Starting phenix.real_space_refine on Thu Sep 18 15:14:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk7_61546/09_2025/9jk7_61546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk7_61546/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jk7_61546/09_2025/9jk7_61546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk7_61546/09_2025/9jk7_61546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jk7_61546/09_2025/9jk7_61546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk7_61546/09_2025/9jk7_61546.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 3.14, per 1000 atoms: 0.18 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 B 141 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS D 141 " - pdb=" SG CYS D 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 141 " - pdb=" SG CYS E 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: 1.84 Conformation dependent library (CDL) restraints added in 902.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 109 through 134 Proline residue: A 123 - end of helix Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 142 through 168 removed outlier: 4.313A pdb=" N GLU A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 204 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.748A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 4.740A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 339 through 369 Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.081A pdb=" N ALA A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 433 through 443 removed outlier: 4.917A pdb=" N ARG A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'B' and resid 110 through 134 Proline residue: B 123 - end of helix Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 142 through 168 removed outlier: 4.313A pdb=" N GLU B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 168 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 204 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.749A pdb=" N VAL B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 removed outlier: 4.740A pdb=" N HIS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 336 Processing helix chain 'B' and resid 339 through 369 Processing helix chain 'B' and resid 386 through 396 removed outlier: 4.081A pdb=" N ALA B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 416 through 430 Processing helix chain 'B' and resid 433 through 443 removed outlier: 4.917A pdb=" N ARG B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'C' and resid 110 through 134 Proline residue: C 123 - end of helix Proline residue: C 130 - end of helix Processing helix chain 'C' and resid 142 through 168 removed outlier: 4.313A pdb=" N GLU C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 204 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.749A pdb=" N VAL C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 283 removed outlier: 4.740A pdb=" N HIS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 339 through 369 Processing helix chain 'C' and resid 386 through 396 removed outlier: 4.081A pdb=" N ALA C 396 " --> pdb=" O GLN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 416 through 430 Processing helix chain 'C' and resid 433 through 443 removed outlier: 4.918A pdb=" N ARG C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR C 441 " --> pdb=" O PHE C 437 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 451 through 455 Processing helix chain 'D' and resid 110 through 134 Proline residue: D 123 - end of helix Proline residue: D 130 - end of helix Processing helix chain 'D' and resid 142 through 168 removed outlier: 4.314A pdb=" N GLU D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 204 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.748A pdb=" N VAL D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 283 removed outlier: 4.741A pdb=" N HIS D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 336 Processing helix chain 'D' and resid 339 through 369 Processing helix chain 'D' and resid 386 through 396 removed outlier: 4.081A pdb=" N ALA D 396 " --> pdb=" O GLN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 416 through 430 Processing helix chain 'D' and resid 433 through 443 removed outlier: 4.917A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 451 through 455 Processing helix chain 'E' and resid 110 through 134 Proline residue: E 123 - end of helix Proline residue: E 130 - end of helix Processing helix chain 'E' and resid 142 through 168 removed outlier: 4.314A pdb=" N GLU E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE E 168 " --> pdb=" O TRP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 204 Processing helix chain 'E' and resid 211 through 238 removed outlier: 3.748A pdb=" N VAL E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 4.740A pdb=" N HIS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 Processing helix chain 'E' and resid 339 through 369 Processing helix chain 'E' and resid 386 through 396 removed outlier: 4.081A pdb=" N ALA E 396 " --> pdb=" O GLN E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 409 Processing helix chain 'E' and resid 416 through 430 Processing helix chain 'E' and resid 433 through 443 removed outlier: 4.917A pdb=" N ARG E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR E 441 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 451 through 455 Processing helix chain 'F' and resid 110 through 134 Proline residue: F 123 - end of helix Proline residue: F 130 - end of helix Processing helix chain 'F' and resid 142 through 168 removed outlier: 4.314A pdb=" N GLU F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 168 " --> pdb=" O TRP F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 204 Processing helix chain 'F' and resid 211 through 238 removed outlier: 3.748A pdb=" N VAL F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 removed outlier: 4.740A pdb=" N HIS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 336 Processing helix chain 'F' and resid 339 through 369 Processing helix chain 'F' and resid 386 through 396 removed outlier: 4.081A pdb=" N ALA F 396 " --> pdb=" O GLN F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 409 Processing helix chain 'F' and resid 416 through 430 Processing helix chain 'F' and resid 433 through 443 removed outlier: 4.917A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR F 441 " --> pdb=" O PHE F 437 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA F 443 " --> pdb=" O GLU F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 450 Processing helix chain 'F' and resid 451 through 455 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.724A pdb=" N TRP A 460 " --> pdb=" O LYS B 498 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 464 " --> pdb=" O GLU B 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 173 through 174 removed outlier: 6.739A pdb=" N PHE A 497 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS A 498 " --> pdb=" O TRP C 460 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU C 462 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER A 500 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER C 464 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A 502 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.638A pdb=" N TRP B 460 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 464 " --> pdb=" O GLU C 502 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 173 through 174 removed outlier: 3.646A pdb=" N TRP D 460 " --> pdb=" O LYS E 498 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 464 " --> pdb=" O GLU E 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 173 through 174 removed outlier: 6.742A pdb=" N PHE D 497 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS D 498 " --> pdb=" O TRP F 460 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU F 462 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER D 500 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER F 464 " --> pdb=" O SER D 500 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU D 502 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.565A pdb=" N TRP E 460 " --> pdb=" O LYS F 498 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 464 " --> pdb=" O GLU F 502 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.41 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.660 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG E 334 TYR 0.022 0.002 TYR A 450 PHE 0.037 0.004 PHE B 260 TRP 0.020 0.002 TRP B 164 HIS 0.008 0.001 HIS F 423 Details of bonding type rmsd covalent geometry : bond 0.00468 (18270) covalent geometry : angle 0.66929 (24762) SS BOND : bond 0.00504 ( 6) SS BOND : angle 0.45044 ( 12) hydrogen bonds : bond 0.10587 ( 1095) hydrogen bonds : angle 5.15878 ( 3195) *********************** 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 : 0.720 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: 0.8111 time to fit residues: 393.6734 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 : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 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 217 GLN A 339 ASN A 403 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN B 217 GLN B 403 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 243 GLN D 339 ASN D 403 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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 = 0.3764 r_free = 0.3764 target = 0.163014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.127443 restraints weight = 19269.451| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.59 r_work: 0.3260 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1793 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= 0.185 Angle : 0.615 8.085 24774 Z= 0.308 Chirality : 0.044 0.193 2808 Planarity : 0.004 0.040 3072 Dihedral : 4.471 19.389 2418 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 9.55 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.18), residues: 2136 helix: 1.36 (0.14), residues: 1248 sheet: 0.30 (0.39), residues: 186 loop : -1.05 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 353 TYR 0.015 0.002 TYR A 450 PHE 0.022 0.003 PHE A 367 TRP 0.016 0.002 TRP F 164 HIS 0.007 0.001 HIS B 423 Details of bonding type rmsd covalent geometry : bond 0.00443 (18270) covalent geometry : angle 0.61535 (24762) SS BOND : bond 0.00065 ( 6) SS BOND : angle 0.30581 ( 12) hydrogen bonds : bond 0.04191 ( 1095) hydrogen bonds : angle 4.46687 ( 3195) *********************** 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 356 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 315 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7496 (tp) cc_final: 0.7121 (mp) REVERT: A 120 PHE cc_start: 0.7201 (t80) cc_final: 0.5457 (m-80) REVERT: A 158 ILE cc_start: 0.8552 (mt) cc_final: 0.8315 (mm) REVERT: A 170 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.5913 (mmt-90) REVERT: A 243 GLN cc_start: 0.8204 (tt0) cc_final: 0.7405 (tt0) REVERT: A 245 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.6818 (mp10) REVERT: A 333 ARG cc_start: 0.6953 (mtm180) cc_final: 0.6400 (tpm170) REVERT: A 385 MET cc_start: 0.8338 (ttp) cc_final: 0.7795 (ttm) REVERT: A 388 ARG cc_start: 0.8011 (tpt170) cc_final: 0.7728 (ttm-80) REVERT: A 404 LYS cc_start: 0.8543 (mtpp) cc_final: 0.7945 (mmtt) REVERT: A 452 LYS cc_start: 0.7742 (mttt) cc_final: 0.6404 (mppt) REVERT: A 513 MET cc_start: 0.7240 (mmp) cc_final: 0.6450 (mmp) REVERT: B 120 PHE cc_start: 0.6889 (t80) cc_final: 0.5172 (m-80) REVERT: B 149 PHE cc_start: 0.7896 (m-80) cc_final: 0.7639 (m-80) REVERT: B 150 ILE cc_start: 0.7124 (mt) cc_final: 0.6803 (mt) REVERT: B 177 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7635 (mtp180) REVERT: B 186 MET cc_start: 0.8022 (mtt) cc_final: 0.7637 (mtp) REVERT: B 341 TYR cc_start: 0.8616 (t80) cc_final: 0.8341 (t80) REVERT: B 404 LYS cc_start: 0.8541 (mtpp) cc_final: 0.7919 (mmtt) REVERT: B 473 LYS cc_start: 0.8062 (pttp) cc_final: 0.7496 (pttm) REVERT: B 513 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7721 (tpp) REVERT: C 120 PHE cc_start: 0.6963 (t80) cc_final: 0.5121 (m-80) REVERT: C 148 LEU cc_start: 0.7936 (mt) cc_final: 0.7731 (mp) REVERT: C 160 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8406 (mt) REVERT: C 186 MET cc_start: 0.8086 (mtt) cc_final: 0.7829 (mtp) REVERT: C 245 GLN cc_start: 0.8684 (mm110) cc_final: 0.8452 (mm110) REVERT: C 255 ASP cc_start: 0.8431 (p0) cc_final: 0.8201 (p0) REVERT: C 349 GLU cc_start: 0.7400 (tt0) cc_final: 0.7156 (tm-30) REVERT: C 371 LYS cc_start: 0.7772 (tttt) cc_final: 0.7462 (ttpt) REVERT: C 404 LYS cc_start: 0.8322 (mtpp) cc_final: 0.7782 (mmtt) REVERT: C 417 MET cc_start: 0.7854 (tmm) cc_final: 0.7613 (tmm) REVERT: C 459 GLN cc_start: 0.8289 (mt0) cc_final: 0.7952 (mm-40) REVERT: C 473 LYS cc_start: 0.8265 (pttp) cc_final: 0.7577 (pttm) REVERT: C 502 GLU cc_start: 0.7185 (tt0) cc_final: 0.6944 (tp30) REVERT: D 118 LEU cc_start: 0.7611 (tp) cc_final: 0.7160 (mp) REVERT: D 120 PHE cc_start: 0.7127 (t80) cc_final: 0.5448 (m-80) REVERT: D 158 ILE cc_start: 0.8567 (mt) cc_final: 0.8327 (mm) REVERT: D 170 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.5919 (mmt-90) REVERT: D 290 LEU cc_start: 0.8537 (mt) cc_final: 0.8296 (mp) REVERT: D 333 ARG cc_start: 0.6874 (mtm180) cc_final: 0.6338 (tpm170) REVERT: D 385 MET cc_start: 0.8432 (ttp) cc_final: 0.8002 (ttm) REVERT: D 404 LYS cc_start: 0.8498 (mtpp) cc_final: 0.7944 (mmtt) REVERT: D 452 LYS cc_start: 0.7797 (mttt) cc_final: 0.6471 (mppt) REVERT: D 513 MET cc_start: 0.7274 (mmp) cc_final: 0.6111 (mmt) REVERT: E 120 PHE cc_start: 0.7011 (t80) cc_final: 0.5378 (m-80) REVERT: E 177 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7733 (mtp85) REVERT: E 186 MET cc_start: 0.8044 (mtt) cc_final: 0.7677 (mtp) REVERT: E 217 GLN cc_start: 0.7234 (mt0) cc_final: 0.6680 (mt0) REVERT: E 290 LEU cc_start: 0.8444 (mt) cc_final: 0.8074 (mt) REVERT: E 341 TYR cc_start: 0.8656 (t80) cc_final: 0.8438 (t80) REVERT: E 388 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6437 (ttt90) REVERT: E 403 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7469 (tm130) REVERT: E 404 LYS cc_start: 0.8573 (mtpp) cc_final: 0.7868 (mmtt) REVERT: E 473 LYS cc_start: 0.8155 (pttp) cc_final: 0.7554 (pttm) REVERT: E 502 GLU cc_start: 0.7544 (tt0) cc_final: 0.6971 (tp30) REVERT: E 513 MET cc_start: 0.7102 (mmp) cc_final: 0.5737 (mmt) REVERT: F 118 LEU cc_start: 0.7446 (tp) cc_final: 0.7047 (mp) REVERT: F 120 PHE cc_start: 0.6957 (t80) cc_final: 0.5126 (m-80) REVERT: F 160 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8425 (mt) REVERT: F 186 MET cc_start: 0.8089 (mtt) cc_final: 0.7840 (mtp) REVERT: F 255 ASP cc_start: 0.8463 (p0) cc_final: 0.8225 (p0) REVERT: F 349 GLU cc_start: 0.7405 (tt0) cc_final: 0.7155 (tm-30) REVERT: F 398 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8535 (ptm) REVERT: F 404 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7795 (mmtt) REVERT: F 439 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7864 (pp20) REVERT: F 459 GLN cc_start: 0.8284 (mt0) cc_final: 0.7969 (mm-40) REVERT: F 470 ASN cc_start: 0.8261 (m110) cc_final: 0.8041 (m110) REVERT: F 473 LYS cc_start: 0.8204 (pttp) cc_final: 0.7505 (pttm) REVERT: F 501 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7063 (tt0) outliers start: 41 outliers final: 10 residues processed: 336 average time/residue: 0.7933 time to fit residues: 292.4346 Evaluate side-chains 308 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 289 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 134 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 126 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 A 470 ASN 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 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** C 470 ASN D 217 GLN D 403 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN D 470 ASN ** 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 403 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.161915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.126027 restraints weight = 19386.651| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.61 r_work: 0.3243 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2183 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= 0.171 Angle : 0.577 7.034 24774 Z= 0.289 Chirality : 0.042 0.207 2808 Planarity : 0.004 0.041 3072 Dihedral : 4.289 18.106 2418 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.64 % Allowed : 11.34 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2136 helix: 1.85 (0.15), residues: 1248 sheet: 0.52 (0.39), residues: 186 loop : -0.74 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 454 TYR 0.015 0.002 TYR D 450 PHE 0.020 0.002 PHE B 367 TRP 0.013 0.002 TRP F 164 HIS 0.005 0.001 HIS D 423 Details of bonding type rmsd covalent geometry : bond 0.00407 (18270) covalent geometry : angle 0.57731 (24762) SS BOND : bond 0.00036 ( 6) SS BOND : angle 0.26716 ( 12) hydrogen bonds : bond 0.03903 ( 1095) hydrogen bonds : angle 4.34801 ( 3195) *********************** 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 351 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7583 (tp) cc_final: 0.7179 (mp) REVERT: A 120 PHE cc_start: 0.7143 (t80) cc_final: 0.5496 (m-80) REVERT: A 158 ILE cc_start: 0.8572 (mt) cc_final: 0.8283 (mm) REVERT: A 170 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6084 (mmt-90) REVERT: A 196 TYR cc_start: 0.8017 (m-80) cc_final: 0.7723 (m-80) REVERT: A 243 GLN cc_start: 0.8213 (tt0) cc_final: 0.7523 (tt0) REVERT: A 245 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: A 333 ARG cc_start: 0.7019 (mtm180) cc_final: 0.6418 (tpm170) REVERT: A 385 MET cc_start: 0.8461 (ttp) cc_final: 0.7928 (ttm) REVERT: A 388 ARG cc_start: 0.7942 (tpt170) cc_final: 0.7638 (ttm-80) REVERT: A 404 LYS cc_start: 0.8561 (mtpp) cc_final: 0.7983 (mmtt) REVERT: A 418 GLU cc_start: 0.7829 (tp30) cc_final: 0.7582 (tp30) REVERT: A 452 LYS cc_start: 0.7660 (mttt) cc_final: 0.6428 (mppt) REVERT: A 473 LYS cc_start: 0.8213 (ptmt) cc_final: 0.7646 (pttm) REVERT: B 120 PHE cc_start: 0.6895 (t80) cc_final: 0.5172 (m-80) REVERT: B 149 PHE cc_start: 0.7969 (m-80) cc_final: 0.7750 (m-80) REVERT: B 177 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7567 (mtp180) REVERT: B 186 MET cc_start: 0.8135 (mtt) cc_final: 0.7780 (mtp) REVERT: B 341 TYR cc_start: 0.8648 (t80) cc_final: 0.8389 (t80) REVERT: B 365 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: B 385 MET cc_start: 0.8401 (ttm) cc_final: 0.8106 (ttm) REVERT: B 388 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.6743 (ttt90) REVERT: B 404 LYS cc_start: 0.8589 (mtpp) cc_final: 0.7962 (mmtt) REVERT: B 473 LYS cc_start: 0.8162 (pttp) cc_final: 0.7631 (pttm) REVERT: C 120 PHE cc_start: 0.6916 (t80) cc_final: 0.5154 (m-80) REVERT: C 148 LEU cc_start: 0.7816 (mt) cc_final: 0.7592 (mp) REVERT: C 177 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7586 (mtp180) REVERT: C 186 MET cc_start: 0.8170 (mtt) cc_final: 0.7962 (mtp) REVERT: C 371 LYS cc_start: 0.7822 (tttt) cc_final: 0.7537 (ttpt) REVERT: C 404 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7818 (mmtt) REVERT: C 417 MET cc_start: 0.7846 (tmm) cc_final: 0.7560 (tmm) REVERT: C 473 LYS cc_start: 0.8274 (pttp) cc_final: 0.7605 (pttm) REVERT: D 118 LEU cc_start: 0.7608 (tp) cc_final: 0.7181 (mp) REVERT: D 120 PHE cc_start: 0.7128 (t80) cc_final: 0.5501 (m-80) REVERT: D 158 ILE cc_start: 0.8586 (mt) cc_final: 0.8297 (mm) REVERT: D 170 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6055 (mmt-90) REVERT: D 196 TYR cc_start: 0.7984 (m-80) cc_final: 0.7710 (m-80) REVERT: D 245 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: D 290 LEU cc_start: 0.8634 (mt) cc_final: 0.8389 (mp) REVERT: D 333 ARG cc_start: 0.7005 (mtm180) cc_final: 0.6390 (tpm170) REVERT: D 385 MET cc_start: 0.8419 (ttp) cc_final: 0.7805 (ttm) REVERT: D 404 LYS cc_start: 0.8566 (mtpp) cc_final: 0.7958 (mmtt) REVERT: D 418 GLU cc_start: 0.7863 (tp30) cc_final: 0.7596 (tp30) REVERT: D 452 LYS cc_start: 0.7678 (mttt) cc_final: 0.6480 (mppt) REVERT: D 473 LYS cc_start: 0.8220 (ptmt) cc_final: 0.7639 (pttm) REVERT: D 513 MET cc_start: 0.7333 (mmp) cc_final: 0.6330 (mmt) REVERT: E 120 PHE cc_start: 0.6995 (t80) cc_final: 0.5435 (m-80) REVERT: E 177 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7591 (mtp180) REVERT: E 186 MET cc_start: 0.8125 (mtt) cc_final: 0.7731 (mtp) REVERT: E 217 GLN cc_start: 0.7293 (mt0) cc_final: 0.6780 (mt0) REVERT: E 341 TYR cc_start: 0.8599 (t80) cc_final: 0.8364 (t80) REVERT: E 365 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: E 371 LYS cc_start: 0.8015 (tttt) cc_final: 0.7581 (ttpt) REVERT: E 388 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6520 (ttt90) REVERT: E 404 LYS cc_start: 0.8552 (mtpp) cc_final: 0.7933 (mmtt) REVERT: E 473 LYS cc_start: 0.8211 (pttp) cc_final: 0.7650 (pttm) REVERT: E 502 GLU cc_start: 0.7480 (tt0) cc_final: 0.6988 (tp30) REVERT: F 120 PHE cc_start: 0.6983 (t80) cc_final: 0.5170 (m-80) REVERT: F 177 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7609 (mtp180) REVERT: F 217 GLN cc_start: 0.7276 (mt0) cc_final: 0.6730 (mt0) REVERT: F 255 ASP cc_start: 0.8484 (p0) cc_final: 0.8279 (p0) REVERT: F 388 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6721 (ttt90) REVERT: F 398 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8534 (ptm) REVERT: F 404 LYS cc_start: 0.8341 (mtpp) cc_final: 0.7839 (mmtt) REVERT: F 422 GLN cc_start: 0.7754 (mt0) cc_final: 0.7222 (mm-40) REVERT: F 439 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7879 (pp20) REVERT: F 473 LYS cc_start: 0.8264 (pttp) cc_final: 0.7614 (pttm) REVERT: F 501 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: F 513 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7455 (mmm) outliers start: 50 outliers final: 14 residues processed: 324 average time/residue: 0.8223 time to fit residues: 291.2960 Evaluate side-chains 309 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 A residue 439 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 273 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 388 ARG Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 513 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 211 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 C 213 GLN C 217 GLN C 470 ASN D 217 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.162470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.127190 restraints weight = 19840.695| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.61 r_work: 0.3254 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18276 Z= 0.166 Angle : 0.563 6.847 24774 Z= 0.281 Chirality : 0.042 0.155 2808 Planarity : 0.004 0.044 3072 Dihedral : 4.202 17.441 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.48 % Allowed : 11.66 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.18), residues: 2136 helix: 2.06 (0.15), residues: 1248 sheet: 0.62 (0.40), residues: 186 loop : -0.59 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 350 TYR 0.015 0.002 TYR D 280 PHE 0.018 0.002 PHE C 367 TRP 0.012 0.002 TRP A 274 HIS 0.005 0.001 HIS D 423 Details of bonding type rmsd covalent geometry : bond 0.00394 (18270) covalent geometry : angle 0.56261 (24762) SS BOND : bond 0.00020 ( 6) SS BOND : angle 0.26393 ( 12) hydrogen bonds : bond 0.03769 ( 1095) hydrogen bonds : angle 4.30382 ( 3195) *********************** 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 363 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7690 (tp) cc_final: 0.7258 (mp) REVERT: A 120 PHE cc_start: 0.7271 (t80) cc_final: 0.5550 (m-80) REVERT: A 158 ILE cc_start: 0.8604 (mt) cc_final: 0.8308 (mm) REVERT: A 170 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6132 (mmt-90) REVERT: A 196 TYR cc_start: 0.8025 (m-80) cc_final: 0.7652 (m-80) REVERT: A 243 GLN cc_start: 0.8135 (tt0) cc_final: 0.7442 (tt0) REVERT: A 245 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: A 333 ARG cc_start: 0.7066 (mtm180) cc_final: 0.6446 (tpm170) REVERT: A 371 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7580 (ttmt) REVERT: A 385 MET cc_start: 0.8436 (ttp) cc_final: 0.8133 (ttm) REVERT: A 404 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8064 (mmtt) REVERT: A 452 LYS cc_start: 0.7669 (mttt) cc_final: 0.6519 (mppt) REVERT: A 473 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7656 (pttm) REVERT: B 120 PHE cc_start: 0.6908 (t80) cc_final: 0.5177 (m-80) REVERT: B 177 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7607 (mtp180) REVERT: B 186 MET cc_start: 0.8162 (mtt) cc_final: 0.7834 (mtp) REVERT: B 217 GLN cc_start: 0.7260 (mt0) cc_final: 0.6776 (mt0) REVERT: B 341 TYR cc_start: 0.8658 (t80) cc_final: 0.8390 (t80) REVERT: B 365 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: B 385 MET cc_start: 0.8442 (ttm) cc_final: 0.8207 (ttm) REVERT: B 388 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.6762 (ttt90) REVERT: B 398 MET cc_start: 0.8960 (ptm) cc_final: 0.8636 (ptm) REVERT: B 404 LYS cc_start: 0.8597 (mtpp) cc_final: 0.7988 (mmtt) REVERT: B 473 LYS cc_start: 0.8241 (pttp) cc_final: 0.7711 (pttm) REVERT: C 120 PHE cc_start: 0.7033 (t80) cc_final: 0.5185 (m-80) REVERT: C 160 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8543 (mt) REVERT: C 177 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7600 (mtp180) REVERT: C 217 GLN cc_start: 0.7325 (mt0) cc_final: 0.6783 (mt0) REVERT: C 371 LYS cc_start: 0.8017 (tttt) cc_final: 0.7628 (ttpt) REVERT: C 404 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7904 (mmtt) REVERT: C 417 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7651 (tmm) REVERT: C 473 LYS cc_start: 0.8283 (pttp) cc_final: 0.7671 (pttm) REVERT: D 118 LEU cc_start: 0.7683 (tp) cc_final: 0.7233 (mp) REVERT: D 120 PHE cc_start: 0.7206 (t80) cc_final: 0.5540 (m-80) REVERT: D 158 ILE cc_start: 0.8616 (mt) cc_final: 0.8324 (mm) REVERT: D 170 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6136 (mmt-90) REVERT: D 196 TYR cc_start: 0.8043 (m-80) cc_final: 0.7672 (m-80) REVERT: D 245 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: D 290 LEU cc_start: 0.8602 (mt) cc_final: 0.8354 (mp) REVERT: D 333 ARG cc_start: 0.7038 (mtm180) cc_final: 0.6404 (tpm170) REVERT: D 349 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7484 (mp0) REVERT: D 371 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7580 (ttmt) REVERT: D 385 MET cc_start: 0.8418 (ttp) cc_final: 0.7795 (ttm) REVERT: D 404 LYS cc_start: 0.8520 (mtpp) cc_final: 0.7999 (mmtt) REVERT: D 418 GLU cc_start: 0.7884 (tp30) cc_final: 0.7667 (tp30) REVERT: D 452 LYS cc_start: 0.7684 (mttt) cc_final: 0.6536 (mppt) REVERT: D 473 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7660 (pttm) REVERT: E 120 PHE cc_start: 0.7005 (t80) cc_final: 0.5437 (m-80) REVERT: E 177 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7608 (mtp180) REVERT: E 186 MET cc_start: 0.8165 (mtt) cc_final: 0.7838 (mtp) REVERT: E 217 GLN cc_start: 0.7313 (mt0) cc_final: 0.6795 (mt0) REVERT: E 365 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: E 371 LYS cc_start: 0.7905 (tttt) cc_final: 0.7405 (ttpt) REVERT: E 388 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6560 (ttt90) REVERT: E 404 LYS cc_start: 0.8579 (mtpp) cc_final: 0.7967 (mmtt) REVERT: E 473 LYS cc_start: 0.8242 (pttp) cc_final: 0.7703 (pttm) REVERT: E 502 GLU cc_start: 0.7374 (tt0) cc_final: 0.7032 (tp30) REVERT: F 120 PHE cc_start: 0.6990 (t80) cc_final: 0.5127 (m-80) REVERT: F 160 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8556 (mt) REVERT: F 177 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7588 (mtp180) REVERT: F 217 GLN cc_start: 0.7266 (mt0) cc_final: 0.6687 (mt0) REVERT: F 398 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (ptm) REVERT: F 404 LYS cc_start: 0.8400 (mtpp) cc_final: 0.7937 (mmtt) REVERT: F 473 LYS cc_start: 0.8293 (pttp) cc_final: 0.7761 (pttm) outliers start: 66 outliers final: 22 residues processed: 332 average time/residue: 0.7979 time to fit residues: 289.3810 Evaluate side-chains 317 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 282 ASP Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 513 MET 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 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 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 365 GLU Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 398 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 9 optimal weight: 4.9990 chunk 115 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 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 D 430 HIS E 213 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 470 ASN F 213 GLN F 430 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.125144 restraints weight = 19690.450| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.60 r_work: 0.3222 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18276 Z= 0.195 Angle : 0.585 7.019 24774 Z= 0.291 Chirality : 0.042 0.159 2808 Planarity : 0.005 0.047 3072 Dihedral : 4.253 17.075 2418 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.22 % Allowed : 12.39 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.18), residues: 2136 helix: 2.05 (0.15), residues: 1248 sheet: 0.67 (0.41), residues: 186 loop : -0.49 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 350 TYR 0.023 0.002 TYR A 280 PHE 0.019 0.002 PHE F 367 TRP 0.012 0.002 TRP A 274 HIS 0.005 0.001 HIS D 423 Details of bonding type rmsd covalent geometry : bond 0.00469 (18270) covalent geometry : angle 0.58549 (24762) SS BOND : bond 0.00049 ( 6) SS BOND : angle 0.26712 ( 12) hydrogen bonds : bond 0.03909 ( 1095) hydrogen bonds : angle 4.34664 ( 3195) *********************** 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 344 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 0.675 Fit side-chains REVERT: A 118 LEU cc_start: 0.7671 (tp) cc_final: 0.7242 (mp) REVERT: A 120 PHE cc_start: 0.7242 (t80) cc_final: 0.5536 (m-80) REVERT: A 158 ILE cc_start: 0.8594 (mt) cc_final: 0.8286 (mm) REVERT: A 170 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6070 (mmt-90) REVERT: A 196 TYR cc_start: 0.8039 (m-80) cc_final: 0.7522 (m-80) REVERT: A 243 GLN cc_start: 0.8130 (tt0) cc_final: 0.7427 (tt0) REVERT: A 245 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: A 333 ARG cc_start: 0.7070 (mtm180) cc_final: 0.6408 (tpm170) REVERT: A 349 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7420 (mp0) REVERT: A 371 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7617 (ttmt) REVERT: A 385 MET cc_start: 0.8405 (ttp) cc_final: 0.7762 (ttm) REVERT: A 404 LYS cc_start: 0.8515 (mtpp) cc_final: 0.7993 (mmtt) REVERT: A 452 LYS cc_start: 0.7697 (mttt) cc_final: 0.6549 (mppt) REVERT: A 473 LYS cc_start: 0.8274 (ptmt) cc_final: 0.7695 (pttm) REVERT: B 120 PHE cc_start: 0.6993 (t80) cc_final: 0.5245 (m-80) REVERT: B 177 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7607 (mtp180) REVERT: B 186 MET cc_start: 0.8131 (mtt) cc_final: 0.7775 (mtp) REVERT: B 217 GLN cc_start: 0.7189 (mt0) cc_final: 0.6686 (mt0) REVERT: B 341 TYR cc_start: 0.8651 (t80) cc_final: 0.8430 (t80) REVERT: B 365 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: B 388 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.6765 (ttt90) REVERT: B 398 MET cc_start: 0.8908 (ptm) cc_final: 0.8611 (ptm) REVERT: B 404 LYS cc_start: 0.8552 (mtpp) cc_final: 0.7910 (mmtt) REVERT: B 473 LYS cc_start: 0.8235 (pttp) cc_final: 0.7674 (pttm) REVERT: C 120 PHE cc_start: 0.6919 (t80) cc_final: 0.5154 (m-80) REVERT: C 160 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8542 (mt) REVERT: C 177 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7648 (mtp180) REVERT: C 354 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8130 (mttt) REVERT: C 404 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7887 (mmtt) REVERT: C 473 LYS cc_start: 0.8344 (pttp) cc_final: 0.7701 (pttm) REVERT: D 118 LEU cc_start: 0.7665 (tp) cc_final: 0.7229 (mp) REVERT: D 120 PHE cc_start: 0.7334 (t80) cc_final: 0.5599 (m-80) REVERT: D 158 ILE cc_start: 0.8604 (mt) cc_final: 0.8297 (mm) REVERT: D 170 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6079 (mmt-90) REVERT: D 196 TYR cc_start: 0.8063 (m-80) cc_final: 0.7541 (m-80) REVERT: D 290 LEU cc_start: 0.8567 (mt) cc_final: 0.8313 (mp) REVERT: D 333 ARG cc_start: 0.7101 (mtm180) cc_final: 0.6414 (tpm170) REVERT: D 371 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7583 (ttmt) REVERT: D 385 MET cc_start: 0.8410 (ttp) cc_final: 0.7794 (ttm) REVERT: D 404 LYS cc_start: 0.8476 (mtpp) cc_final: 0.7944 (mmtt) REVERT: D 452 LYS cc_start: 0.7740 (mttt) cc_final: 0.6586 (mppt) REVERT: D 473 LYS cc_start: 0.8176 (ptmt) cc_final: 0.7594 (pttm) REVERT: E 120 PHE cc_start: 0.7052 (t80) cc_final: 0.5414 (m-80) REVERT: E 177 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7613 (mtp180) REVERT: E 186 MET cc_start: 0.8162 (mtt) cc_final: 0.7813 (mtp) REVERT: E 217 GLN cc_start: 0.7286 (mt0) cc_final: 0.6750 (mt0) REVERT: E 365 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: E 388 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6545 (ttt90) REVERT: E 404 LYS cc_start: 0.8537 (mtpp) cc_final: 0.7892 (mmtt) REVERT: E 465 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: E 473 LYS cc_start: 0.8254 (pttp) cc_final: 0.7682 (pttm) REVERT: E 502 GLU cc_start: 0.7484 (tt0) cc_final: 0.7014 (tp30) REVERT: F 120 PHE cc_start: 0.6929 (t80) cc_final: 0.5176 (m-80) REVERT: F 160 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8558 (mt) REVERT: F 177 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7658 (mtp180) REVERT: F 217 GLN cc_start: 0.7264 (mt0) cc_final: 0.6675 (mt0) REVERT: F 354 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8096 (mttt) REVERT: F 398 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8563 (ptm) REVERT: F 404 LYS cc_start: 0.8356 (mtpp) cc_final: 0.7898 (mmtt) REVERT: F 452 LYS cc_start: 0.7979 (mttt) cc_final: 0.6565 (mppt) REVERT: F 473 LYS cc_start: 0.8278 (pttp) cc_final: 0.7795 (pttm) outliers start: 61 outliers final: 26 residues processed: 312 average time/residue: 0.7862 time to fit residues: 267.4577 Evaluate side-chains 314 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 282 ASP 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 160 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 354 LYS 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 238 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 513 MET 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 465 GLU Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 466 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 213 GLN C 217 GLN C 430 HIS C 470 ASN D 217 GLN D 245 GLN D 403 GLN D 411 GLN E 213 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN 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 = 0.3703 r_free = 0.3703 target = 0.158022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121216 restraints weight = 19331.610| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.71 r_work: 0.3181 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18276 Z= 0.213 Angle : 0.607 8.927 24774 Z= 0.300 Chirality : 0.043 0.172 2808 Planarity : 0.005 0.049 3072 Dihedral : 4.301 16.960 2418 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.43 % Allowed : 12.71 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.18), residues: 2136 helix: 1.99 (0.14), residues: 1248 sheet: 0.67 (0.41), residues: 186 loop : -0.44 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 252 TYR 0.027 0.002 TYR D 280 PHE 0.019 0.002 PHE E 367 TRP 0.013 0.002 TRP A 274 HIS 0.005 0.001 HIS D 423 Details of bonding type rmsd covalent geometry : bond 0.00516 (18270) covalent geometry : angle 0.60670 (24762) SS BOND : bond 0.00059 ( 6) SS BOND : angle 0.29300 ( 12) hydrogen bonds : bond 0.03993 ( 1095) hydrogen bonds : angle 4.39424 ( 3195) *********************** 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 346 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 281 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7571 (tp) cc_final: 0.7137 (mp) REVERT: A 120 PHE cc_start: 0.7156 (t80) cc_final: 0.5434 (m-80) REVERT: A 158 ILE cc_start: 0.8519 (mt) cc_final: 0.8203 (mm) REVERT: A 170 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.5987 (mmt-90) REVERT: A 196 TYR cc_start: 0.8107 (m-80) cc_final: 0.7598 (m-80) REVERT: A 243 GLN cc_start: 0.8039 (tt0) cc_final: 0.7319 (tt0) REVERT: A 245 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: A 333 ARG cc_start: 0.7128 (mtm180) cc_final: 0.6431 (tpm170) REVERT: A 388 ARG cc_start: 0.7995 (tpt170) cc_final: 0.7569 (ttm-80) REVERT: A 404 LYS cc_start: 0.8424 (mtpp) cc_final: 0.7822 (mmtt) REVERT: A 452 LYS cc_start: 0.7573 (mttt) cc_final: 0.6375 (mppt) REVERT: A 473 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7641 (pttm) REVERT: A 502 GLU cc_start: 0.7632 (tt0) cc_final: 0.7149 (tp30) REVERT: B 120 PHE cc_start: 0.7018 (t80) cc_final: 0.5128 (m-80) REVERT: B 177 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7526 (mtp180) REVERT: B 186 MET cc_start: 0.8092 (mtt) cc_final: 0.7719 (mtp) REVERT: B 217 GLN cc_start: 0.7104 (mt0) cc_final: 0.6594 (mt0) REVERT: B 282 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8436 (m-30) REVERT: B 341 TYR cc_start: 0.8624 (t80) cc_final: 0.8375 (t80) REVERT: B 388 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.6731 (ttt90) REVERT: B 404 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7735 (mmtt) REVERT: B 473 LYS cc_start: 0.8181 (pttp) cc_final: 0.7577 (pttm) REVERT: C 120 PHE cc_start: 0.6924 (t80) cc_final: 0.5140 (m-80) REVERT: C 177 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7534 (mtp180) REVERT: C 404 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7752 (mmtt) REVERT: C 473 LYS cc_start: 0.8348 (pttp) cc_final: 0.7648 (pttm) REVERT: D 118 LEU cc_start: 0.7573 (tp) cc_final: 0.7130 (mp) REVERT: D 120 PHE cc_start: 0.7168 (t80) cc_final: 0.5429 (m-80) REVERT: D 158 ILE cc_start: 0.8526 (mt) cc_final: 0.8207 (mm) REVERT: D 170 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.5947 (mmt-90) REVERT: D 177 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7537 (mtp180) REVERT: D 196 TYR cc_start: 0.8120 (m-80) cc_final: 0.7621 (m-80) REVERT: D 245 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8334 (mm-40) REVERT: D 290 LEU cc_start: 0.8558 (mt) cc_final: 0.8313 (mp) REVERT: D 333 ARG cc_start: 0.7107 (mtm180) cc_final: 0.6405 (tpm170) REVERT: D 371 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7611 (ttmt) REVERT: D 385 MET cc_start: 0.8376 (ttp) cc_final: 0.7643 (ttm) REVERT: D 388 ARG cc_start: 0.7991 (tpt170) cc_final: 0.7569 (ttm-80) REVERT: D 404 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7822 (mmtt) REVERT: D 452 LYS cc_start: 0.7605 (mttt) cc_final: 0.6398 (mppt) REVERT: D 473 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7563 (pttm) REVERT: D 502 GLU cc_start: 0.7638 (tt0) cc_final: 0.7123 (tp30) REVERT: E 120 PHE cc_start: 0.6941 (t80) cc_final: 0.5293 (m-80) REVERT: E 177 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7527 (mtp180) REVERT: E 186 MET cc_start: 0.8061 (mtt) cc_final: 0.7685 (mtp) REVERT: E 217 GLN cc_start: 0.7194 (mt0) cc_final: 0.6646 (mt0) REVERT: E 365 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: E 371 LYS cc_start: 0.7836 (tttt) cc_final: 0.7461 (ttpt) REVERT: E 388 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6550 (ttt90) REVERT: E 404 LYS cc_start: 0.8455 (mtpp) cc_final: 0.7738 (mmtt) REVERT: E 473 LYS cc_start: 0.8177 (pttp) cc_final: 0.7569 (pttm) REVERT: E 502 GLU cc_start: 0.7661 (tt0) cc_final: 0.7022 (tp30) REVERT: F 120 PHE cc_start: 0.6876 (t80) cc_final: 0.5093 (m-80) REVERT: F 177 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7532 (mtp180) REVERT: F 398 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8569 (ptm) REVERT: F 404 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7782 (mmtt) REVERT: F 452 LYS cc_start: 0.7842 (mttt) cc_final: 0.6400 (mppt) REVERT: F 473 LYS cc_start: 0.8290 (pttp) cc_final: 0.7779 (pttm) outliers start: 65 outliers final: 26 residues processed: 309 average time/residue: 0.7553 time to fit residues: 254.5474 Evaluate side-chains 312 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 282 ASP 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 282 ASP 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 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 245 GLN Chi-restraints excluded: chain D residue 255 ASP 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 273 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 Chi-restraints excluded: chain F residue 398 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 157 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 217 GLN A 403 GLN A 411 GLN B 213 GLN B 403 GLN B 470 ASN C 213 GLN C 217 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 403 GLN E 470 ASN F 213 GLN F 217 GLN F 470 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.166767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.132005 restraints weight = 19871.847| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.55 r_work: 0.3279 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18276 Z= 0.167 Angle : 0.561 8.529 24774 Z= 0.280 Chirality : 0.041 0.167 2808 Planarity : 0.004 0.049 3072 Dihedral : 4.152 16.002 2418 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.64 % Allowed : 13.87 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.18), residues: 2136 helix: 2.14 (0.14), residues: 1248 sheet: 0.71 (0.41), residues: 186 loop : -0.36 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 350 TYR 0.019 0.002 TYR D 280 PHE 0.018 0.002 PHE F 149 TRP 0.015 0.002 TRP C 274 HIS 0.004 0.001 HIS D 423 Details of bonding type rmsd covalent geometry : bond 0.00401 (18270) covalent geometry : angle 0.56111 (24762) SS BOND : bond 0.00029 ( 6) SS BOND : angle 0.29604 ( 12) hydrogen bonds : bond 0.03741 ( 1095) hydrogen bonds : angle 4.30939 ( 3195) *********************** 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 332 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 0.743 Fit side-chains REVERT: A 118 LEU cc_start: 0.7745 (tp) cc_final: 0.7313 (mp) REVERT: A 120 PHE cc_start: 0.7198 (t80) cc_final: 0.5551 (m-80) REVERT: A 158 ILE cc_start: 0.8679 (mt) cc_final: 0.8398 (mm) REVERT: A 170 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6200 (mmt-90) REVERT: A 196 TYR cc_start: 0.8127 (m-80) cc_final: 0.7637 (m-80) REVERT: A 243 GLN cc_start: 0.8057 (tt0) cc_final: 0.7438 (tt0) REVERT: A 245 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: A 333 ARG cc_start: 0.7202 (mtm180) cc_final: 0.6527 (tpm170) REVERT: A 388 ARG cc_start: 0.8080 (tpt170) cc_final: 0.7717 (ttm-80) REVERT: A 404 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8085 (mmtt) REVERT: A 452 LYS cc_start: 0.7739 (mttt) cc_final: 0.6653 (mppt) REVERT: A 473 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7809 (pttm) REVERT: B 120 PHE cc_start: 0.7038 (t80) cc_final: 0.5421 (m-80) REVERT: B 177 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7656 (mtp180) REVERT: B 186 MET cc_start: 0.8228 (mtt) cc_final: 0.7896 (mtp) REVERT: B 217 GLN cc_start: 0.7280 (mt0) cc_final: 0.6798 (mt0) REVERT: B 341 TYR cc_start: 0.8709 (t80) cc_final: 0.8488 (t80) REVERT: B 388 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.6810 (ttt90) REVERT: B 404 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8002 (mmtt) REVERT: B 465 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: B 473 LYS cc_start: 0.8263 (pttp) cc_final: 0.7760 (pttm) REVERT: C 120 PHE cc_start: 0.6941 (t80) cc_final: 0.5224 (m-80) REVERT: C 160 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8614 (mt) REVERT: C 177 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7721 (mtp180) REVERT: C 404 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7977 (mmtt) REVERT: C 473 LYS cc_start: 0.8350 (pttp) cc_final: 0.7794 (pttm) REVERT: D 118 LEU cc_start: 0.7719 (tp) cc_final: 0.7279 (mp) REVERT: D 120 PHE cc_start: 0.7156 (t80) cc_final: 0.5512 (m-80) REVERT: D 158 ILE cc_start: 0.8676 (mt) cc_final: 0.8400 (mm) REVERT: D 170 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6188 (mmt-90) REVERT: D 177 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7645 (mtp180) REVERT: D 196 TYR cc_start: 0.8164 (m-80) cc_final: 0.7681 (m-80) REVERT: D 290 LEU cc_start: 0.8562 (mt) cc_final: 0.8318 (mp) REVERT: D 333 ARG cc_start: 0.7219 (mtm180) cc_final: 0.6542 (tpm170) REVERT: D 371 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7569 (ttmt) REVERT: D 385 MET cc_start: 0.8423 (ttp) cc_final: 0.7710 (ttm) REVERT: D 404 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8023 (mmtt) REVERT: D 452 LYS cc_start: 0.7794 (mttt) cc_final: 0.6672 (mppt) REVERT: D 473 LYS cc_start: 0.8263 (ptmt) cc_final: 0.7739 (pttm) REVERT: D 513 MET cc_start: 0.7849 (tpp) cc_final: 0.7619 (tpt) REVERT: E 120 PHE cc_start: 0.6973 (t80) cc_final: 0.5456 (m-80) REVERT: E 177 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7691 (mtp180) REVERT: E 186 MET cc_start: 0.8210 (mtt) cc_final: 0.7873 (mtp) REVERT: E 217 GLN cc_start: 0.7378 (mt0) cc_final: 0.6840 (mt0) REVERT: E 365 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: E 388 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6594 (ttt90) REVERT: E 404 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8027 (mmtt) REVERT: E 473 LYS cc_start: 0.8269 (pttp) cc_final: 0.7765 (pttm) REVERT: E 502 GLU cc_start: 0.7493 (tt0) cc_final: 0.7083 (tp30) REVERT: F 120 PHE cc_start: 0.6942 (t80) cc_final: 0.5201 (m-80) REVERT: F 160 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8623 (mt) REVERT: F 177 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7714 (mtp180) REVERT: F 217 GLN cc_start: 0.7352 (mt0) cc_final: 0.6813 (mt0) REVERT: F 398 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8542 (ptm) REVERT: F 404 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8010 (mmtt) REVERT: F 452 LYS cc_start: 0.8034 (mttt) cc_final: 0.6693 (mppt) REVERT: F 473 LYS cc_start: 0.8346 (pttp) cc_final: 0.7800 (pttm) outliers start: 50 outliers final: 19 residues processed: 305 average time/residue: 0.7628 time to fit residues: 254.3134 Evaluate side-chains 305 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 282 ASP 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 D residue 255 ASP 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 365 GLU Chi-restraints excluded: chain E residue 388 ARG Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 398 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 206 optimal weight: 0.6980 chunk 122 optimal weight: 0.0170 chunk 51 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 403 GLN B 403 GLN B 470 ASN C 217 GLN C 470 ASN D 217 GLN D 245 GLN D 403 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 470 ASN F 470 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.168253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133651 restraints weight = 19675.346| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.56 r_work: 0.3344 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18276 Z= 0.139 Angle : 0.537 8.874 24774 Z= 0.269 Chirality : 0.040 0.163 2808 Planarity : 0.004 0.048 3072 Dihedral : 4.023 16.481 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.22 % Allowed : 14.72 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.19), residues: 2136 helix: 2.33 (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 ARG 0.006 0.000 ARG F 350 TYR 0.015 0.001 TYR D 280 PHE 0.018 0.002 PHE F 149 TRP 0.017 0.002 TRP C 274 HIS 0.003 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00327 (18270) covalent geometry : angle 0.53713 (24762) SS BOND : bond 0.00020 ( 6) SS BOND : angle 0.29882 ( 12) hydrogen bonds : bond 0.03514 ( 1095) hydrogen bonds : angle 4.23031 ( 3195) *********************** 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: 42 poor density : 298 time to evaluate : 0.994 Fit side-chains REVERT: A 118 LEU cc_start: 0.7760 (tp) cc_final: 0.7322 (mp) REVERT: A 120 PHE cc_start: 0.7172 (t80) cc_final: 0.5497 (m-80) REVERT: A 158 ILE cc_start: 0.8674 (mt) cc_final: 0.8379 (mm) REVERT: A 170 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6146 (mmt-90) REVERT: A 196 TYR cc_start: 0.8132 (m-80) cc_final: 0.7644 (m-80) REVERT: A 243 GLN cc_start: 0.8043 (tt0) cc_final: 0.7379 (tt0) REVERT: A 245 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: A 333 ARG cc_start: 0.7207 (mtm180) cc_final: 0.6542 (tpm170) REVERT: A 388 ARG cc_start: 0.8088 (tpt170) cc_final: 0.7759 (ttm-80) REVERT: A 404 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8019 (mmtt) REVERT: A 452 LYS cc_start: 0.7712 (mttt) cc_final: 0.6616 (mppt) REVERT: A 473 LYS cc_start: 0.8265 (ptmt) cc_final: 0.7783 (pttm) REVERT: B 120 PHE cc_start: 0.6864 (t80) cc_final: 0.5202 (m-80) REVERT: B 177 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7578 (mtp180) REVERT: B 186 MET cc_start: 0.8186 (mtt) cc_final: 0.7896 (mtp) REVERT: B 217 GLN cc_start: 0.7368 (mt0) cc_final: 0.6903 (mt0) REVERT: B 341 TYR cc_start: 0.8698 (t80) cc_final: 0.8439 (t80) REVERT: B 385 MET cc_start: 0.8387 (ttm) cc_final: 0.8178 (ttm) REVERT: B 388 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.6800 (ttt90) REVERT: B 404 LYS cc_start: 0.8590 (mtpp) cc_final: 0.7973 (mmtt) REVERT: B 465 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: B 473 LYS cc_start: 0.8214 (pttp) cc_final: 0.7729 (pttm) REVERT: C 120 PHE cc_start: 0.6877 (t80) cc_final: 0.5135 (m-80) REVERT: C 160 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8584 (mt) REVERT: C 177 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7679 (mtp180) REVERT: C 217 GLN cc_start: 0.7312 (mt0) cc_final: 0.6790 (mt0) REVERT: C 339 ASN cc_start: 0.8071 (t0) cc_final: 0.7865 (t160) REVERT: C 371 LYS cc_start: 0.8074 (tttt) cc_final: 0.7716 (ttpt) REVERT: C 404 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7938 (mmtt) REVERT: C 473 LYS cc_start: 0.8324 (pttp) cc_final: 0.7868 (pttm) REVERT: D 118 LEU cc_start: 0.7732 (tp) cc_final: 0.7285 (mp) REVERT: D 120 PHE cc_start: 0.7153 (t80) cc_final: 0.5464 (m-80) REVERT: D 158 ILE cc_start: 0.8670 (mt) cc_final: 0.8380 (mm) REVERT: D 170 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6127 (mmt-90) REVERT: D 196 TYR cc_start: 0.8153 (m-80) cc_final: 0.7670 (m-80) REVERT: D 290 LEU cc_start: 0.8544 (mt) cc_final: 0.8270 (mp) REVERT: D 333 ARG cc_start: 0.7264 (mtm180) cc_final: 0.6543 (tpm170) REVERT: D 371 LYS cc_start: 0.7736 (ttpt) cc_final: 0.7500 (ttmt) REVERT: D 388 ARG cc_start: 0.8051 (tpt170) cc_final: 0.7703 (ttm-80) REVERT: D 404 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8030 (mmtt) REVERT: D 452 LYS cc_start: 0.7781 (mttt) cc_final: 0.6679 (mppt) REVERT: D 473 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7760 (pttm) REVERT: E 120 PHE cc_start: 0.6932 (t80) cc_final: 0.5402 (m-80) REVERT: E 177 ARG cc_start: 0.8192 (mtt180) cc_final: 0.7606 (mtp180) REVERT: E 186 MET cc_start: 0.8168 (mtt) cc_final: 0.7864 (mtp) REVERT: E 217 GLN cc_start: 0.7358 (mt0) cc_final: 0.6842 (mt0) REVERT: E 365 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: E 371 LYS cc_start: 0.7754 (tttt) cc_final: 0.7353 (ttpt) REVERT: E 403 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7519 (tm130) REVERT: E 404 LYS cc_start: 0.8614 (mtpp) cc_final: 0.7989 (mmtt) REVERT: E 473 LYS cc_start: 0.8215 (pttp) cc_final: 0.7722 (pttm) REVERT: E 502 GLU cc_start: 0.7454 (tt0) cc_final: 0.7095 (tp30) REVERT: F 120 PHE cc_start: 0.6886 (t80) cc_final: 0.5123 (m-80) REVERT: F 160 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8604 (mt) REVERT: F 217 GLN cc_start: 0.7354 (mt0) cc_final: 0.6798 (mt0) REVERT: F 339 ASN cc_start: 0.8109 (t0) cc_final: 0.7887 (t160) REVERT: F 398 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8477 (ptm) REVERT: F 404 LYS cc_start: 0.8410 (mtpp) cc_final: 0.7966 (mmtt) REVERT: F 452 LYS cc_start: 0.7948 (mttt) cc_final: 0.6653 (mppt) REVERT: F 473 LYS cc_start: 0.8262 (pttp) cc_final: 0.7810 (pttm) outliers start: 42 outliers final: 19 residues processed: 319 average time/residue: 0.7784 time to fit residues: 272.0433 Evaluate side-chains 321 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 293 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 B residue 152 VAL 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 255 ASP 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 365 GLU Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 398 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 144 optimal weight: 6.9990 chunk 196 optimal weight: 0.5980 chunk 71 optimal weight: 0.0370 chunk 75 optimal weight: 3.9990 chunk 78 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 403 GLN B 403 GLN B 470 ASN C 403 GLN C 470 ASN D 217 GLN D 403 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 470 ASN F 470 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.168830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134430 restraints weight = 19648.341| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.54 r_work: 0.3354 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18276 Z= 0.132 Angle : 0.536 7.813 24774 Z= 0.268 Chirality : 0.040 0.171 2808 Planarity : 0.004 0.047 3072 Dihedral : 3.987 16.543 2418 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.06 % Allowed : 15.35 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.19), residues: 2136 helix: 2.40 (0.14), residues: 1248 sheet: 1.06 (0.42), residues: 180 loop : -0.33 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 350 TYR 0.013 0.001 TYR F 280 PHE 0.021 0.002 PHE F 149 TRP 0.016 0.002 TRP C 274 HIS 0.003 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00311 (18270) covalent geometry : angle 0.53574 (24762) SS BOND : bond 0.00013 ( 6) SS BOND : angle 0.29431 ( 12) hydrogen bonds : bond 0.03468 ( 1095) hydrogen bonds : angle 4.21667 ( 3195) *********************** 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 344 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 305 time to evaluate : 0.779 Fit side-chains REVERT: A 118 LEU cc_start: 0.7750 (tp) cc_final: 0.7308 (mp) REVERT: A 120 PHE cc_start: 0.7150 (t80) cc_final: 0.5480 (m-80) REVERT: A 158 ILE cc_start: 0.8672 (mt) cc_final: 0.8372 (mm) REVERT: A 170 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6159 (mmt-90) REVERT: A 196 TYR cc_start: 0.8117 (m-80) cc_final: 0.7616 (m-80) REVERT: A 243 GLN cc_start: 0.8035 (tt0) cc_final: 0.7369 (tt0) REVERT: A 245 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: A 333 ARG cc_start: 0.7248 (mtm180) cc_final: 0.6541 (tpm170) REVERT: A 388 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7751 (ttm-80) REVERT: A 404 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8080 (mmtt) REVERT: A 452 LYS cc_start: 0.7750 (mttt) cc_final: 0.6605 (mppt) REVERT: A 473 LYS cc_start: 0.8258 (ptmt) cc_final: 0.7770 (pttm) REVERT: B 120 PHE cc_start: 0.6807 (t80) cc_final: 0.5204 (m-80) REVERT: B 170 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6140 (mmt180) REVERT: B 177 ARG cc_start: 0.8161 (mtt180) cc_final: 0.7584 (mtp180) REVERT: B 186 MET cc_start: 0.8174 (mtt) cc_final: 0.7842 (mtp) REVERT: B 217 GLN cc_start: 0.7354 (mt0) cc_final: 0.6880 (mt0) REVERT: B 341 TYR cc_start: 0.8666 (t80) cc_final: 0.8426 (t80) REVERT: B 388 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.6808 (ttt90) REVERT: B 398 MET cc_start: 0.8910 (ptm) cc_final: 0.8670 (ptm) REVERT: B 403 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7466 (tm130) REVERT: B 404 LYS cc_start: 0.8585 (mtpp) cc_final: 0.7958 (mmtt) REVERT: B 465 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: B 473 LYS cc_start: 0.8226 (pttp) cc_final: 0.7750 (pttm) REVERT: C 120 PHE cc_start: 0.6836 (t80) cc_final: 0.5126 (m-80) REVERT: C 160 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8594 (mt) REVERT: C 177 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7677 (mtp180) REVERT: C 217 GLN cc_start: 0.7322 (mt0) cc_final: 0.6783 (mt0) REVERT: C 339 ASN cc_start: 0.8095 (t0) cc_final: 0.7857 (t160) REVERT: C 371 LYS cc_start: 0.8069 (tttt) cc_final: 0.7715 (ttpt) REVERT: C 404 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7923 (mmtt) REVERT: C 432 MET cc_start: 0.8621 (mtp) cc_final: 0.8380 (mtm) REVERT: C 473 LYS cc_start: 0.8293 (pttp) cc_final: 0.7852 (pttm) REVERT: D 118 LEU cc_start: 0.7730 (tp) cc_final: 0.7371 (mt) REVERT: D 120 PHE cc_start: 0.7183 (t80) cc_final: 0.5472 (m-80) REVERT: D 158 ILE cc_start: 0.8678 (mt) cc_final: 0.8380 (mm) REVERT: D 196 TYR cc_start: 0.8130 (m-80) cc_final: 0.7639 (m-80) REVERT: D 290 LEU cc_start: 0.8531 (mt) cc_final: 0.8263 (mp) REVERT: D 371 LYS cc_start: 0.7652 (ttpt) cc_final: 0.7448 (ttmt) REVERT: D 385 MET cc_start: 0.8453 (ttp) cc_final: 0.7964 (ttm) REVERT: D 388 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7723 (ttm-80) REVERT: D 404 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8033 (mmtt) REVERT: D 452 LYS cc_start: 0.7820 (mttt) cc_final: 0.6666 (mppt) REVERT: D 473 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7740 (pttm) REVERT: E 120 PHE cc_start: 0.6845 (t80) cc_final: 0.5366 (m-80) REVERT: E 177 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7620 (mtp180) REVERT: E 186 MET cc_start: 0.8183 (mtt) cc_final: 0.7846 (mtp) REVERT: E 217 GLN cc_start: 0.7363 (mt0) cc_final: 0.6834 (mt0) REVERT: E 371 LYS cc_start: 0.7739 (tttt) cc_final: 0.7291 (ttpt) REVERT: E 404 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8018 (mmtt) REVERT: E 473 LYS cc_start: 0.8210 (pttp) cc_final: 0.7722 (pttm) REVERT: E 502 GLU cc_start: 0.7429 (tt0) cc_final: 0.7028 (tp30) REVERT: F 120 PHE cc_start: 0.6835 (t80) cc_final: 0.5108 (m-80) REVERT: F 160 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8609 (mt) REVERT: F 177 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7695 (mtp180) REVERT: F 217 GLN cc_start: 0.7357 (mt0) cc_final: 0.6802 (mt0) REVERT: F 339 ASN cc_start: 0.8031 (t0) cc_final: 0.7822 (t160) REVERT: F 404 LYS cc_start: 0.8391 (mtpp) cc_final: 0.7981 (mmtt) REVERT: F 452 LYS cc_start: 0.7960 (mttt) cc_final: 0.6687 (mppt) REVERT: F 473 LYS cc_start: 0.8264 (pttp) cc_final: 0.7822 (pttm) outliers start: 39 outliers final: 20 residues processed: 321 average time/residue: 0.8026 time to fit residues: 281.7664 Evaluate side-chains 320 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 B residue 152 VAL Chi-restraints excluded: chain B residue 170 ARG 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 187 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 255 ASP 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 384 VAL Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 51 optimal weight: 0.8980 chunk 132 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 403 GLN B 470 ASN C 213 GLN C 403 GLN C 470 ASN D 217 GLN D 403 GLN D 422 GLN 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 470 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.167005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132283 restraints weight = 19685.035| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.54 r_work: 0.3335 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18276 Z= 0.179 Angle : 0.578 9.173 24774 Z= 0.286 Chirality : 0.042 0.212 2808 Planarity : 0.005 0.048 3072 Dihedral : 4.128 16.593 2418 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.90 % Allowed : 15.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.18), residues: 2136 helix: 2.24 (0.14), residues: 1248 sheet: 0.77 (0.41), residues: 186 loop : -0.31 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 350 TYR 0.022 0.002 TYR D 280 PHE 0.026 0.002 PHE F 149 TRP 0.011 0.002 TRP E 164 HIS 0.003 0.001 HIS F 423 Details of bonding type rmsd covalent geometry : bond 0.00430 (18270) covalent geometry : angle 0.57799 (24762) SS BOND : bond 0.00044 ( 6) SS BOND : angle 0.27044 ( 12) hydrogen bonds : bond 0.03747 ( 1095) hydrogen bonds : angle 4.30069 ( 3195) ********************** 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 325 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.798 Fit side-chains REVERT: A 118 LEU cc_start: 0.7752 (tp) cc_final: 0.7309 (mp) REVERT: A 120 PHE cc_start: 0.7208 (t80) cc_final: 0.5507 (m-80) REVERT: A 158 ILE cc_start: 0.8687 (mt) cc_final: 0.8381 (mm) REVERT: A 170 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6196 (mmt-90) REVERT: A 177 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7607 (mtp180) REVERT: A 196 TYR cc_start: 0.8138 (m-80) cc_final: 0.7626 (m-80) REVERT: A 243 GLN cc_start: 0.8045 (tt0) cc_final: 0.7380 (tt0) REVERT: A 245 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7075 (mp10) REVERT: A 404 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8091 (mmtt) REVERT: A 452 LYS cc_start: 0.7796 (mttt) cc_final: 0.6622 (mppt) REVERT: A 473 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7787 (pttm) REVERT: B 120 PHE cc_start: 0.6832 (t80) cc_final: 0.5190 (m-80) REVERT: B 170 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7135 (mmt180) REVERT: B 177 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7672 (mtp180) REVERT: B 186 MET cc_start: 0.8208 (mtt) cc_final: 0.7905 (mtp) REVERT: B 217 GLN cc_start: 0.7367 (mt0) cc_final: 0.6900 (mt0) REVERT: B 341 TYR cc_start: 0.8716 (t80) cc_final: 0.8460 (t80) REVERT: B 349 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7574 (mp0) REVERT: B 388 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.6801 (ttt90) REVERT: B 404 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8044 (mmtt) REVERT: B 473 LYS cc_start: 0.8251 (pttp) cc_final: 0.7761 (pttm) REVERT: C 120 PHE cc_start: 0.6867 (t80) cc_final: 0.5142 (m-80) REVERT: C 160 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8606 (mt) REVERT: C 177 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7717 (mtp180) REVERT: C 217 GLN cc_start: 0.7350 (mt0) cc_final: 0.6824 (mt0) REVERT: C 339 ASN cc_start: 0.8125 (t0) cc_final: 0.7886 (t160) REVERT: C 404 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7943 (mmtt) REVERT: C 432 MET cc_start: 0.8735 (mtp) cc_final: 0.8459 (mtm) REVERT: C 452 LYS cc_start: 0.7958 (mttt) cc_final: 0.6691 (mppt) REVERT: C 473 LYS cc_start: 0.8309 (pttp) cc_final: 0.7863 (pttm) REVERT: D 118 LEU cc_start: 0.7750 (tp) cc_final: 0.7299 (mp) REVERT: D 120 PHE cc_start: 0.7197 (t80) cc_final: 0.5484 (m-80) REVERT: D 158 ILE cc_start: 0.8688 (mt) cc_final: 0.8388 (mm) REVERT: D 177 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7626 (mtp180) REVERT: D 196 TYR cc_start: 0.8166 (m-80) cc_final: 0.7607 (m-80) REVERT: D 290 LEU cc_start: 0.8548 (mt) cc_final: 0.8280 (mp) REVERT: D 371 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7559 (ttmt) REVERT: D 385 MET cc_start: 0.8567 (ttp) cc_final: 0.8112 (ttm) REVERT: D 388 ARG cc_start: 0.8062 (tpt170) cc_final: 0.7726 (ttm-80) REVERT: D 404 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8036 (mmtt) REVERT: D 452 LYS cc_start: 0.7848 (mttt) cc_final: 0.6664 (mppt) REVERT: D 473 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7752 (pttm) REVERT: D 513 MET cc_start: 0.7966 (tpp) cc_final: 0.7720 (tpt) REVERT: E 120 PHE cc_start: 0.6896 (t80) cc_final: 0.5388 (m-80) REVERT: E 177 ARG cc_start: 0.8278 (mtt180) cc_final: 0.7712 (mtp180) REVERT: E 186 MET cc_start: 0.8205 (mtt) cc_final: 0.7910 (mtp) REVERT: E 217 GLN cc_start: 0.7422 (mt0) cc_final: 0.6893 (mt0) REVERT: E 349 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7616 (mp0) REVERT: E 371 LYS cc_start: 0.7828 (tttt) cc_final: 0.7397 (ttpt) REVERT: E 404 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8024 (mmtt) REVERT: E 473 LYS cc_start: 0.8346 (pttp) cc_final: 0.7855 (pttm) REVERT: E 502 GLU cc_start: 0.7509 (tt0) cc_final: 0.7107 (tp30) REVERT: F 120 PHE cc_start: 0.6879 (t80) cc_final: 0.5138 (m-80) REVERT: F 160 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8624 (mt) REVERT: F 217 GLN cc_start: 0.7381 (mt0) cc_final: 0.6821 (mt0) REVERT: F 339 ASN cc_start: 0.8116 (t0) cc_final: 0.7879 (t160) REVERT: F 388 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6672 (ttt90) REVERT: F 404 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7958 (mmtt) REVERT: F 422 GLN cc_start: 0.7623 (mt0) cc_final: 0.7139 (mm-40) REVERT: F 452 LYS cc_start: 0.7881 (mttt) cc_final: 0.6659 (mppt) REVERT: F 473 LYS cc_start: 0.8315 (pttp) cc_final: 0.7881 (pttm) outliers start: 36 outliers final: 20 residues processed: 304 average time/residue: 0.8552 time to fit residues: 283.3804 Evaluate side-chains 314 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 288 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 392 GLN Chi-restraints excluded: chain A residue 439 GLU 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 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 255 ASP 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 492 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 388 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 149 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 179 optimal weight: 0.0770 chunk 190 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 217 GLN A 403 GLN A 422 GLN B 213 GLN B 403 GLN B 470 ASN C 213 GLN C 403 GLN C 470 ASN D 217 GLN D 403 GLN E 213 GLN ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN 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 = 0.3830 r_free = 0.3830 target = 0.168185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133613 restraints weight = 19788.650| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.55 r_work: 0.3356 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18276 Z= 0.145 Angle : 0.550 8.519 24774 Z= 0.275 Chirality : 0.041 0.208 2808 Planarity : 0.004 0.047 3072 Dihedral : 4.040 16.320 2418 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.74 % Allowed : 15.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.18), residues: 2136 helix: 2.32 (0.14), residues: 1248 sheet: 1.02 (0.42), residues: 180 loop : -0.30 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 350 TYR 0.016 0.002 TYR D 280 PHE 0.026 0.002 PHE F 149 TRP 0.016 0.002 TRP C 274 HIS 0.003 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00344 (18270) covalent geometry : angle 0.55024 (24762) SS BOND : bond 0.00010 ( 6) SS BOND : angle 0.29354 ( 12) hydrogen bonds : bond 0.03574 ( 1095) hydrogen bonds : angle 4.27044 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7324.72 seconds wall clock time: 125 minutes 37.02 seconds (7537.02 seconds total)