Starting phenix.real_space_refine on Mon May 19 02:00:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk7_61546/05_2025/9jk7_61546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk7_61546/05_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_61546/05_2025/9jk7_61546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk7_61546/05_2025/9jk7_61546.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk7_61546/05_2025/9jk7_61546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk7_61546/05_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-5687/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: 7.24, 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=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 141 " - pdb=" SG CYS E 145 " distance=2.03 Simple disulfide: pdb=" SG CYS D 141 " - pdb=" SG CYS D 145 " distance=2.03 Simple disulfide: pdb=" SG CYS F 141 " - pdb=" SG CYS F 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: 4.33 Conformation dependent library (CDL) restraints added in 2.1 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: 1.53 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: 5.36 Time building geometry restraints manager: 5.09 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 - 21.01: 672 21.01 - 31.51: 110 31.51 - 42.02: 40 42.02 - 52.52: 12 Dihedral angle restraints: 10932 sinusoidal: 4476 harmonic: 6456 Sorted by residual: dihedral pdb=" CB CYS D 141 " pdb=" SG CYS D 141 " pdb=" SG CYS D 145 " pdb=" CB CYS D 145 " ideal model delta sinusoidal sigma weight residual -86.00 -138.52 52.52 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " pdb=" SG CYS E 145 " pdb=" CB CYS E 145 " ideal model delta sinusoidal sigma weight residual -86.00 -138.51 52.51 1 1.00e+01 1.00e-02 3.76e+01 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 ... (remaining 10929 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: 2.22 - 2.75: 2740 2.75 - 3.29: 17406 3.29 - 3.83: 31400 3.83 - 4.36: 37066 4.36 - 4.90: 64594 Nonbonded interactions: 153206 Sorted by model distance: nonbonded pdb=" OG1 THR E 433 " pdb=" O THR F 254 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR D 433 " pdb=" O THR E 254 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR A 433 " pdb=" O THR B 254 " model vdw 2.218 3.040 nonbonded pdb=" O SER A 500 " pdb=" N LEU C 462 " model vdw 2.224 3.120 nonbonded pdb=" O SER D 500 " pdb=" N LEU F 462 " model vdw 2.273 3.120 ... (remaining 153201 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: 0.13 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 35.060 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.470 ------------------------------------------------------------------------------- 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 18276 Z= 0.202 Angle : 0.669 7.303 24774 Z= 0.375 Chirality : 0.046 0.296 2808 Planarity : 0.004 0.045 3072 Dihedral : 7.686 45.725 6702 Min Nonbonded Distance : 2.218 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 Details of bonding type rmsd hydrogen bonds : bond 0.10587 ( 1095) hydrogen bonds : angle 5.15878 ( 3195) SS BOND : bond 0.00504 ( 6) SS BOND : angle 0.45044 ( 12) covalent geometry : bond 0.00468 (18270) covalent geometry : angle 0.66929 (24762) *********************** 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 : 1.936 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: 1.4939 time to fit residues: 727.8616 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 : 3.175 ------------------------------------------------------------------------------- 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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3780 r_free = 0.3780 target = 0.164612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.129202 restraints weight = 19174.580| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.60 r_work: 0.3280 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18276 Z= 0.161 Angle : 0.589 7.564 24774 Z= 0.297 Chirality : 0.043 0.183 2808 Planarity : 0.004 0.040 3072 Dihedral : 4.384 19.148 2418 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.95 % Allowed : 9.70 % 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: 0.83 (0.18), residues: 2136 helix: 1.47 (0.14), residues: 1248 sheet: 0.35 (0.39), residues: 186 loop : -1.05 (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 0.021 0.003 PHE C 260 TYR 0.015 0.002 TYR B 342 ARG 0.005 0.000 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1095) hydrogen bonds : angle 4.42405 ( 3195) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.30329 ( 12) covalent geometry : bond 0.00376 (18270) covalent geometry : angle 0.58960 (24762) *********************** 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 360 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 323 time to evaluate : 2.095 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: 0.7163 (t80) cc_final: 0.5474 (m-80) REVERT: A 158 ILE cc_start: 0.8559 (mt) cc_final: 0.8325 (mm) REVERT: A 170 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.5910 (mmt-90) REVERT: A 243 GLN cc_start: 0.8201 (tt0) cc_final: 0.7406 (tt0) REVERT: A 245 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: A 333 ARG cc_start: 0.6911 (mtm180) cc_final: 0.6363 (tpm170) REVERT: A 385 MET cc_start: 0.8249 (ttp) cc_final: 0.7751 (ttm) REVERT: A 404 LYS cc_start: 0.8530 (mtpp) cc_final: 0.7932 (mmtt) REVERT: A 452 LYS cc_start: 0.7727 (mttt) cc_final: 0.6388 (mppt) REVERT: A 513 MET cc_start: 0.7207 (mmp) cc_final: 0.6455 (mmp) REVERT: B 120 PHE cc_start: 0.6801 (t80) cc_final: 0.5131 (m-80) REVERT: B 149 PHE cc_start: 0.7895 (m-80) cc_final: 0.7607 (m-80) REVERT: B 177 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7602 (mtp180) REVERT: B 186 MET cc_start: 0.7976 (mtt) cc_final: 0.7612 (mtp) REVERT: B 341 TYR cc_start: 0.8610 (t80) cc_final: 0.8333 (t80) REVERT: B 404 LYS cc_start: 0.8536 (mtpp) cc_final: 0.7908 (mmtt) REVERT: B 473 LYS cc_start: 0.8040 (pttp) cc_final: 0.7467 (pttm) REVERT: B 510 LYS cc_start: 0.7272 (mmtt) cc_final: 0.7072 (mmmm) REVERT: C 120 PHE cc_start: 0.6958 (t80) cc_final: 0.5130 (m-80) REVERT: C 160 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8401 (mt) REVERT: C 186 MET cc_start: 0.8100 (mtt) cc_final: 0.7842 (mtp) REVERT: C 255 ASP cc_start: 0.8397 (p0) cc_final: 0.8168 (p0) REVERT: C 353 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7699 (mtt180) REVERT: C 371 LYS cc_start: 0.7720 (tttt) cc_final: 0.7314 (ttpt) REVERT: C 398 MET cc_start: 0.8801 (ptm) cc_final: 0.8591 (ptm) REVERT: C 404 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7780 (mmtt) REVERT: C 417 MET cc_start: 0.7783 (tmm) cc_final: 0.7537 (tmm) REVERT: C 470 ASN cc_start: 0.8140 (m110) cc_final: 0.7931 (m110) REVERT: C 473 LYS cc_start: 0.8285 (pttp) cc_final: 0.7587 (pttm) REVERT: C 502 GLU cc_start: 0.7222 (tt0) cc_final: 0.6881 (tp30) REVERT: D 118 LEU cc_start: 0.7597 (tp) cc_final: 0.7243 (mt) REVERT: D 120 PHE cc_start: 0.7103 (t80) cc_final: 0.5467 (m-80) REVERT: D 158 ILE cc_start: 0.8578 (mt) cc_final: 0.8325 (mm) REVERT: D 170 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6001 (mmt-90) REVERT: D 290 LEU cc_start: 0.8504 (mt) cc_final: 0.8250 (mp) REVERT: D 333 ARG cc_start: 0.6875 (mtm180) cc_final: 0.6363 (tpm170) REVERT: D 385 MET cc_start: 0.8369 (ttp) cc_final: 0.7920 (ttm) REVERT: D 404 LYS cc_start: 0.8490 (mtpp) cc_final: 0.7938 (mmtt) REVERT: D 452 LYS cc_start: 0.7782 (mttt) cc_final: 0.6450 (mppt) REVERT: D 513 MET cc_start: 0.7208 (mmp) cc_final: 0.6091 (mmt) REVERT: E 120 PHE cc_start: 0.6976 (t80) cc_final: 0.5378 (m-80) REVERT: E 177 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7581 (mtp180) REVERT: E 186 MET cc_start: 0.7997 (mtt) cc_final: 0.7639 (mtp) REVERT: E 217 GLN cc_start: 0.7220 (mt0) cc_final: 0.6674 (mt0) REVERT: E 290 LEU cc_start: 0.8444 (mt) cc_final: 0.8063 (mt) REVERT: E 341 TYR cc_start: 0.8579 (t80) cc_final: 0.8370 (t80) REVERT: E 354 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8079 (mtmm) REVERT: E 403 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7459 (tm130) REVERT: E 404 LYS cc_start: 0.8562 (mtpp) cc_final: 0.7857 (mmtt) REVERT: E 473 LYS cc_start: 0.8172 (pttp) cc_final: 0.7542 (pttm) REVERT: E 502 GLU cc_start: 0.7554 (tt0) cc_final: 0.6972 (tp30) REVERT: E 513 MET cc_start: 0.6991 (mmp) cc_final: 0.5708 (mmt) REVERT: F 118 LEU cc_start: 0.7456 (tp) cc_final: 0.7052 (mp) REVERT: F 120 PHE cc_start: 0.7011 (t80) cc_final: 0.5194 (m-80) REVERT: F 160 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8415 (mt) REVERT: F 186 MET cc_start: 0.8092 (mtt) cc_final: 0.7840 (mtp) REVERT: F 255 ASP cc_start: 0.8402 (p0) cc_final: 0.8160 (p0) REVERT: F 349 GLU cc_start: 0.7430 (tt0) cc_final: 0.7174 (tm-30) REVERT: F 371 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7513 (mtpt) REVERT: F 398 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8547 (ptm) REVERT: F 404 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7787 (mmtt) REVERT: F 416 THR cc_start: 0.8369 (p) cc_final: 0.8000 (t) REVERT: F 473 LYS cc_start: 0.8250 (pttp) cc_final: 0.7545 (pttm) REVERT: F 501 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7039 (tt0) outliers start: 37 outliers final: 11 residues processed: 341 average time/residue: 1.3985 time to fit residues: 528.3366 Evaluate side-chains 305 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 286 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 160 LEU 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: 0.5980 chunk 84 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 0.0570 chunk 72 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 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 217 GLN ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.180009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148803 restraints weight = 19510.910| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.48 r_work: 0.3564 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18276 Z= 0.141 Angle : 0.545 6.718 24774 Z= 0.274 Chirality : 0.041 0.191 2808 Planarity : 0.004 0.041 3072 Dihedral : 4.154 17.724 2418 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.69 % Allowed : 11.45 % Favored : 85.86 % 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: 1.49 (0.18), residues: 2136 helix: 1.99 (0.15), residues: 1248 sheet: 0.55 (0.39), residues: 186 loop : -0.73 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 274 HIS 0.004 0.001 HIS A 423 PHE 0.019 0.002 PHE E 367 TYR 0.013 0.001 TYR D 450 ARG 0.005 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 1095) hydrogen bonds : angle 4.27878 ( 3195) SS BOND : bond 0.00050 ( 6) SS BOND : angle 0.27173 ( 12) covalent geometry : bond 0.00330 (18270) covalent geometry : angle 0.54545 (24762) *********************** 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 356 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7654 (tp) cc_final: 0.7335 (mt) REVERT: A 120 PHE cc_start: 0.7123 (t80) cc_final: 0.5569 (m-80) REVERT: A 158 ILE cc_start: 0.8639 (mt) cc_final: 0.8376 (mm) REVERT: A 170 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6201 (mmt-90) REVERT: A 243 GLN cc_start: 0.8242 (tt0) cc_final: 0.7578 (tt0) REVERT: A 245 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: A 333 ARG cc_start: 0.7058 (mtm180) cc_final: 0.6459 (tpm170) REVERT: A 385 MET cc_start: 0.8419 (ttp) cc_final: 0.7906 (ttm) REVERT: A 404 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8139 (mmtt) REVERT: A 418 GLU cc_start: 0.7717 (tp30) cc_final: 0.7479 (tp30) REVERT: A 452 LYS cc_start: 0.7721 (mttt) cc_final: 0.6516 (mppt) REVERT: A 473 LYS cc_start: 0.8304 (ptmt) cc_final: 0.7773 (pttm) REVERT: B 120 PHE cc_start: 0.6896 (t80) cc_final: 0.5226 (m-80) REVERT: B 149 PHE cc_start: 0.7913 (m-80) cc_final: 0.7625 (m-80) REVERT: B 177 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7541 (mtp180) REVERT: B 186 MET cc_start: 0.8179 (mtt) cc_final: 0.7787 (mtp) REVERT: B 341 TYR cc_start: 0.8670 (t80) cc_final: 0.8461 (t80) REVERT: B 365 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: B 388 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.6809 (ttt90) REVERT: B 404 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8122 (mmtt) REVERT: B 473 LYS cc_start: 0.8136 (pttp) cc_final: 0.7613 (pttm) REVERT: C 118 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7435 (mt) REVERT: C 120 PHE cc_start: 0.6914 (t80) cc_final: 0.5147 (m-80) REVERT: C 126 PHE cc_start: 0.8194 (m-10) cc_final: 0.7916 (m-10) REVERT: C 160 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 217 GLN cc_start: 0.7326 (mt0) cc_final: 0.6755 (mt0) REVERT: C 371 LYS cc_start: 0.7776 (tttt) cc_final: 0.7392 (ttpt) REVERT: C 404 LYS cc_start: 0.8411 (mtpp) cc_final: 0.7954 (mmtt) REVERT: C 417 MET cc_start: 0.7855 (tmm) cc_final: 0.7583 (tmm) REVERT: C 473 LYS cc_start: 0.8338 (pttp) cc_final: 0.7726 (pttm) REVERT: C 502 GLU cc_start: 0.7314 (tt0) cc_final: 0.7020 (tp30) REVERT: D 118 LEU cc_start: 0.7696 (tp) cc_final: 0.7317 (mt) REVERT: D 120 PHE cc_start: 0.7059 (t80) cc_final: 0.5549 (m-80) REVERT: D 158 ILE cc_start: 0.8648 (mt) cc_final: 0.8387 (mm) REVERT: D 170 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6200 (mmt-90) REVERT: D 245 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: D 290 LEU cc_start: 0.8584 (mt) cc_final: 0.8323 (mp) REVERT: D 333 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6432 (tpm170) REVERT: D 349 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7608 (mp0) REVERT: D 385 MET cc_start: 0.8419 (ttp) cc_final: 0.7827 (ttm) REVERT: D 404 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8121 (mmtt) REVERT: D 418 GLU cc_start: 0.7863 (tp30) cc_final: 0.7608 (tp30) REVERT: D 452 LYS cc_start: 0.7727 (mttt) cc_final: 0.6510 (mppt) REVERT: D 473 LYS cc_start: 0.8284 (ptmt) cc_final: 0.7757 (pttm) REVERT: D 513 MET cc_start: 0.7151 (mmp) cc_final: 0.6236 (mmt) REVERT: E 120 PHE cc_start: 0.6906 (t80) cc_final: 0.5416 (m-80) REVERT: E 177 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7622 (mtp180) REVERT: E 186 MET cc_start: 0.8180 (mtt) cc_final: 0.7805 (mtp) REVERT: E 217 GLN cc_start: 0.7350 (mt0) cc_final: 0.6847 (mt0) REVERT: E 290 LEU cc_start: 0.8519 (mt) cc_final: 0.8165 (mt) REVERT: E 341 TYR cc_start: 0.8642 (t80) cc_final: 0.8440 (t80) REVERT: E 365 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: E 371 LYS cc_start: 0.7854 (tttt) cc_final: 0.7313 (ttpt) REVERT: E 388 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6539 (ttt90) REVERT: E 404 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8079 (mmtt) REVERT: E 473 LYS cc_start: 0.8244 (pttp) cc_final: 0.7678 (pttm) REVERT: E 502 GLU cc_start: 0.7359 (tt0) cc_final: 0.7016 (tp30) REVERT: F 120 PHE cc_start: 0.6911 (t80) cc_final: 0.5140 (m-80) REVERT: F 160 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8567 (mt) REVERT: F 217 GLN cc_start: 0.7243 (mt0) cc_final: 0.6714 (mt0) REVERT: F 371 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7546 (mtpt) REVERT: F 388 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6739 (ttt90) REVERT: F 404 LYS cc_start: 0.8400 (mtpp) cc_final: 0.7961 (mmtt) REVERT: F 422 GLN cc_start: 0.7677 (mt0) cc_final: 0.7193 (mm110) REVERT: F 473 LYS cc_start: 0.8322 (pttp) cc_final: 0.7760 (pttm) REVERT: F 501 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: F 502 GLU cc_start: 0.7233 (tt0) cc_final: 0.6972 (tp30) REVERT: F 513 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7184 (tpp) outliers start: 51 outliers final: 11 residues processed: 331 average time/residue: 1.4202 time to fit residues: 519.3122 Evaluate side-chains 310 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 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 160 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 513 MET 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 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 388 ARG 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: 0.8980 chunk 31 optimal weight: 0.0270 chunk 185 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 215 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 403 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147804 restraints weight = 19599.941| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.49 r_work: 0.3555 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18276 Z= 0.141 Angle : 0.539 6.849 24774 Z= 0.269 Chirality : 0.040 0.141 2808 Planarity : 0.004 0.044 3072 Dihedral : 4.073 17.192 2418 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.22 % Allowed : 12.18 % 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: 1.80 (0.18), residues: 2136 helix: 2.24 (0.15), residues: 1248 sheet: 0.70 (0.40), residues: 186 loop : -0.59 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 274 HIS 0.004 0.001 HIS D 423 PHE 0.015 0.002 PHE D 367 TYR 0.012 0.001 TYR A 450 ARG 0.004 0.000 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 1095) hydrogen bonds : angle 4.22173 ( 3195) SS BOND : bond 0.00034 ( 6) SS BOND : angle 0.26060 ( 12) covalent geometry : bond 0.00329 (18270) covalent geometry : angle 0.53929 (24762) *********************** 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 368 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7688 (tp) cc_final: 0.7353 (mt) REVERT: A 120 PHE cc_start: 0.7147 (t80) cc_final: 0.5598 (m-80) REVERT: A 158 ILE cc_start: 0.8644 (mt) cc_final: 0.8375 (mm) REVERT: A 170 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6159 (mmt-90) REVERT: A 196 TYR cc_start: 0.8147 (m-80) cc_final: 0.7597 (m-80) REVERT: A 243 GLN cc_start: 0.8186 (tt0) cc_final: 0.7505 (tt0) REVERT: A 245 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.6976 (mp10) REVERT: A 333 ARG cc_start: 0.7042 (mtm180) cc_final: 0.6446 (tpm170) REVERT: A 349 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7595 (mp0) REVERT: A 385 MET cc_start: 0.8402 (ttp) cc_final: 0.7762 (ttm) REVERT: A 404 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8124 (mmtt) REVERT: A 418 GLU cc_start: 0.7711 (tp30) cc_final: 0.7483 (tp30) REVERT: A 452 LYS cc_start: 0.7678 (mttt) cc_final: 0.6548 (mppt) REVERT: A 473 LYS cc_start: 0.8353 (ptmt) cc_final: 0.7797 (pttm) REVERT: B 120 PHE cc_start: 0.6882 (t80) cc_final: 0.5224 (m-80) REVERT: B 149 PHE cc_start: 0.7976 (m-80) cc_final: 0.7709 (m-80) REVERT: B 177 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7616 (mtp180) REVERT: B 186 MET cc_start: 0.8154 (mtt) cc_final: 0.7823 (mtp) REVERT: B 341 TYR cc_start: 0.8638 (t80) cc_final: 0.8400 (t80) REVERT: B 365 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: B 388 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.6808 (ttt90) REVERT: B 404 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8096 (mmtt) REVERT: B 473 LYS cc_start: 0.8193 (pttp) cc_final: 0.7658 (pttm) REVERT: C 120 PHE cc_start: 0.6919 (t80) cc_final: 0.5148 (m-80) REVERT: C 160 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8570 (mt) REVERT: C 217 GLN cc_start: 0.7385 (mt0) cc_final: 0.6785 (mt0) REVERT: C 371 LYS cc_start: 0.7929 (tttt) cc_final: 0.7500 (ttpt) REVERT: C 404 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7962 (mmtt) REVERT: C 417 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7571 (tmm) REVERT: C 473 LYS cc_start: 0.8361 (pttp) cc_final: 0.7761 (pttm) REVERT: C 502 GLU cc_start: 0.7287 (tt0) cc_final: 0.6992 (tp30) REVERT: D 118 LEU cc_start: 0.7692 (tp) cc_final: 0.7300 (mt) REVERT: D 120 PHE cc_start: 0.7041 (t80) cc_final: 0.5524 (m-80) REVERT: D 158 ILE cc_start: 0.8658 (mt) cc_final: 0.8387 (mm) REVERT: D 170 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6142 (mmt-90) REVERT: D 245 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.6874 (mp10) REVERT: D 290 LEU cc_start: 0.8561 (mt) cc_final: 0.8303 (mp) REVERT: D 333 ARG cc_start: 0.7037 (mtm180) cc_final: 0.6426 (tpm170) REVERT: D 349 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7546 (mp0) REVERT: D 371 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7515 (ttpt) REVERT: D 385 MET cc_start: 0.8455 (ttp) cc_final: 0.7797 (ttm) REVERT: D 404 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8114 (mmtt) REVERT: D 418 GLU cc_start: 0.7790 (tp30) cc_final: 0.7543 (tp30) REVERT: D 452 LYS cc_start: 0.7675 (mttt) cc_final: 0.6531 (mppt) REVERT: D 473 LYS cc_start: 0.8322 (ptmt) cc_final: 0.7789 (pttm) REVERT: D 513 MET cc_start: 0.7286 (mmp) cc_final: 0.6284 (mmt) REVERT: E 120 PHE cc_start: 0.6902 (t80) cc_final: 0.5361 (m-80) REVERT: E 186 MET cc_start: 0.8161 (mtt) cc_final: 0.7832 (mtp) REVERT: E 217 GLN cc_start: 0.7344 (mt0) cc_final: 0.6840 (mt0) REVERT: E 282 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: E 290 LEU cc_start: 0.8512 (mt) cc_final: 0.8160 (mt) REVERT: E 365 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: E 371 LYS cc_start: 0.7776 (tttt) cc_final: 0.7311 (ttpt) REVERT: E 388 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6569 (ttt90) REVERT: E 404 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8068 (mmtt) REVERT: E 473 LYS cc_start: 0.8216 (pttp) cc_final: 0.7680 (pttm) REVERT: E 502 GLU cc_start: 0.7377 (tt0) cc_final: 0.7060 (tp30) REVERT: E 513 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7002 (tpp) REVERT: F 118 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7445 (mt) REVERT: F 120 PHE cc_start: 0.6870 (t80) cc_final: 0.5127 (m-80) REVERT: F 160 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8578 (mt) REVERT: F 217 GLN cc_start: 0.7239 (mt0) cc_final: 0.6693 (mt0) REVERT: F 371 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7679 (mtpt) REVERT: F 404 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7991 (mmtt) REVERT: F 473 LYS cc_start: 0.8328 (pttp) cc_final: 0.7792 (pttm) REVERT: F 502 GLU cc_start: 0.7230 (tt0) cc_final: 0.6998 (tp30) outliers start: 61 outliers final: 21 residues processed: 337 average time/residue: 1.4567 time to fit residues: 541.1975 Evaluate side-chains 328 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 294 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 238 GLU Chi-restraints excluded: chain A residue 245 GLN 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 B residue 418 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 C residue 466 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 245 GLN 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 418 GLU Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain E residue 513 MET 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: 0.8980 chunk 175 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 217 GLN B 243 GLN B 403 GLN B 470 ASN C 213 GLN C 403 GLN D 213 GLN D 217 GLN D 245 GLN D 403 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 470 ASN F 213 GLN F 403 GLN 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 = 0.3726 r_free = 0.3726 target = 0.160924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124812 restraints weight = 19735.048| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.65 r_work: 0.3253 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18276 Z= 0.193 Angle : 0.588 7.264 24774 Z= 0.292 Chirality : 0.043 0.210 2808 Planarity : 0.004 0.047 3072 Dihedral : 4.254 17.380 2418 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.22 % Allowed : 12.50 % Favored : 84.28 % 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: 2.12 (0.14), residues: 1248 sheet: 0.67 (0.40), residues: 186 loop : -0.50 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 164 HIS 0.005 0.001 HIS D 423 PHE 0.017 0.002 PHE D 367 TYR 0.020 0.002 TYR D 280 ARG 0.004 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1095) hydrogen bonds : angle 4.32122 ( 3195) SS BOND : bond 0.00027 ( 6) SS BOND : angle 0.25836 ( 12) covalent geometry : bond 0.00462 (18270) covalent geometry : angle 0.58838 (24762) *********************** 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 356 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 295 time to evaluate : 1.888 Fit side-chains REVERT: A 118 LEU cc_start: 0.7678 (tp) cc_final: 0.7254 (mp) REVERT: A 120 PHE cc_start: 0.7317 (t80) cc_final: 0.5594 (m-80) REVERT: A 158 ILE cc_start: 0.8599 (mt) cc_final: 0.8301 (mm) REVERT: A 170 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6050 (mmt-90) REVERT: A 196 TYR cc_start: 0.8173 (m-80) cc_final: 0.7535 (m-80) REVERT: A 243 GLN cc_start: 0.8148 (tt0) cc_final: 0.7448 (tt0) REVERT: A 245 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: A 333 ARG cc_start: 0.7085 (mtm180) cc_final: 0.6430 (tpm170) REVERT: A 349 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7435 (mp0) REVERT: A 385 MET cc_start: 0.8365 (ttp) cc_final: 0.8134 (ttm) REVERT: A 404 LYS cc_start: 0.8525 (mtpp) cc_final: 0.7975 (mmtt) REVERT: A 452 LYS cc_start: 0.7637 (mttt) cc_final: 0.6468 (mppt) REVERT: A 473 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7672 (pttm) REVERT: B 120 PHE cc_start: 0.6970 (t80) cc_final: 0.5241 (m-80) REVERT: B 177 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7619 (mtp180) REVERT: B 186 MET cc_start: 0.8155 (mtt) cc_final: 0.7810 (mtp) REVERT: B 341 TYR cc_start: 0.8669 (t80) cc_final: 0.8455 (t80) REVERT: B 365 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: B 371 LYS cc_start: 0.8069 (tttt) cc_final: 0.7675 (ttpt) REVERT: B 388 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.6789 (ttt90) REVERT: B 404 LYS cc_start: 0.8600 (mtpp) cc_final: 0.7982 (mmtt) REVERT: B 473 LYS cc_start: 0.8227 (pttp) cc_final: 0.7686 (pttm) REVERT: C 120 PHE cc_start: 0.7030 (t80) cc_final: 0.5186 (m-80) REVERT: C 177 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7569 (mtp180) REVERT: C 217 GLN cc_start: 0.7339 (mt0) cc_final: 0.6734 (mt0) REVERT: C 371 LYS cc_start: 0.8066 (tttt) cc_final: 0.7641 (ttpt) REVERT: C 404 LYS cc_start: 0.8351 (mtpp) cc_final: 0.7899 (mmtt) REVERT: C 417 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7789 (tmm) REVERT: C 473 LYS cc_start: 0.8302 (pttp) cc_final: 0.7815 (pttm) REVERT: D 118 LEU cc_start: 0.7701 (tp) cc_final: 0.7195 (mp) REVERT: D 120 PHE cc_start: 0.7162 (t80) cc_final: 0.5511 (m-80) REVERT: D 158 ILE cc_start: 0.8607 (mt) cc_final: 0.8305 (mm) REVERT: D 170 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6059 (mmt-90) REVERT: D 196 TYR cc_start: 0.8200 (m-80) cc_final: 0.7405 (m-80) REVERT: D 290 LEU cc_start: 0.8640 (mt) cc_final: 0.8399 (mp) REVERT: D 333 ARG cc_start: 0.7081 (mtm180) cc_final: 0.6387 (tpm170) REVERT: D 354 LYS cc_start: 0.8432 (mttt) cc_final: 0.8231 (mtmm) REVERT: D 371 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7579 (ttmt) REVERT: D 385 MET cc_start: 0.8346 (ttp) cc_final: 0.8087 (ttm) REVERT: D 404 LYS cc_start: 0.8514 (mtpp) cc_final: 0.7976 (mmtt) REVERT: D 452 LYS cc_start: 0.7688 (mttt) cc_final: 0.6489 (mppt) REVERT: D 473 LYS cc_start: 0.8188 (ptmt) cc_final: 0.7623 (pttm) REVERT: E 120 PHE cc_start: 0.7020 (t80) cc_final: 0.5433 (m-80) REVERT: E 177 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7619 (mtp180) REVERT: E 186 MET cc_start: 0.8184 (mtt) cc_final: 0.7839 (mtp) REVERT: E 217 GLN cc_start: 0.7316 (mt0) cc_final: 0.6797 (mt0) REVERT: E 365 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: E 371 LYS cc_start: 0.7926 (tttt) cc_final: 0.7459 (ttpt) REVERT: E 388 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6634 (ttt90) REVERT: E 404 LYS cc_start: 0.8541 (mtpp) cc_final: 0.7904 (mmtt) REVERT: E 473 LYS cc_start: 0.8241 (pttp) cc_final: 0.7685 (pttm) REVERT: E 502 GLU cc_start: 0.7477 (tt0) cc_final: 0.6995 (tp30) REVERT: F 120 PHE cc_start: 0.7029 (t80) cc_final: 0.5186 (m-80) REVERT: F 126 PHE cc_start: 0.8278 (m-10) cc_final: 0.8028 (m-10) REVERT: F 177 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7676 (mtp180) REVERT: F 217 GLN cc_start: 0.7276 (mt0) cc_final: 0.6687 (mt0) REVERT: F 371 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7814 (mtpt) REVERT: F 404 LYS cc_start: 0.8376 (mtpp) cc_final: 0.7923 (mmtt) REVERT: F 473 LYS cc_start: 0.8357 (pttp) cc_final: 0.7798 (pttm) outliers start: 61 outliers final: 23 residues processed: 325 average time/residue: 1.5799 time to fit residues: 561.9486 Evaluate side-chains 311 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 281 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 418 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 C residue 417 MET Chi-restraints excluded: chain C residue 466 GLU 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 439 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 148 LEU 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 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 282 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 111 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 135 optimal weight: 0.0050 chunk 155 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 143 optimal weight: 0.0970 chunk 215 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.2250 ------------------------------------------------------------------------------- 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 B 213 GLN B 217 GLN B 403 GLN B 470 ASN C 213 GLN C 470 ASN D 213 GLN D 217 GLN D 403 GLN E 213 GLN E 403 GLN F 213 GLN F 470 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.172367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.138327 restraints weight = 19606.979| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.54 r_work: 0.3421 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18276 Z= 0.108 Angle : 0.501 6.635 24774 Z= 0.254 Chirality : 0.039 0.140 2808 Planarity : 0.004 0.047 3072 Dihedral : 3.869 15.457 2418 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.43 % Allowed : 13.66 % Favored : 83.91 % 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: 2.13 (0.19), residues: 2136 helix: 2.47 (0.15), residues: 1248 sheet: 1.09 (0.41), residues: 180 loop : -0.46 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 274 HIS 0.002 0.001 HIS A 423 PHE 0.013 0.001 PHE F 149 TYR 0.009 0.001 TYR B 450 ARG 0.005 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 1095) hydrogen bonds : angle 4.15769 ( 3195) SS BOND : bond 0.00062 ( 6) SS BOND : angle 0.27498 ( 12) covalent geometry : bond 0.00243 (18270) covalent geometry : angle 0.50106 (24762) *********************** 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 369 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 time to evaluate : 2.023 Fit side-chains REVERT: A 118 LEU cc_start: 0.7734 (tp) cc_final: 0.7344 (mt) REVERT: A 120 PHE cc_start: 0.7066 (t80) cc_final: 0.5498 (m-80) REVERT: A 158 ILE cc_start: 0.8648 (mt) cc_final: 0.8369 (mm) REVERT: A 170 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6107 (mmt-90) REVERT: A 196 TYR cc_start: 0.8175 (m-80) cc_final: 0.7651 (m-80) REVERT: A 243 GLN cc_start: 0.8098 (tt0) cc_final: 0.7465 (tt0) REVERT: A 245 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7011 (mp10) REVERT: A 333 ARG cc_start: 0.7163 (mtm180) cc_final: 0.6491 (tpm170) REVERT: A 388 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7612 (ttm-80) REVERT: A 404 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8021 (mmtt) REVERT: A 452 LYS cc_start: 0.7676 (mttt) cc_final: 0.6556 (mppt) REVERT: A 473 LYS cc_start: 0.8279 (ptmt) cc_final: 0.7762 (pttm) REVERT: B 120 PHE cc_start: 0.6856 (t80) cc_final: 0.5165 (m-80) REVERT: B 177 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7523 (mtp180) REVERT: B 186 MET cc_start: 0.8128 (mtt) cc_final: 0.7846 (mtp) REVERT: B 217 GLN cc_start: 0.7196 (mt0) cc_final: 0.6746 (mt0) REVERT: B 339 ASN cc_start: 0.8151 (t0) cc_final: 0.7942 (t0) REVERT: B 341 TYR cc_start: 0.8625 (t80) cc_final: 0.8419 (t80) REVERT: B 365 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: B 388 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.6819 (ttt90) REVERT: B 404 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8023 (mmtt) REVERT: B 465 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: B 473 LYS cc_start: 0.8188 (pttp) cc_final: 0.7731 (pttm) REVERT: C 120 PHE cc_start: 0.6848 (t80) cc_final: 0.5223 (m-80) REVERT: C 126 PHE cc_start: 0.8033 (m-10) cc_final: 0.7671 (m-10) REVERT: C 160 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8556 (mt) REVERT: C 217 GLN cc_start: 0.7338 (mt0) cc_final: 0.6773 (mt0) REVERT: C 371 LYS cc_start: 0.7874 (tttt) cc_final: 0.7515 (ttpt) REVERT: C 404 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7848 (mmtt) REVERT: C 473 LYS cc_start: 0.8241 (pttp) cc_final: 0.7786 (pttm) REVERT: D 118 LEU cc_start: 0.7696 (tp) cc_final: 0.7305 (mt) REVERT: D 120 PHE cc_start: 0.7001 (t80) cc_final: 0.5457 (m-80) REVERT: D 158 ILE cc_start: 0.8635 (mt) cc_final: 0.8352 (mm) REVERT: D 170 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6075 (mmt-90) REVERT: D 196 TYR cc_start: 0.8174 (m-80) cc_final: 0.7635 (m-80) REVERT: D 290 LEU cc_start: 0.8494 (mt) cc_final: 0.8210 (mp) REVERT: D 333 ARG cc_start: 0.7199 (mtm180) cc_final: 0.6474 (tpm170) REVERT: D 385 MET cc_start: 0.8405 (ttp) cc_final: 0.7791 (ttm) REVERT: D 388 ARG cc_start: 0.7877 (ttt90) cc_final: 0.7625 (ttm-80) REVERT: D 404 LYS cc_start: 0.8456 (mtpp) cc_final: 0.8016 (mmtt) REVERT: D 431 ASP cc_start: 0.8492 (m-30) cc_final: 0.8237 (m-30) REVERT: D 452 LYS cc_start: 0.7736 (mttt) cc_final: 0.6565 (mppt) REVERT: D 473 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7710 (pttm) REVERT: E 120 PHE cc_start: 0.6859 (t80) cc_final: 0.5319 (m-80) REVERT: E 186 MET cc_start: 0.8126 (mtt) cc_final: 0.7844 (mtp) REVERT: E 217 GLN cc_start: 0.7332 (mt0) cc_final: 0.6828 (mt0) REVERT: E 371 LYS cc_start: 0.7580 (tttt) cc_final: 0.7169 (ttpt) REVERT: E 388 ARG cc_start: 0.7872 (ttt90) cc_final: 0.6760 (ttt90) REVERT: E 404 LYS cc_start: 0.8564 (mtpp) cc_final: 0.7955 (mmtt) REVERT: E 465 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7232 (pt0) REVERT: E 473 LYS cc_start: 0.8164 (pttp) cc_final: 0.7696 (pttm) REVERT: E 502 GLU cc_start: 0.7311 (tt0) cc_final: 0.6940 (tp30) REVERT: F 120 PHE cc_start: 0.6939 (t80) cc_final: 0.5187 (m-80) REVERT: F 126 PHE cc_start: 0.8174 (m-10) cc_final: 0.7895 (m-10) REVERT: F 160 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8576 (mt) REVERT: F 177 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7566 (mtp180) REVERT: F 217 GLN cc_start: 0.7204 (mt0) cc_final: 0.6654 (mt0) REVERT: F 371 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7669 (mtpt) REVERT: F 404 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7857 (mmtt) REVERT: F 473 LYS cc_start: 0.8209 (pttp) cc_final: 0.7767 (pttm) outliers start: 46 outliers final: 15 residues processed: 345 average time/residue: 1.3870 time to fit residues: 531.0593 Evaluate side-chains 329 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 306 time to evaluate : 2.271 ------------------------------------------------------------------------------- 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 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 B residue 465 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 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 477 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 465 GLU 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: 0.9990 chunk 207 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 chunk 135 optimal weight: 0.0060 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 213 GLN B 403 GLN B 470 ASN C 339 ASN C 403 GLN C 470 ASN D 217 GLN D 245 GLN D 403 GLN D 411 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN F 339 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 = 0.3836 r_free = 0.3836 target = 0.168938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134062 restraints weight = 19640.240| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.57 r_work: 0.3357 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18276 Z= 0.155 Angle : 0.548 7.731 24774 Z= 0.272 Chirality : 0.041 0.199 2808 Planarity : 0.004 0.047 3072 Dihedral : 4.045 16.344 2418 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.27 % Allowed : 14.72 % Favored : 83.02 % 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: 2.07 (0.18), residues: 2136 helix: 2.39 (0.14), residues: 1248 sheet: 1.03 (0.41), residues: 180 loop : -0.41 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 274 HIS 0.004 0.001 HIS D 423 PHE 0.018 0.002 PHE F 149 TYR 0.015 0.002 TYR D 280 ARG 0.004 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 1095) hydrogen bonds : angle 4.21091 ( 3195) SS BOND : bond 0.00026 ( 6) SS BOND : angle 0.27023 ( 12) covalent geometry : bond 0.00369 (18270) covalent geometry : angle 0.54835 (24762) *********************** 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 338 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 295 time to evaluate : 2.053 Fit side-chains REVERT: A 118 LEU cc_start: 0.7732 (tp) cc_final: 0.7279 (mp) REVERT: A 120 PHE cc_start: 0.7132 (t80) cc_final: 0.5483 (m-80) REVERT: A 158 ILE cc_start: 0.8665 (mt) cc_final: 0.8369 (mm) REVERT: A 170 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6136 (mmt-90) REVERT: A 196 TYR cc_start: 0.8214 (m-80) cc_final: 0.7680 (m-80) REVERT: A 243 GLN cc_start: 0.8057 (tt0) cc_final: 0.7425 (tt0) REVERT: A 245 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: A 333 ARG cc_start: 0.7161 (mtm180) cc_final: 0.6481 (tpm170) REVERT: A 385 MET cc_start: 0.8587 (ttp) cc_final: 0.8077 (ttm) REVERT: A 388 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7616 (ttm-80) REVERT: A 404 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8028 (mmtt) REVERT: A 452 LYS cc_start: 0.7768 (mttt) cc_final: 0.6648 (mppt) REVERT: A 473 LYS cc_start: 0.8308 (ptmt) cc_final: 0.7787 (pttm) REVERT: B 120 PHE cc_start: 0.6879 (t80) cc_final: 0.5156 (m-80) REVERT: B 177 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7655 (mtp180) REVERT: B 186 MET cc_start: 0.8214 (mtt) cc_final: 0.7853 (mtp) REVERT: B 217 GLN cc_start: 0.7232 (mt0) cc_final: 0.6769 (mt0) REVERT: B 341 TYR cc_start: 0.8664 (t80) cc_final: 0.8420 (t80) REVERT: B 365 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: B 371 LYS cc_start: 0.7861 (tttt) cc_final: 0.7483 (ttpt) REVERT: B 388 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.6860 (ttt90) REVERT: B 404 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8042 (mmtt) REVERT: B 465 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: B 473 LYS cc_start: 0.8215 (pttp) cc_final: 0.7730 (pttm) REVERT: C 120 PHE cc_start: 0.6888 (t80) cc_final: 0.5112 (m-80) REVERT: C 126 PHE cc_start: 0.8068 (m-10) cc_final: 0.7681 (m-10) REVERT: C 160 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8569 (mt) REVERT: C 177 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7604 (mtp180) REVERT: C 217 GLN cc_start: 0.7369 (mt0) cc_final: 0.6778 (mt0) REVERT: C 371 LYS cc_start: 0.8022 (tttt) cc_final: 0.7619 (ttpt) REVERT: C 404 LYS cc_start: 0.8329 (mtpp) cc_final: 0.7888 (mmtt) REVERT: C 473 LYS cc_start: 0.8310 (pttp) cc_final: 0.7807 (pttm) REVERT: D 118 LEU cc_start: 0.7727 (tp) cc_final: 0.7325 (mt) REVERT: D 120 PHE cc_start: 0.7064 (t80) cc_final: 0.5438 (m-80) REVERT: D 158 ILE cc_start: 0.8661 (mt) cc_final: 0.8372 (mm) REVERT: D 196 TYR cc_start: 0.8208 (m-80) cc_final: 0.7660 (m-80) REVERT: D 290 LEU cc_start: 0.8541 (mt) cc_final: 0.8252 (mp) REVERT: D 388 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7688 (ttm-80) REVERT: D 398 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8554 (ptm) REVERT: D 404 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8004 (mmtt) REVERT: D 432 MET cc_start: 0.8635 (mtp) cc_final: 0.8344 (mtm) REVERT: D 452 LYS cc_start: 0.7724 (mttt) cc_final: 0.6545 (mppt) REVERT: D 473 LYS cc_start: 0.8260 (ptmt) cc_final: 0.7730 (pttm) REVERT: E 120 PHE cc_start: 0.6898 (t80) cc_final: 0.5295 (m-80) REVERT: E 177 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7660 (mtp180) REVERT: E 186 MET cc_start: 0.8201 (mtt) cc_final: 0.7837 (mtp) REVERT: E 217 GLN cc_start: 0.7314 (mt0) cc_final: 0.6799 (mt0) REVERT: E 371 LYS cc_start: 0.7749 (tttt) cc_final: 0.7326 (ttpt) REVERT: E 388 ARG cc_start: 0.7852 (ttt90) cc_final: 0.6776 (ttt90) REVERT: E 404 LYS cc_start: 0.8597 (mtpp) cc_final: 0.7980 (mmtt) REVERT: E 465 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: E 473 LYS cc_start: 0.8208 (pttp) cc_final: 0.7707 (pttm) REVERT: E 502 GLU cc_start: 0.7429 (tt0) cc_final: 0.7072 (tp30) REVERT: F 120 PHE cc_start: 0.6948 (t80) cc_final: 0.5156 (m-80) REVERT: F 160 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8571 (mt) REVERT: F 177 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7596 (mtp180) REVERT: F 217 GLN cc_start: 0.7234 (mt0) cc_final: 0.6669 (mt0) REVERT: F 404 LYS cc_start: 0.8394 (mtpp) cc_final: 0.7942 (mmtt) REVERT: F 452 LYS cc_start: 0.7970 (mttt) cc_final: 0.6657 (mppt) REVERT: F 473 LYS cc_start: 0.8290 (pttp) cc_final: 0.7848 (pttm) outliers start: 43 outliers final: 18 residues processed: 313 average time/residue: 1.4918 time to fit residues: 514.5400 Evaluate side-chains 319 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 388 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 476 ILE 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 B residue 418 GLU Chi-restraints excluded: chain B residue 465 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 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 388 ARG Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 465 GLU 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: 1.9990 chunk 159 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 206 optimal weight: 0.5980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 B 213 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN B 470 ASN C 213 GLN C 403 GLN C 470 ASN D 213 GLN D 217 GLN D 245 GLN D 403 GLN E 213 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 HIS E 470 ASN F 470 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.168010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133227 restraints weight = 19680.516| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.55 r_work: 0.3359 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18276 Z= 0.169 Angle : 0.565 7.901 24774 Z= 0.280 Chirality : 0.042 0.196 2808 Planarity : 0.004 0.049 3072 Dihedral : 4.107 16.372 2418 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.74 % Allowed : 14.45 % Favored : 82.81 % 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: 1.99 (0.18), residues: 2136 helix: 2.30 (0.14), residues: 1248 sheet: 0.99 (0.41), residues: 180 loop : -0.38 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 274 HIS 0.005 0.001 HIS D 423 PHE 0.019 0.002 PHE F 149 TYR 0.019 0.002 TYR D 280 ARG 0.005 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1095) hydrogen bonds : angle 4.26304 ( 3195) SS BOND : bond 0.00028 ( 6) SS BOND : angle 0.25944 ( 12) covalent geometry : bond 0.00404 (18270) covalent geometry : angle 0.56474 (24762) *********************** 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 340 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7758 (tp) cc_final: 0.7315 (mp) REVERT: A 120 PHE cc_start: 0.7220 (t80) cc_final: 0.5488 (m-80) REVERT: A 170 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6170 (mmt-90) REVERT: A 196 TYR cc_start: 0.8173 (m-80) cc_final: 0.7578 (m-80) REVERT: A 243 GLN cc_start: 0.8043 (tt0) cc_final: 0.7400 (tt0) REVERT: A 245 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: A 333 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6511 (tpm170) REVERT: A 388 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7703 (ttm-80) REVERT: A 404 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8033 (mmtt) REVERT: A 452 LYS cc_start: 0.7787 (mttt) cc_final: 0.6662 (mppt) REVERT: A 473 LYS cc_start: 0.8305 (ptmt) cc_final: 0.7788 (pttm) REVERT: B 120 PHE cc_start: 0.6874 (t80) cc_final: 0.5115 (m-80) REVERT: B 177 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7675 (mtp180) REVERT: B 186 MET cc_start: 0.8222 (mtt) cc_final: 0.7845 (mtp) REVERT: B 341 TYR cc_start: 0.8718 (t80) cc_final: 0.8475 (t80) REVERT: B 365 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: B 371 LYS cc_start: 0.7947 (tttt) cc_final: 0.7653 (ttpt) REVERT: B 388 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.6857 (ttt90) REVERT: B 404 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8051 (mmtt) REVERT: B 465 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: B 473 LYS cc_start: 0.8235 (pttp) cc_final: 0.7746 (pttm) REVERT: C 120 PHE cc_start: 0.7008 (t80) cc_final: 0.5208 (m-80) REVERT: C 177 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7687 (mtp180) REVERT: C 217 GLN cc_start: 0.7381 (mt0) cc_final: 0.6796 (mt0) REVERT: C 371 LYS cc_start: 0.8071 (tttt) cc_final: 0.7712 (ttpt) REVERT: C 404 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7934 (mmtt) REVERT: C 473 LYS cc_start: 0.8315 (pttp) cc_final: 0.7788 (pttm) REVERT: D 118 LEU cc_start: 0.7758 (tp) cc_final: 0.7357 (mt) REVERT: D 120 PHE cc_start: 0.7125 (t80) cc_final: 0.5459 (m-80) REVERT: D 158 ILE cc_start: 0.8676 (mt) cc_final: 0.8386 (mm) REVERT: D 170 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6127 (mmt-90) REVERT: D 196 TYR cc_start: 0.8199 (m-80) cc_final: 0.7576 (m-80) REVERT: D 290 LEU cc_start: 0.8554 (mt) cc_final: 0.8275 (mp) REVERT: D 385 MET cc_start: 0.8584 (ttp) cc_final: 0.8145 (ttm) REVERT: D 388 ARG cc_start: 0.7910 (ttt90) cc_final: 0.7689 (ttm-80) REVERT: D 398 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8605 (ptm) REVERT: D 404 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8053 (mmtt) REVERT: D 432 MET cc_start: 0.8617 (mtp) cc_final: 0.8336 (mtm) REVERT: D 452 LYS cc_start: 0.7857 (mttt) cc_final: 0.6666 (mppt) REVERT: D 473 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7779 (pttm) REVERT: E 120 PHE cc_start: 0.6836 (t80) cc_final: 0.5195 (m-80) REVERT: E 177 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7685 (mtp180) REVERT: E 186 MET cc_start: 0.8199 (mtt) cc_final: 0.7867 (mtp) REVERT: E 217 GLN cc_start: 0.7321 (mt0) cc_final: 0.6799 (mt0) REVERT: E 371 LYS cc_start: 0.7782 (tttt) cc_final: 0.7381 (ttpt) REVERT: E 388 ARG cc_start: 0.7876 (ttt90) cc_final: 0.6820 (ttt90) REVERT: E 398 MET cc_start: 0.8777 (ptp) cc_final: 0.8503 (ptm) REVERT: E 404 LYS cc_start: 0.8629 (mtpp) cc_final: 0.7992 (mmtt) REVERT: E 465 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: E 473 LYS cc_start: 0.8236 (pttp) cc_final: 0.7725 (pttm) REVERT: E 502 GLU cc_start: 0.7485 (tt0) cc_final: 0.7066 (tp30) REVERT: F 120 PHE cc_start: 0.7033 (t80) cc_final: 0.5162 (m-80) REVERT: F 126 PHE cc_start: 0.8217 (m-10) cc_final: 0.7994 (m-10) REVERT: F 160 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8576 (mt) REVERT: F 177 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7714 (mtp180) REVERT: F 217 GLN cc_start: 0.7311 (mt0) cc_final: 0.6736 (mt0) REVERT: F 371 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7687 (mtmt) REVERT: F 404 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7953 (mmtt) REVERT: F 452 LYS cc_start: 0.7984 (mttt) cc_final: 0.6684 (mppt) REVERT: F 473 LYS cc_start: 0.8290 (pttp) cc_final: 0.7861 (pttm) outliers start: 52 outliers final: 20 residues processed: 312 average time/residue: 1.5773 time to fit residues: 542.7836 Evaluate side-chains 311 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 388 ARG 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 B residue 418 GLU Chi-restraints excluded: chain B residue 465 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 C residue 465 GLU 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 398 MET 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 465 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 209 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 178 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 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 213 GLN A 217 GLN A 403 GLN B 217 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN B 411 GLN B 470 ASN C 213 GLN C 403 GLN C 470 ASN D 213 GLN D 217 GLN D 245 GLN D 403 GLN D 422 GLN E 213 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.170256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.135862 restraints weight = 19747.203| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.55 r_work: 0.3379 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18276 Z= 0.126 Angle : 0.526 8.916 24774 Z= 0.263 Chirality : 0.040 0.163 2808 Planarity : 0.004 0.048 3072 Dihedral : 3.950 17.592 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.06 % Allowed : 15.51 % Favored : 82.44 % 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: 2.15 (0.18), residues: 2136 helix: 2.45 (0.14), residues: 1248 sheet: 1.07 (0.42), residues: 180 loop : -0.37 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 274 HIS 0.003 0.001 HIS D 423 PHE 0.022 0.002 PHE F 149 TYR 0.012 0.001 TYR C 280 ARG 0.006 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 1095) hydrogen bonds : angle 4.19706 ( 3195) SS BOND : bond 0.00039 ( 6) SS BOND : angle 0.28292 ( 12) covalent geometry : bond 0.00293 (18270) covalent geometry : angle 0.52643 (24762) *********************** 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 338 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 299 time to evaluate : 2.604 Fit side-chains REVERT: A 118 LEU cc_start: 0.7773 (tp) cc_final: 0.7373 (mt) REVERT: A 120 PHE cc_start: 0.7110 (t80) cc_final: 0.5468 (m-80) REVERT: A 196 TYR cc_start: 0.8222 (m-80) cc_final: 0.7701 (m-80) REVERT: A 243 GLN cc_start: 0.8034 (tt0) cc_final: 0.7426 (tt0) REVERT: A 245 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: A 333 ARG cc_start: 0.7240 (mtm180) cc_final: 0.6533 (tpm170) REVERT: A 388 ARG cc_start: 0.7936 (ttt90) cc_final: 0.7711 (ttm-80) REVERT: A 452 LYS cc_start: 0.7805 (mttt) cc_final: 0.6635 (mppt) REVERT: A 473 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7790 (pttm) REVERT: B 120 PHE cc_start: 0.6832 (t80) cc_final: 0.5139 (m-80) REVERT: B 170 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6100 (mmt180) REVERT: B 177 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7582 (mtp180) REVERT: B 186 MET cc_start: 0.8187 (mtt) cc_final: 0.7873 (mtp) REVERT: B 341 TYR cc_start: 0.8624 (t80) cc_final: 0.8393 (t80) REVERT: B 365 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: B 371 LYS cc_start: 0.7738 (tttt) cc_final: 0.7385 (ttpt) REVERT: B 388 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.6833 (ttt90) REVERT: B 403 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7472 (tm130) REVERT: B 404 LYS cc_start: 0.8597 (mtpp) cc_final: 0.7992 (mmtt) REVERT: B 465 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: B 473 LYS cc_start: 0.8240 (pttp) cc_final: 0.7757 (pttm) REVERT: C 120 PHE cc_start: 0.6918 (t80) cc_final: 0.5124 (m-80) REVERT: C 160 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8561 (mt) REVERT: C 177 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7560 (mtp180) REVERT: C 217 GLN cc_start: 0.7341 (mt0) cc_final: 0.6749 (mt0) REVERT: C 371 LYS cc_start: 0.7993 (tttt) cc_final: 0.7599 (ttpt) REVERT: C 404 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7927 (mmtt) REVERT: C 473 LYS cc_start: 0.8292 (pttp) cc_final: 0.7830 (pttm) REVERT: D 118 LEU cc_start: 0.7737 (tp) cc_final: 0.7330 (mt) REVERT: D 120 PHE cc_start: 0.7082 (t80) cc_final: 0.5448 (m-80) REVERT: D 149 PHE cc_start: 0.7624 (m-80) cc_final: 0.7117 (m-10) REVERT: D 158 ILE cc_start: 0.8660 (mt) cc_final: 0.8369 (mm) REVERT: D 170 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6039 (mmt-90) REVERT: D 196 TYR cc_start: 0.8178 (m-80) cc_final: 0.7579 (m-80) REVERT: D 290 LEU cc_start: 0.8505 (mt) cc_final: 0.8217 (mp) REVERT: D 385 MET cc_start: 0.8595 (ttp) cc_final: 0.8041 (ttm) REVERT: D 404 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8020 (mmtt) REVERT: D 432 MET cc_start: 0.8604 (mtp) cc_final: 0.8356 (mtm) REVERT: D 452 LYS cc_start: 0.7857 (mttt) cc_final: 0.6645 (mppt) REVERT: D 473 LYS cc_start: 0.8307 (ptmt) cc_final: 0.7766 (pttm) REVERT: E 120 PHE cc_start: 0.6772 (t80) cc_final: 0.5310 (m-80) REVERT: E 177 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7606 (mtp180) REVERT: E 186 MET cc_start: 0.8169 (mtt) cc_final: 0.7858 (mtp) REVERT: E 217 GLN cc_start: 0.7302 (mt0) cc_final: 0.6810 (mt0) REVERT: E 371 LYS cc_start: 0.7643 (tttt) cc_final: 0.7231 (ttpt) REVERT: E 388 ARG cc_start: 0.7875 (ttt90) cc_final: 0.6812 (ttt90) REVERT: E 404 LYS cc_start: 0.8565 (mtpp) cc_final: 0.7953 (mmtt) REVERT: E 473 LYS cc_start: 0.8231 (pttp) cc_final: 0.7727 (pttm) REVERT: E 502 GLU cc_start: 0.7408 (tt0) cc_final: 0.6982 (tp30) REVERT: F 120 PHE cc_start: 0.6897 (t80) cc_final: 0.5126 (m-80) REVERT: F 126 PHE cc_start: 0.8155 (m-10) cc_final: 0.7928 (m-10) REVERT: F 160 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8576 (mt) REVERT: F 177 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7638 (mtp180) REVERT: F 217 GLN cc_start: 0.7299 (mt0) cc_final: 0.6709 (mt0) REVERT: F 404 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7947 (mmtt) REVERT: F 452 LYS cc_start: 0.7954 (mttt) cc_final: 0.6646 (mppt) REVERT: F 473 LYS cc_start: 0.8284 (pttp) cc_final: 0.7856 (pttm) outliers start: 39 outliers final: 20 residues processed: 315 average time/residue: 1.4831 time to fit residues: 515.4948 Evaluate side-chains 316 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 288 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 A residue 476 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 465 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 465 GLU 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 439 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 152 VAL 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 513 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 217 GLN A 403 GLN A 411 GLN B 213 GLN B 217 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN B 415 HIS B 470 ASN C 213 GLN C 339 ASN C 403 GLN C 470 ASN D 213 GLN D 217 GLN D 245 GLN D 403 GLN D 422 GLN E 213 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN F 339 ASN F 470 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.167821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132975 restraints weight = 19731.687| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.55 r_work: 0.3330 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18276 Z= 0.177 Angle : 0.578 9.046 24774 Z= 0.286 Chirality : 0.042 0.176 2808 Planarity : 0.004 0.049 3072 Dihedral : 4.127 16.737 2418 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.79 % Allowed : 15.98 % Favored : 82.23 % 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: 1.97 (0.18), residues: 2136 helix: 2.27 (0.14), residues: 1248 sheet: 0.99 (0.42), residues: 180 loop : -0.35 (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 0.025 0.002 PHE F 149 TYR 0.020 0.002 TYR A 280 ARG 0.006 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1095) hydrogen bonds : angle 4.28574 ( 3195) SS BOND : bond 0.00037 ( 6) SS BOND : angle 0.25963 ( 12) covalent geometry : bond 0.00425 (18270) covalent geometry : angle 0.57856 (24762) ********************** 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 319 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 1.852 Fit side-chains REVERT: A 118 LEU cc_start: 0.7766 (tp) cc_final: 0.7327 (mp) REVERT: A 120 PHE cc_start: 0.7255 (t80) cc_final: 0.5519 (m-80) REVERT: A 158 ILE cc_start: 0.8681 (mt) cc_final: 0.8388 (mm) REVERT: A 196 TYR cc_start: 0.8195 (m-80) cc_final: 0.7592 (m-80) REVERT: A 243 GLN cc_start: 0.8041 (tt0) cc_final: 0.7410 (tt0) REVERT: A 245 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: A 333 ARG cc_start: 0.7249 (mtm180) cc_final: 0.6538 (tpm170) REVERT: A 404 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8085 (mmtt) REVERT: A 452 LYS cc_start: 0.7839 (mttt) cc_final: 0.6620 (mppt) REVERT: A 473 LYS cc_start: 0.8309 (ptmt) cc_final: 0.7800 (pttm) REVERT: A 513 MET cc_start: 0.8063 (tpp) cc_final: 0.7849 (tpt) REVERT: B 120 PHE cc_start: 0.6909 (t80) cc_final: 0.5174 (m-80) REVERT: B 170 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7125 (mmt180) REVERT: B 177 ARG cc_start: 0.8237 (mtt180) cc_final: 0.7679 (mtp180) REVERT: B 186 MET cc_start: 0.8235 (mtt) cc_final: 0.7908 (mtp) REVERT: B 217 GLN cc_start: 0.7277 (mt0) cc_final: 0.6820 (mt0) REVERT: B 341 TYR cc_start: 0.8733 (t80) cc_final: 0.8482 (t80) REVERT: B 371 LYS cc_start: 0.7902 (tttt) cc_final: 0.7619 (ttpt) REVERT: B 388 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.6872 (ttt90) REVERT: B 404 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8080 (mmtt) REVERT: B 465 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: B 473 LYS cc_start: 0.8239 (pttp) cc_final: 0.7748 (pttm) REVERT: C 120 PHE cc_start: 0.6994 (t80) cc_final: 0.5156 (m-80) REVERT: C 126 PHE cc_start: 0.8056 (m-10) cc_final: 0.7740 (m-10) REVERT: C 160 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8575 (mt) REVERT: C 177 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7712 (mtp180) REVERT: C 217 GLN cc_start: 0.7408 (mt0) cc_final: 0.6848 (mt0) REVERT: C 371 LYS cc_start: 0.8103 (tttt) cc_final: 0.7760 (ttpt) REVERT: C 404 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7945 (mmtt) REVERT: C 473 LYS cc_start: 0.8321 (pttp) cc_final: 0.7774 (pttm) REVERT: D 118 LEU cc_start: 0.7769 (tp) cc_final: 0.7360 (mt) REVERT: D 120 PHE cc_start: 0.7219 (t80) cc_final: 0.5482 (m-80) REVERT: D 148 LEU cc_start: 0.8007 (mt) cc_final: 0.7721 (mp) REVERT: D 158 ILE cc_start: 0.8679 (mt) cc_final: 0.8392 (mm) REVERT: D 170 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6121 (mmt-90) REVERT: D 177 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7608 (mtp180) REVERT: D 196 TYR cc_start: 0.8197 (m-80) cc_final: 0.7587 (m-80) REVERT: D 290 LEU cc_start: 0.8550 (mt) cc_final: 0.8269 (mp) REVERT: D 385 MET cc_start: 0.8575 (ttp) cc_final: 0.7962 (ttm) REVERT: D 404 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8063 (mmtt) REVERT: D 432 MET cc_start: 0.8614 (mtp) cc_final: 0.8338 (mtm) REVERT: D 452 LYS cc_start: 0.7905 (mttt) cc_final: 0.6659 (mppt) REVERT: D 473 LYS cc_start: 0.8322 (ptmt) cc_final: 0.7787 (pttm) REVERT: E 120 PHE cc_start: 0.6890 (t80) cc_final: 0.5425 (m-80) REVERT: E 177 ARG cc_start: 0.8272 (mtt180) cc_final: 0.7708 (mtp180) REVERT: E 186 MET cc_start: 0.8216 (mtt) cc_final: 0.7889 (mtp) REVERT: E 217 GLN cc_start: 0.7399 (mt0) cc_final: 0.6905 (mt0) REVERT: E 371 LYS cc_start: 0.7790 (tttt) cc_final: 0.7349 (ttpt) REVERT: E 388 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6834 (ttt90) REVERT: E 404 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8005 (mmtt) REVERT: E 473 LYS cc_start: 0.8246 (pttp) cc_final: 0.7736 (pttm) REVERT: E 502 GLU cc_start: 0.7472 (tt0) cc_final: 0.7061 (tp30) REVERT: F 120 PHE cc_start: 0.7032 (t80) cc_final: 0.5198 (m-80) REVERT: F 126 PHE cc_start: 0.8228 (m-10) cc_final: 0.7816 (m-10) REVERT: F 160 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8570 (mt) REVERT: F 177 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7732 (mtp180) REVERT: F 217 GLN cc_start: 0.7364 (mt0) cc_final: 0.6794 (mt0) REVERT: F 404 LYS cc_start: 0.8361 (mtpp) cc_final: 0.7948 (mmtt) REVERT: F 452 LYS cc_start: 0.7935 (mttt) cc_final: 0.6654 (mppt) REVERT: F 473 LYS cc_start: 0.8286 (pttp) cc_final: 0.7861 (pttm) REVERT: F 513 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6872 (mmm) outliers start: 34 outliers final: 18 residues processed: 299 average time/residue: 1.5573 time to fit residues: 511.0094 Evaluate side-chains 305 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL 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 B residue 418 GLU Chi-restraints excluded: chain B residue 465 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 465 GLU 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 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 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 513 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.0000 chunk 167 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 162 optimal weight: 0.0570 chunk 134 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 203 optimal weight: 0.8980 chunk 154 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 overall best weight: 0.2902 ------------------------------------------------------------------------------- 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 B 213 GLN B 470 ASN C 213 GLN C 403 GLN C 470 ASN D 213 GLN D 217 GLN D 245 GLN D 403 GLN D 422 GLN E 213 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 = 0.3869 r_free = 0.3869 target = 0.171855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.137661 restraints weight = 19666.186| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.56 r_work: 0.3416 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18276 Z= 0.114 Angle : 0.520 9.097 24774 Z= 0.261 Chirality : 0.040 0.153 2808 Planarity : 0.004 0.048 3072 Dihedral : 3.894 16.233 2418 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.79 % Allowed : 15.82 % Favored : 82.38 % 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: 2.21 (0.18), residues: 2136 helix: 2.49 (0.14), residues: 1248 sheet: 1.15 (0.42), residues: 180 loop : -0.35 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 274 HIS 0.003 0.001 HIS E 423 PHE 0.025 0.002 PHE F 149 TYR 0.010 0.001 TYR C 280 ARG 0.007 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 1095) hydrogen bonds : angle 4.19020 ( 3195) SS BOND : bond 0.00041 ( 6) SS BOND : angle 0.29214 ( 12) covalent geometry : bond 0.00259 (18270) covalent geometry : angle 0.52013 (24762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13573.80 seconds wall clock time: 234 minutes 30.45 seconds (14070.45 seconds total)