 0.7704 (pttm) REVERT: E 502 GLU cc_start: 0.7273 (tt0) cc_final: 0.6957 (tp30) REVERT: F 120 PHE cc_start: 0.6908 (t80) cc_final: 0.5160 (m-80) REVERT: F 160 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8564 (mt) REVERT: F 177 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7621 (mtp180) REVERT: F 217 GLN cc_start: 0.7374 (mt0) cc_final: 0.6871 (mt0) REVERT: F 349 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6933 (tm-30) REVERT: F 371 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7666 (mtmt) REVERT: F 404 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7903 (mmtt) REVERT: F 473 LYS cc_start: 0.8199 (pttp) cc_final: 0.7771 (pttm) outliers start: 36 outliers final: 18 residues processed: 327 average time/residue: 1.4714 time to fit residues: 532.5972 Evaluate side-chains 319 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 296 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 164 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 206 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 217 GLN A 403 GLN A 430 HIS B 403 GLN B 415 HIS B 470 ASN C 339 ASN C 403 GLN C 430 HIS C 470 ASN D 245 GLN D 403 GLN D 411 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 415 HIS E 430 HIS E 470 ASN F 339 ASN F 430 HIS F 470 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129027 restraints weight = 20223.633| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.74 r_work: 0.3468 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18270 Z= 0.350 Angle : 0.621 8.560 24762 Z= 0.304 Chirality : 0.044 0.181 2808 Planarity : 0.005 0.047 3072 Dihedral : 4.269 16.322 2418 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.43 % Allowed : 14.66 % Favored : 82.91 % 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: 1.86 (0.18), residues: 2136 helix: 2.18 (0.14), residues: 1248 sheet: 0.71 (0.41), residues: 186 loop : -0.35 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 274 HIS 0.005 0.001 HIS D 423 PHE 0.022 0.003 PHE E 367 TYR 0.027 0.002 TYR A 280 ARG 0.005 0.001 ARG C 252 *********************** 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 333 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 287 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7665 (tp) cc_final: 0.7225 (mp) REVERT: A 120 PHE cc_start: 0.7289 (t80) cc_final: 0.5500 (m-80) REVERT: A 158 ILE cc_start: 0.8612 (mt) cc_final: 0.8296 (mm) REVERT: A 170 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6061 (mmt-90) REVERT: A 196 TYR cc_start: 0.8196 (m-80) cc_final: 0.7585 (m-80) REVERT: A 243 GLN cc_start: 0.8120 (tt0) cc_final: 0.7419 (tt0) REVERT: A 245 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: A 404 LYS cc_start: 0.8505 (mtpp) cc_final: 0.7919 (mmtt) REVERT: A 452 LYS cc_start: 0.7764 (mttt) cc_final: 0.6495 (mppt) REVERT: A 473 LYS cc_start: 0.8317 (ptmt) cc_final: 0.7708 (pttm) REVERT: B 120 PHE cc_start: 0.6952 (t80) cc_final: 0.5140 (m-80) REVERT: B 170 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.5921 (mmt180) REVERT: B 177 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7584 (mtp180) REVERT: B 186 MET cc_start: 0.8198 (mtt) cc_final: 0.7763 (mtp) REVERT: B 341 TYR cc_start: 0.8737 (t80) cc_final: 0.8515 (t80) REVERT: B 371 LYS cc_start: 0.8019 (tttt) cc_final: 0.7568 (ttpt) REVERT: B 388 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.6754 (ttt90) REVERT: B 404 LYS cc_start: 0.8580 (mtpp) cc_final: 0.7956 (mmtt) REVERT: B 473 LYS cc_start: 0.8213 (pttp) cc_final: 0.7640 (pttm) REVERT: C 120 PHE cc_start: 0.6882 (t80) cc_final: 0.5110 (m-80) REVERT: C 177 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7580 (mtp180) REVERT: C 217 GLN cc_start: 0.7122 (mt0) cc_final: 0.6528 (mt0) REVERT: C 404 LYS cc_start: 0.8385 (mtpp) cc_final: 0.7877 (mmtt) REVERT: C 452 LYS cc_start: 0.7874 (mttt) cc_final: 0.6466 (mppt) REVERT: C 473 LYS cc_start: 0.8327 (pttp) cc_final: 0.7826 (pttm) REVERT: D 118 LEU cc_start: 0.7697 (tp) cc_final: 0.7243 (mp) REVERT: D 120 PHE cc_start: 0.7281 (t80) cc_final: 0.5495 (m-80) REVERT: D 158 ILE cc_start: 0.8627 (mt) cc_final: 0.8316 (mm) REVERT: D 196 TYR cc_start: 0.8058 (m-80) cc_final: 0.7603 (m-80) REVERT: D 290 LEU cc_start: 0.8558 (mt) cc_final: 0.8286 (mp) REVERT: D 385 MET cc_start: 0.8371 (ttp) cc_final: 0.7611 (ttm) REVERT: D 404 LYS cc_start: 0.8521 (mtpp) cc_final: 0.7945 (mmtt) REVERT: D 452 LYS cc_start: 0.7779 (mttt) cc_final: 0.6492 (mppt) REVERT: D 473 LYS cc_start: 0.8332 (ptmt) cc_final: 0.7707 (pttm) REVERT: E 120 PHE cc_start: 0.6782 (t80) cc_final: 0.5049 (m-80) REVERT: E 177 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7618 (mtp180) REVERT: E 186 MET cc_start: 0.8179 (mtt) cc_final: 0.7743 (mtp) REVERT: E 217 GLN cc_start: 0.7288 (mt0) cc_final: 0.6769 (mt0) REVERT: E 371 LYS cc_start: 0.7847 (tttt) cc_final: 0.7490 (ttpt) REVERT: E 388 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6760 (ttt90) REVERT: E 404 LYS cc_start: 0.8567 (mtpp) cc_final: 0.7905 (mmtt) REVERT: E 473 LYS cc_start: 0.8219 (pttp) cc_final: 0.7628 (pttm) REVERT: E 502 GLU cc_start: 0.7679 (tt0) cc_final: 0.7052 (tp30) REVERT: F 120 PHE cc_start: 0.6900 (t80) cc_final: 0.5139 (m-80) REVERT: F 177 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7589 (mtp180) REVERT: F 217 GLN cc_start: 0.7370 (mt0) cc_final: 0.6797 (mt0) REVERT: F 353 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7726 (ttm-80) REVERT: F 371 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7654 (mtmt) REVERT: F 404 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7931 (mmtt) REVERT: F 452 LYS cc_start: 0.7873 (mttt) cc_final: 0.6450 (mppt) REVERT: F 473 LYS cc_start: 0.8323 (pttp) cc_final: 0.7743 (pttm) outliers start: 46 outliers final: 18 residues processed: 310 average time/residue: 1.6944 time to fit residues: 581.6716 Evaluate side-chains 301 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 279 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 214 optimal weight: 0.0770 chunk 151 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 217 GLN A 403 GLN A 411 GLN B 217 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN B 470 ASN C 403 GLN C 470 ASN D 217 GLN D 245 GLN D 403 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN E 470 ASN F 470 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.168134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133718 restraints weight = 19932.030| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.55 r_work: 0.3356 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18270 Z= 0.229 Angle : 0.555 9.378 24762 Z= 0.275 Chirality : 0.041 0.170 2808 Planarity : 0.004 0.048 3072 Dihedral : 4.058 15.752 2418 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.64 % Allowed : 15.72 % 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: 2.04 (0.18), residues: 2136 helix: 2.34 (0.14), residues: 1248 sheet: 0.96 (0.42), residues: 180 loop : -0.33 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 274 HIS 0.003 0.001 HIS A 423 PHE 0.018 0.002 PHE C 149 TYR 0.016 0.002 TYR F 280 ARG 0.006 0.000 ARG F 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 322 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 2.156 Fit side-chains REVERT: A 118 LEU cc_start: 0.7752 (tp) cc_final: 0.7308 (mp) REVERT: A 120 PHE cc_start: 0.7215 (t80) cc_final: 0.5483 (m-80) REVERT: A 158 ILE cc_start: 0.8669 (mt) cc_final: 0.8382 (mm) REVERT: A 170 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6208 (mmt-90) REVERT: A 196 TYR cc_start: 0.8202 (m-80) cc_final: 0.7619 (m-80) REVERT: A 243 GLN cc_start: 0.8057 (tt0) cc_final: 0.7421 (tt0) REVERT: A 245 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: A 333 ARG cc_start: 0.7205 (mtm180) cc_final: 0.6515 (tpm170) REVERT: A 388 ARG cc_start: 0.7900 (ttt90) cc_final: 0.7689 (ttm-80) REVERT: A 404 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8109 (mmtt) REVERT: A 452 LYS cc_start: 0.7846 (mttt) cc_final: 0.6673 (mppt) REVERT: A 473 LYS cc_start: 0.8284 (ptmt) cc_final: 0.7787 (pttm) REVERT: B 120 PHE cc_start: 0.6898 (t80) cc_final: 0.5148 (m-80) REVERT: B 170 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6140 (mmt180) REVERT: B 177 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7658 (mtp180) REVERT: B 186 MET cc_start: 0.8225 (mtt) cc_final: 0.7909 (mtp) REVERT: B 341 TYR cc_start: 0.8739 (t80) cc_final: 0.8462 (t80) REVERT: B 371 LYS cc_start: 0.7865 (tttt) cc_final: 0.7550 (ttpt) REVERT: B 388 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.6832 (ttt90) REVERT: B 404 LYS cc_start: 0.8598 (mtpp) cc_final: 0.7969 (mmtt) REVERT: B 473 LYS cc_start: 0.8241 (pttp) cc_final: 0.7743 (pttm) REVERT: C 120 PHE cc_start: 0.6851 (t80) cc_final: 0.5150 (m-80) REVERT: C 177 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7797 (mtp85) REVERT: C 217 GLN cc_start: 0.7256 (mt0) cc_final: 0.6695 (mt0) REVERT: C 371 LYS cc_start: 0.8070 (tttt) cc_final: 0.7806 (ttpt) REVERT: C 404 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7936 (mmtt) REVERT: C 432 MET cc_start: 0.8654 (mtp) cc_final: 0.8275 (mtm) REVERT: C 473 LYS cc_start: 0.8312 (pttp) cc_final: 0.7762 (pttm) REVERT: D 118 LEU cc_start: 0.7771 (tp) cc_final: 0.7367 (mt) REVERT: D 120 PHE cc_start: 0.7208 (t80) cc_final: 0.5469 (m-80) REVERT: D 158 ILE cc_start: 0.8669 (mt) cc_final: 0.8382 (mm) REVERT: D 196 TYR cc_start: 0.8107 (m-80) cc_final: 0.7677 (m-80) REVERT: D 290 LEU cc_start: 0.8537 (mt) cc_final: 0.8263 (mp) REVERT: D 385 MET cc_start: 0.8367 (ttp) cc_final: 0.7607 (ttm) REVERT: D 388 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7684 (ttm-80) REVERT: D 404 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8013 (mmtt) REVERT: D 452 LYS cc_start: 0.7887 (mttt) cc_final: 0.6684 (mppt) REVERT: D 473 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7773 (pttm) REVERT: E 120 PHE cc_start: 0.6851 (t80) cc_final: 0.5206 (m-80) REVERT: E 177 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7680 (mtp180) REVERT: E 186 MET cc_start: 0.8197 (mtt) cc_final: 0.7917 (mtp) REVERT: E 217 GLN cc_start: 0.7364 (mt0) cc_final: 0.6857 (mt0) REVERT: E 404 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8030 (mmtt) REVERT: E 473 LYS cc_start: 0.8250 (pttp) cc_final: 0.7744 (pttm) REVERT: E 502 GLU cc_start: 0.7456 (tt0) cc_final: 0.7114 (tp30) REVERT: F 120 PHE cc_start: 0.6875 (t80) cc_final: 0.5142 (m-80) REVERT: F 126 PHE cc_start: 0.8095 (m-10) cc_final: 0.7801 (m-10) REVERT: F 160 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8604 (mt) REVERT: F 177 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7718 (mtp180) REVERT: F 217 GLN cc_start: 0.7425 (mt0) cc_final: 0.6881 (mt0) REVERT: F 371 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7734 (mtmt) REVERT: F 404 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8017 (mmtt) REVERT: F 452 LYS cc_start: 0.7988 (mttt) cc_final: 0.6680 (mppt) REVERT: F 473 LYS cc_start: 0.8280 (pttp) cc_final: 0.7844 (pttm) outliers start: 31 outliers final: 14 residues processed: 305 average time/residue: 1.6081 time to fit residues: 538.2225 Evaluate side-chains 299 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 281 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 100 optimal weight: 0.5980 chunk 177 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 403 GLN A 422 GLN B 217 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN B 411 GLN B 470 ASN C 403 GLN C 470 ASN D 217 GLN D 403 GLN D 422 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN F 470 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.169597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.135476 restraints weight = 19868.092| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.54 r_work: 0.3389 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18270 Z= 0.195 Angle : 0.539 9.450 24762 Z= 0.269 Chirality : 0.040 0.167 2808 Planarity : 0.004 0.047 3072 Dihedral : 3.979 16.917 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.21 % Allowed : 16.46 % Favored : 82.33 % 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: 2.14 (0.18), residues: 2136 helix: 2.43 (0.14), residues: 1248 sheet: 1.03 (0.42), residues: 180 loop : -0.33 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 274 HIS 0.005 0.001 HIS C 348 PHE 0.023 0.002 PHE C 126 TYR 0.012 0.001 TYR F 280 ARG 0.007 0.000 ARG F 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 308 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 285 time to evaluate : 2.725 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7749 (tp) cc_final: 0.7399 (mt) REVERT: A 120 PHE cc_start: 0.7171 (t80) cc_final: 0.5464 (m-80) REVERT: A 158 ILE cc_start: 0.8654 (mt) cc_final: 0.8351 (mm) REVERT: A 170 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6133 (mmt-90) REVERT: A 196 TYR cc_start: 0.8200 (m-80) cc_final: 0.7697 (m-80) REVERT: A 243 GLN cc_start: 0.8039 (tt0) cc_final: 0.7424 (tt0) REVERT: A 245 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: A 333 ARG cc_start: 0.7251 (mtm180) cc_final: 0.6523 (tpm170) REVERT: A 388 ARG cc_start: 0.7916 (ttt90) cc_final: 0.7691 (ttm-80) REVERT: A 404 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8014 (mmtt) REVERT: A 431 ASP cc_start: 0.8517 (m-30) cc_final: 0.8246 (m-30) REVERT: A 452 LYS cc_start: 0.7830 (mttt) cc_final: 0.6630 (mppt) REVERT: A 473 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7759 (pttm) REVERT: B 120 PHE cc_start: 0.6854 (t80) cc_final: 0.5179 (m-80) REVERT: B 170 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6114 (mmt180) REVERT: B 177 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7599 (mtp180) REVERT: B 186 MET cc_start: 0.8193 (mtt) cc_final: 0.7880 (mtp) REVERT: B 341 TYR cc_start: 0.8689 (t80) cc_final: 0.8447 (t80) REVERT: B 371 LYS cc_start: 0.7805 (tttt) cc_final: 0.7441 (ttpt) REVERT: B 388 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.6814 (ttt90) REVERT: B 403 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7535 (tm130) REVERT: B 404 LYS cc_start: 0.8582 (mtpp) cc_final: 0.7949 (mmtt) REVERT: B 473 LYS cc_start: 0.8253 (pttp) cc_final: 0.7766 (pttm) REVERT: C 120 PHE cc_start: 0.6936 (t80) cc_final: 0.5251 (m-80) REVERT: C 177 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7586 (mtp180) REVERT: C 217 GLN cc_start: 0.7271 (mt0) cc_final: 0.6716 (mt0) REVERT: C 371 LYS cc_start: 0.8017 (tttt) cc_final: 0.7621 (ttpt) REVERT: C 404 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7903 (mmtt) REVERT: C 432 MET cc_start: 0.8658 (mtp) cc_final: 0.8275 (mtm) REVERT: C 473 LYS cc_start: 0.8300 (pttp) cc_final: 0.7814 (pttm) REVERT: D 118 LEU cc_start: 0.7760 (tp) cc_final: 0.7359 (mt) REVERT: D 120 PHE cc_start: 0.7186 (t80) cc_final: 0.5458 (m-80) REVERT: D 196 TYR cc_start: 0.8099 (m-80) cc_final: 0.7744 (m-80) REVERT: D 290 LEU cc_start: 0.8510 (mt) cc_final: 0.8217 (mp) REVERT: D 333 ARG cc_start: 0.7348 (mtm180) cc_final: 0.6512 (tpm170) REVERT: D 388 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7698 (ttm-80) REVERT: D 404 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8079 (mmtt) REVERT: D 431 ASP cc_start: 0.8514 (m-30) cc_final: 0.8255 (m-30) REVERT: D 452 LYS cc_start: 0.7856 (mttt) cc_final: 0.6628 (mppt) REVERT: D 473 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7746 (pttm) REVERT: E 120 PHE cc_start: 0.6786 (t80) cc_final: 0.5177 (m-80) REVERT: E 177 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7611 (mtp180) REVERT: E 186 MET cc_start: 0.8160 (mtt) cc_final: 0.7832 (mtp) REVERT: E 217 GLN cc_start: 0.7458 (mt0) cc_final: 0.6889 (mt0) REVERT: E 371 LYS cc_start: 0.7678 (tttt) cc_final: 0.7234 (ttpt) REVERT: E 404 LYS cc_start: 0.8585 (mtpp) cc_final: 0.7958 (mmtt) REVERT: E 473 LYS cc_start: 0.8203 (pttp) cc_final: 0.7706 (pttm) REVERT: E 502 GLU cc_start: 0.7400 (tt0) cc_final: 0.7021 (tp30) REVERT: F 120 PHE cc_start: 0.6923 (t80) cc_final: 0.5119 (m-80) REVERT: F 160 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8593 (mt) REVERT: F 177 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7688 (mtp180) REVERT: F 217 GLN cc_start: 0.7415 (mt0) cc_final: 0.6871 (mt0) REVERT: F 353 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7867 (ttm-80) REVERT: F 371 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7719 (mtmt) REVERT: F 404 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7892 (mmtt) REVERT: F 452 LYS cc_start: 0.7922 (mttt) cc_final: 0.6645 (mppt) REVERT: F 473 LYS cc_start: 0.8231 (pttp) cc_final: 0.7804 (pttm) outliers start: 23 outliers final: 16 residues processed: 294 average time/residue: 1.6040 time to fit residues: 518.9493 Evaluate side-chains 298 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 203 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 217 GLN A 403 GLN A 422 GLN B 217 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN B 470 ASN C 403 GLN C 470 ASN D 217 GLN D 403 GLN D 422 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN F 403 GLN F 470 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.167556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133050 restraints weight = 19839.268| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.54 r_work: 0.3360 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18270 Z= 0.269 Angle : 0.577 8.996 24762 Z= 0.286 Chirality : 0.042 0.178 2808 Planarity : 0.004 0.048 3072 Dihedral : 4.114 15.894 2418 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.64 % Allowed : 16.19 % Favored : 82.17 % 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: 2.01 (0.18), residues: 2136 helix: 2.30 (0.14), residues: 1248 sheet: 0.93 (0.41), residues: 180 loop : -0.31 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 274 HIS 0.004 0.001 HIS D 423 PHE 0.040 0.002 PHE C 126 TYR 0.019 0.002 TYR F 280 ARG 0.006 0.000 ARG F 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13617.02 seconds wall clock time: 241 minutes 1.25 seconds (14461.25 seconds total)