Starting phenix.real_space_refine on Thu Sep 18 15:19:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jka_61549/09_2025/9jka_61549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jka_61549/09_2025/9jka_61549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jka_61549/09_2025/9jka_61549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jka_61549/09_2025/9jka_61549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jka_61549/09_2025/9jka_61549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jka_61549/09_2025/9jka_61549.map" } resolution = 2.5 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 11706 2.51 5 N 3084 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s 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: 2.69, per 1000 atoms: 0.15 Number of scatterers: 17820 At special positions: 0 Unit cell: (99.51, 89.88, 219.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2970 8.00 N 3084 7.00 C 11706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=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: 1.24 Conformation dependent library (CDL) restraints added in 799.2 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: 84 helices and 12 sheets defined 62.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 109 through 134 Proline residue: A 123 - end of helix Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 142 through 168 removed outlier: 4.048A pdb=" N GLU A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 204 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS A 509 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 134 Proline residue: B 123 - end of helix Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 168 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 204 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 336 Processing helix chain 'B' and resid 339 through 368 removed outlier: 3.598A pdb=" N TYR B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 416 through 430 Processing helix chain 'B' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 456 through 459 Processing helix chain 'B' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS B 509 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 Proline residue: C 123 - end of helix Proline residue: C 130 - end of helix Processing helix chain 'C' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 204 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA C 396 " --> pdb=" O GLN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 416 through 430 Processing helix chain 'C' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR C 441 " --> pdb=" O PHE C 437 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 456 through 459 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS C 509 " --> pdb=" O PRO C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 134 Proline residue: D 123 - end of helix Proline residue: D 130 - end of helix Processing helix chain 'D' and resid 142 through 168 removed outlier: 4.048A pdb=" N GLU D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 204 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 336 Processing helix chain 'D' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA D 396 " --> pdb=" O GLN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 416 through 430 Processing helix chain 'D' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 456 through 459 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS D 509 " --> pdb=" O PRO D 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 134 Proline residue: E 123 - end of helix Proline residue: E 130 - end of helix Processing helix chain 'E' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 168 " --> pdb=" O TRP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 204 Processing helix chain 'E' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 Processing helix chain 'E' and resid 339 through 368 removed outlier: 3.598A pdb=" N TYR E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA E 396 " --> pdb=" O GLN E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 409 Processing helix chain 'E' and resid 416 through 430 Processing helix chain 'E' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR E 441 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 456 through 459 Processing helix chain 'E' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS E 509 " --> pdb=" O PRO E 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 134 Proline residue: F 123 - end of helix Proline residue: F 130 - end of helix Processing helix chain 'F' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 168 " --> pdb=" O TRP F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 204 Processing helix chain 'F' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 336 Processing helix chain 'F' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 396 removed outlier: 4.116A pdb=" N ALA F 396 " --> pdb=" O GLN F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 409 Processing helix chain 'F' and resid 416 through 430 Processing helix chain 'F' and resid 433 through 443 removed outlier: 4.951A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR F 441 " --> pdb=" O PHE F 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA F 443 " --> pdb=" O GLU F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 450 Processing helix chain 'F' and resid 456 through 459 Processing helix chain 'F' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS F 509 " --> pdb=" O PRO F 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.920A pdb=" N TRP A 460 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.586A pdb=" N LYS A 371 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 173 through 174 removed outlier: 6.487A pdb=" N PHE A 497 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS A 498 " --> pdb=" O TRP C 460 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU C 462 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER A 500 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 512 removed outlier: 3.595A pdb=" N LYS B 371 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.755A pdb=" N TRP B 460 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AA7, first strand: chain 'D' and resid 173 through 174 removed outlier: 3.678A pdb=" N TRP D 460 " --> pdb=" O LYS E 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 371 through 372 Processing sheet with id=AA9, first strand: chain 'F' and resid 173 through 174 removed outlier: 6.627A pdb=" N PHE D 497 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS D 498 " --> pdb=" O TRP F 460 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU F 462 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER D 500 " --> pdb=" O LEU F 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 511 through 512 removed outlier: 3.511A pdb=" N LYS E 371 " --> pdb=" O VAL D 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.869A pdb=" N TRP E 460 " --> pdb=" O LYS F 498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 511 through 512 1086 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5102 1.34 - 1.45: 3097 1.45 - 1.57: 9969 1.57 - 1.69: 0 1.69 - 1.80: 102 Bond restraints: 18270 Sorted by residual: bond pdb=" CA THR C 122 " pdb=" C THR C 122 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.26e-02 6.30e+03 1.84e+00 bond pdb=" CA THR D 122 " pdb=" C THR D 122 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.26e-02 6.30e+03 1.82e+00 bond pdb=" CA THR B 122 " pdb=" C THR B 122 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.26e-02 6.30e+03 1.80e+00 bond pdb=" CB TRP E 274 " pdb=" CG TRP E 274 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.78e+00 bond pdb=" CA THR E 122 " pdb=" C THR E 122 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.26e-02 6.30e+03 1.77e+00 ... (remaining 18265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 23116 1.56 - 3.11: 1299 3.11 - 4.67: 249 4.67 - 6.23: 62 6.23 - 7.78: 36 Bond angle restraints: 24762 Sorted by residual: angle pdb=" CA PRO F 130 " pdb=" C PRO F 130 " pdb=" N PRO F 131 " ideal model delta sigma weight residual 117.93 122.37 -4.44 1.20e+00 6.94e-01 1.37e+01 angle pdb=" CA PRO C 130 " pdb=" C PRO C 130 " pdb=" N PRO C 131 " ideal model delta sigma weight residual 117.93 122.37 -4.44 1.20e+00 6.94e-01 1.37e+01 angle pdb=" CA PRO E 130 " pdb=" C PRO E 130 " pdb=" N PRO E 131 " ideal model delta sigma weight residual 117.93 122.37 -4.44 1.20e+00 6.94e-01 1.37e+01 angle pdb=" CA PRO B 130 " pdb=" C PRO B 130 " pdb=" N PRO B 131 " ideal model delta sigma weight residual 117.93 122.34 -4.41 1.20e+00 6.94e-01 1.35e+01 angle pdb=" CA PRO A 130 " pdb=" C PRO A 130 " pdb=" N PRO A 131 " ideal model delta sigma weight residual 117.93 122.34 -4.41 1.20e+00 6.94e-01 1.35e+01 ... (remaining 24757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.59: 9820 10.59 - 21.19: 904 21.19 - 31.78: 142 31.78 - 42.37: 48 42.37 - 52.96: 18 Dihedral angle restraints: 10932 sinusoidal: 4476 harmonic: 6456 Sorted by residual: dihedral pdb=" CB CYS B 141 " pdb=" SG CYS B 141 " pdb=" SG CYS B 145 " pdb=" CB CYS B 145 " ideal model delta sinusoidal sigma weight residual -86.00 -138.96 52.96 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS F 141 " pdb=" SG CYS F 141 " pdb=" SG CYS F 145 " pdb=" CB CYS F 145 " ideal model delta sinusoidal sigma weight residual -86.00 -138.95 52.95 1 1.00e+01 1.00e-02 3.82e+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 -138.94 52.94 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 10929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1563 0.034 - 0.068: 729 0.068 - 0.102: 329 0.102 - 0.136: 133 0.136 - 0.170: 54 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA LEU F 129 " pdb=" N LEU F 129 " pdb=" C LEU F 129 " pdb=" CB LEU F 129 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA LEU E 129 " pdb=" N LEU E 129 " pdb=" C LEU E 129 " pdb=" CB LEU E 129 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA LEU B 129 " pdb=" N LEU B 129 " pdb=" C LEU B 129 " pdb=" CB LEU B 129 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 2805 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 260 " 0.014 2.00e-02 2.50e+03 2.20e-02 8.50e+00 pdb=" CG PHE B 260 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 260 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 260 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 260 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 260 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 260 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 260 " -0.014 2.00e-02 2.50e+03 2.19e-02 8.39e+00 pdb=" CG PHE D 260 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE D 260 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE D 260 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 260 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE D 260 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE D 260 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 260 " -0.014 2.00e-02 2.50e+03 2.19e-02 8.36e+00 pdb=" CG PHE F 260 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE F 260 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE F 260 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 260 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE F 260 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE F 260 " 0.002 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4218 2.79 - 3.32: 15877 3.32 - 3.85: 30875 3.85 - 4.37: 35728 4.37 - 4.90: 62858 Nonbonded interactions: 149556 Sorted by model distance: nonbonded pdb=" OE2 GLU C 347 " pdb=" OH TYR E 343 " model vdw 2.264 3.040 nonbonded pdb=" O ALA C 444 " pdb=" OH TYR C 450 " model vdw 2.268 3.040 nonbonded pdb=" O ALA E 444 " pdb=" OH TYR E 450 " model vdw 2.268 3.040 nonbonded pdb=" O ALA D 444 " pdb=" OH TYR D 450 " model vdw 2.268 3.040 nonbonded pdb=" O ALA F 444 " pdb=" OH TYR F 450 " model vdw 2.268 3.040 ... (remaining 149551 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.310 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:5.720 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 18276 Z= 0.274 Angle : 0.902 7.783 24774 Z= 0.501 Chirality : 0.052 0.170 2808 Planarity : 0.007 0.053 3072 Dihedral : 8.501 52.931 6702 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.23 (0.15), residues: 2136 helix: -1.44 (0.12), residues: 1200 sheet: 1.47 (0.38), residues: 168 loop : -2.01 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 252 TYR 0.020 0.003 TYR D 279 PHE 0.045 0.006 PHE B 260 TRP 0.025 0.002 TRP D 164 HIS 0.012 0.002 HIS E 423 Details of bonding type rmsd covalent geometry : bond 0.00663 (18270) covalent geometry : angle 0.90196 (24762) SS BOND : bond 0.00100 ( 6) SS BOND : angle 0.67318 ( 12) hydrogen bonds : bond 0.11301 ( 1086) hydrogen bonds : angle 6.21183 ( 3159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8567 (tp) cc_final: 0.8272 (tm) REVERT: A 217 GLN cc_start: 0.7433 (mt0) cc_final: 0.7162 (mt0) REVERT: A 222 LEU cc_start: 0.7935 (tp) cc_final: 0.7684 (tp) REVERT: A 344 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 350 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6844 (ttm110) REVERT: A 418 GLU cc_start: 0.7634 (tp30) cc_final: 0.7292 (tp30) REVERT: A 422 GLN cc_start: 0.7628 (mt0) cc_final: 0.7003 (mt0) REVERT: B 135 ARG cc_start: 0.7199 (ttt180) cc_final: 0.6944 (tpt-90) REVERT: B 341 TYR cc_start: 0.8206 (t80) cc_final: 0.7774 (t80) REVERT: B 350 ARG cc_start: 0.7348 (ttm110) cc_final: 0.7093 (ttm110) REVERT: B 385 MET cc_start: 0.8593 (ttp) cc_final: 0.8149 (ttp) REVERT: B 403 GLN cc_start: 0.7952 (tt0) cc_final: 0.7748 (tt0) REVERT: B 418 GLU cc_start: 0.7989 (tp30) cc_final: 0.7607 (tp30) REVERT: B 422 GLN cc_start: 0.7766 (mt0) cc_final: 0.7464 (mm110) REVERT: B 435 LYS cc_start: 0.7679 (ttmp) cc_final: 0.7282 (tptp) REVERT: C 172 LYS cc_start: 0.8251 (pttp) cc_final: 0.7510 (mtpp) REVERT: C 344 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 385 MET cc_start: 0.8820 (ttp) cc_final: 0.8539 (ttp) REVERT: C 404 LYS cc_start: 0.8378 (mttm) cc_final: 0.8106 (mttm) REVERT: C 418 GLU cc_start: 0.7942 (tp30) cc_final: 0.7430 (tp30) REVERT: C 422 GLN cc_start: 0.7615 (mt0) cc_final: 0.7255 (mt0) REVERT: C 513 MET cc_start: 0.7389 (tpp) cc_final: 0.7088 (tpp) REVERT: D 213 GLN cc_start: 0.7984 (tt0) cc_final: 0.7593 (tm-30) REVERT: D 217 GLN cc_start: 0.7458 (mt0) cc_final: 0.7225 (mt0) REVERT: D 341 TYR cc_start: 0.7997 (t80) cc_final: 0.7623 (t80) REVERT: D 344 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7275 (mt-10) REVERT: D 347 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7494 (mt-10) REVERT: D 349 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 350 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6867 (ttm110) REVERT: D 385 MET cc_start: 0.8741 (ttp) cc_final: 0.8512 (ttp) REVERT: D 418 GLU cc_start: 0.7816 (tp30) cc_final: 0.7598 (tp30) REVERT: D 422 GLN cc_start: 0.7701 (mt0) cc_final: 0.7182 (mm-40) REVERT: D 435 LYS cc_start: 0.7833 (ttmp) cc_final: 0.7425 (tptp) REVERT: E 117 LEU cc_start: 0.8819 (tp) cc_final: 0.8616 (tm) REVERT: E 120 PHE cc_start: 0.7504 (t80) cc_final: 0.7018 (m-80) REVERT: E 170 ARG cc_start: 0.7369 (mtt180) cc_final: 0.7155 (mmp80) REVERT: E 172 LYS cc_start: 0.8306 (pttp) cc_final: 0.7542 (mtpp) REVERT: E 341 TYR cc_start: 0.8426 (t80) cc_final: 0.8029 (t80) REVERT: E 344 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 350 ARG cc_start: 0.7181 (ttm110) cc_final: 0.6852 (ttm110) REVERT: E 404 LYS cc_start: 0.8502 (mttm) cc_final: 0.8300 (mtmm) REVERT: E 418 GLU cc_start: 0.7950 (tp30) cc_final: 0.7457 (tp30) REVERT: E 435 LYS cc_start: 0.7614 (ttmp) cc_final: 0.7298 (tptp) REVERT: F 120 PHE cc_start: 0.7384 (t80) cc_final: 0.7172 (m-80) REVERT: F 172 LYS cc_start: 0.8230 (pttp) cc_final: 0.7474 (mtpp) REVERT: F 344 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7397 (mt-10) REVERT: F 385 MET cc_start: 0.8804 (ttp) cc_final: 0.8544 (ttp) REVERT: F 404 LYS cc_start: 0.8380 (mttm) cc_final: 0.8110 (mttm) REVERT: F 418 GLU cc_start: 0.7944 (tp30) cc_final: 0.7412 (tp30) REVERT: F 422 GLN cc_start: 0.7624 (mt0) cc_final: 0.7251 (mt0) REVERT: F 513 MET cc_start: 0.7402 (tpp) cc_final: 0.7199 (tpp) outliers start: 0 outliers final: 1 residues processed: 489 average time/residue: 0.8779 time to fit residues: 463.9035 Evaluate side-chains 301 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 282 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 411 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN B 411 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN C 412 GLN C 415 HIS C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN D 451 HIS E 411 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 GLN F 415 HIS F 449 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101317 restraints weight = 21378.265| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.05 r_work: 0.3104 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18276 Z= 0.153 Angle : 0.548 7.383 24774 Z= 0.287 Chirality : 0.040 0.142 2808 Planarity : 0.005 0.042 3072 Dihedral : 4.417 48.394 2420 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.69 % Allowed : 11.39 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.55 (0.17), residues: 2136 helix: 1.17 (0.14), residues: 1212 sheet: 1.75 (0.39), residues: 168 loop : -1.28 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 482 TYR 0.010 0.002 TYR F 450 PHE 0.025 0.003 PHE B 149 TRP 0.018 0.002 TRP B 164 HIS 0.004 0.001 HIS E 423 Details of bonding type rmsd covalent geometry : bond 0.00354 (18270) covalent geometry : angle 0.54817 (24762) SS BOND : bond 0.00133 ( 6) SS BOND : angle 0.56573 ( 12) hydrogen bonds : bond 0.03499 ( 1086) hydrogen bonds : angle 4.22222 ( 3159) *********************** 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 376 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 325 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5420 (mmp-170) REVERT: A 182 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7139 (ttp80) REVERT: A 217 GLN cc_start: 0.7497 (mt0) cc_final: 0.7216 (mt0) REVERT: A 344 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7965 (mt-10) REVERT: A 350 ARG cc_start: 0.7524 (ttm110) cc_final: 0.7051 (ttm110) REVERT: A 364 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7952 (mt-10) REVERT: A 418 GLU cc_start: 0.8591 (tp30) cc_final: 0.8208 (tp30) REVERT: A 422 GLN cc_start: 0.8150 (mt0) cc_final: 0.7715 (mt0) REVERT: B 172 LYS cc_start: 0.8397 (pttt) cc_final: 0.8181 (pttm) REVERT: B 182 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7021 (ttm170) REVERT: B 213 GLN cc_start: 0.7836 (tt0) cc_final: 0.7497 (tm-30) REVERT: B 341 TYR cc_start: 0.8596 (t80) cc_final: 0.8184 (t80) REVERT: B 350 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7303 (ttm110) REVERT: B 418 GLU cc_start: 0.8757 (tp30) cc_final: 0.8211 (tp30) REVERT: B 422 GLN cc_start: 0.8324 (mt0) cc_final: 0.8009 (mt0) REVERT: B 435 LYS cc_start: 0.8286 (ttmp) cc_final: 0.7583 (tptt) REVERT: C 172 LYS cc_start: 0.8442 (pttp) cc_final: 0.7488 (mmmt) REVERT: C 190 PHE cc_start: 0.8141 (t80) cc_final: 0.7873 (t80) REVERT: C 344 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7764 (mt-10) REVERT: C 364 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: C 400 ARG cc_start: 0.8087 (tpm-80) cc_final: 0.7526 (tpp-160) REVERT: C 418 GLU cc_start: 0.8799 (tp30) cc_final: 0.8192 (tp30) REVERT: C 422 GLN cc_start: 0.8149 (mt0) cc_final: 0.7807 (mt0) REVERT: C 513 MET cc_start: 0.7560 (tpp) cc_final: 0.7093 (tpp) REVERT: D 120 PHE cc_start: 0.6722 (m-80) cc_final: 0.6239 (t80) REVERT: D 344 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7892 (mt-10) REVERT: D 350 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7193 (ttm110) REVERT: D 364 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7783 (mt-10) REVERT: D 402 MET cc_start: 0.9052 (tpt) cc_final: 0.8792 (tpp) REVERT: D 418 GLU cc_start: 0.8621 (tp30) cc_final: 0.8294 (tp30) REVERT: E 120 PHE cc_start: 0.7468 (t80) cc_final: 0.7014 (m-80) REVERT: E 170 ARG cc_start: 0.7884 (mtt180) cc_final: 0.6937 (mmp80) REVERT: E 195 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 217 GLN cc_start: 0.7869 (mt0) cc_final: 0.7523 (mm-40) REVERT: E 341 TYR cc_start: 0.8663 (t80) cc_final: 0.8277 (t80) REVERT: E 344 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7895 (mt-10) REVERT: E 350 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7286 (ttm110) REVERT: E 412 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7624 (mp10) REVERT: E 418 GLU cc_start: 0.8644 (tp30) cc_final: 0.8170 (tp30) REVERT: F 120 PHE cc_start: 0.7364 (t80) cc_final: 0.7080 (m-80) REVERT: F 172 LYS cc_start: 0.8447 (pttp) cc_final: 0.7467 (mtpp) REVERT: F 190 PHE cc_start: 0.8143 (t80) cc_final: 0.7843 (t80) REVERT: F 344 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7806 (mt-10) REVERT: F 364 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: F 400 ARG cc_start: 0.8077 (tpm-80) cc_final: 0.7527 (tpp-160) REVERT: F 418 GLU cc_start: 0.8804 (tp30) cc_final: 0.8186 (tp30) REVERT: F 422 GLN cc_start: 0.8143 (mt0) cc_final: 0.7787 (mt0) REVERT: F 513 MET cc_start: 0.7259 (tpp) cc_final: 0.6858 (tpp) outliers start: 51 outliers final: 8 residues processed: 349 average time/residue: 0.7730 time to fit residues: 295.0307 Evaluate side-chains 298 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 286 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 134 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 160 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 126 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS E 243 GLN E 412 GLN E 449 GLN F 449 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101010 restraints weight = 21479.269| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.06 r_work: 0.3099 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18276 Z= 0.125 Angle : 0.524 8.489 24774 Z= 0.265 Chirality : 0.038 0.137 2808 Planarity : 0.004 0.038 3072 Dihedral : 4.028 13.828 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.58 % Allowed : 13.82 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.60 (0.18), residues: 2136 helix: 2.11 (0.14), residues: 1212 sheet: 1.87 (0.40), residues: 168 loop : -0.93 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 210 TYR 0.013 0.001 TYR A 341 PHE 0.026 0.002 PHE B 149 TRP 0.018 0.002 TRP B 134 HIS 0.004 0.001 HIS E 423 Details of bonding type rmsd covalent geometry : bond 0.00287 (18270) covalent geometry : angle 0.52373 (24762) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.63416 ( 12) hydrogen bonds : bond 0.03221 ( 1086) hydrogen bonds : angle 4.04902 ( 3159) *********************** 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 348 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.5648 (mmp-170) REVERT: A 182 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7138 (ttp80) REVERT: A 217 GLN cc_start: 0.7496 (mt0) cc_final: 0.7204 (mt0) REVERT: A 344 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7978 (mt-10) REVERT: A 350 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7044 (ttm110) REVERT: A 364 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7826 (mt-10) REVERT: A 402 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (tpp) REVERT: A 418 GLU cc_start: 0.8649 (tp30) cc_final: 0.8345 (tp30) REVERT: B 117 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8251 (tm) REVERT: B 172 LYS cc_start: 0.8382 (pttt) cc_final: 0.8177 (pttm) REVERT: B 182 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7055 (ttp-110) REVERT: B 341 TYR cc_start: 0.8617 (t80) cc_final: 0.8235 (t80) REVERT: B 350 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7435 (ttm110) REVERT: B 371 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8308 (ttpp) REVERT: B 418 GLU cc_start: 0.8751 (tp30) cc_final: 0.8154 (tp30) REVERT: B 422 GLN cc_start: 0.8302 (mt0) cc_final: 0.7943 (mt0) REVERT: C 172 LYS cc_start: 0.8439 (pttp) cc_final: 0.7509 (mtpt) REVERT: C 190 PHE cc_start: 0.8157 (t80) cc_final: 0.7899 (t80) REVERT: C 344 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7860 (mt-10) REVERT: C 364 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: C 400 ARG cc_start: 0.8137 (tpm-80) cc_final: 0.7538 (tpp-160) REVERT: C 418 GLU cc_start: 0.8804 (tp30) cc_final: 0.8179 (tp30) REVERT: C 422 GLN cc_start: 0.8133 (mt0) cc_final: 0.7783 (mt0) REVERT: C 513 MET cc_start: 0.7626 (tpp) cc_final: 0.7135 (tpp) REVERT: D 344 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7938 (mt-10) REVERT: D 350 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7157 (ttm110) REVERT: D 418 GLU cc_start: 0.8672 (tp30) cc_final: 0.8371 (tp30) REVERT: E 120 PHE cc_start: 0.7468 (t80) cc_final: 0.6973 (m-80) REVERT: E 170 ARG cc_start: 0.7917 (mtt180) cc_final: 0.6984 (mmp80) REVERT: E 186 MET cc_start: 0.8283 (mmt) cc_final: 0.7673 (mtp) REVERT: E 195 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8059 (p) REVERT: E 217 GLN cc_start: 0.7597 (mt0) cc_final: 0.7347 (mm-40) REVERT: E 341 TYR cc_start: 0.8631 (t80) cc_final: 0.8240 (t80) REVERT: E 344 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7895 (mt-10) REVERT: E 350 ARG cc_start: 0.7634 (ttm110) cc_final: 0.7275 (ttm110) REVERT: E 418 GLU cc_start: 0.8608 (tp30) cc_final: 0.8132 (tp30) REVERT: F 118 LEU cc_start: 0.8096 (tp) cc_final: 0.7791 (tt) REVERT: F 120 PHE cc_start: 0.7393 (t80) cc_final: 0.7052 (m-80) REVERT: F 172 LYS cc_start: 0.8445 (pttp) cc_final: 0.7550 (mtpt) REVERT: F 190 PHE cc_start: 0.8148 (t80) cc_final: 0.7856 (t80) REVERT: F 344 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7814 (mt-10) REVERT: F 364 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: F 400 ARG cc_start: 0.8108 (tpm-80) cc_final: 0.7518 (tpp-160) REVERT: F 418 GLU cc_start: 0.8800 (tp30) cc_final: 0.8188 (tp30) REVERT: F 422 GLN cc_start: 0.8137 (mt0) cc_final: 0.7793 (mt0) REVERT: F 513 MET cc_start: 0.7239 (tpp) cc_final: 0.6789 (tpp) outliers start: 49 outliers final: 8 residues processed: 322 average time/residue: 0.7631 time to fit residues: 269.3492 Evaluate side-chains 294 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 280 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 412 GLN Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 96 optimal weight: 0.1980 chunk 39 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 211 optimal weight: 0.0270 chunk 103 optimal weight: 0.0060 chunk 50 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS F 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103430 restraints weight = 21433.871| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.06 r_work: 0.3135 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18276 Z= 0.099 Angle : 0.489 8.123 24774 Z= 0.247 Chirality : 0.037 0.141 2808 Planarity : 0.003 0.035 3072 Dihedral : 3.776 13.738 2418 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.16 % Allowed : 15.24 % 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: 2.22 (0.18), residues: 2136 helix: 2.67 (0.14), residues: 1206 sheet: 1.90 (0.39), residues: 168 loop : -0.67 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.010 0.001 TYR A 341 PHE 0.026 0.002 PHE B 149 TRP 0.018 0.001 TRP B 134 HIS 0.002 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00221 (18270) covalent geometry : angle 0.48900 (24762) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.46948 ( 12) hydrogen bonds : bond 0.02911 ( 1086) hydrogen bonds : angle 3.89223 ( 3159) *********************** 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 340 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 299 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: A 170 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.5522 (mmp-170) REVERT: A 182 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7172 (ttp-170) REVERT: A 217 GLN cc_start: 0.7420 (mt0) cc_final: 0.7161 (mt0) REVERT: A 344 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 350 ARG cc_start: 0.7452 (ttm110) cc_final: 0.7014 (ttm110) REVERT: A 364 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7720 (mt-10) REVERT: A 417 MET cc_start: 0.8004 (ttp) cc_final: 0.7794 (ttm) REVERT: A 418 GLU cc_start: 0.8692 (tp30) cc_final: 0.8324 (tp30) REVERT: B 149 PHE cc_start: 0.7917 (m-80) cc_final: 0.7177 (m-80) REVERT: B 182 ARG cc_start: 0.7727 (ttm170) cc_final: 0.7051 (ttp-110) REVERT: B 213 GLN cc_start: 0.7814 (tt0) cc_final: 0.7445 (tm-30) REVERT: B 341 TYR cc_start: 0.8616 (t80) cc_final: 0.8217 (t80) REVERT: B 350 ARG cc_start: 0.7660 (ttm110) cc_final: 0.7158 (ttm110) REVERT: B 371 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8287 (ttpp) REVERT: B 418 GLU cc_start: 0.8763 (tp30) cc_final: 0.8149 (tp30) REVERT: B 422 GLN cc_start: 0.8301 (mt0) cc_final: 0.7944 (mt0) REVERT: C 172 LYS cc_start: 0.8491 (pttp) cc_final: 0.7520 (mtpt) REVERT: C 190 PHE cc_start: 0.8103 (t80) cc_final: 0.7871 (t80) REVERT: C 344 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7839 (mt-10) REVERT: C 364 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: C 371 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8207 (ptmm) REVERT: C 400 ARG cc_start: 0.7981 (tpm-80) cc_final: 0.7583 (tpm-80) REVERT: C 418 GLU cc_start: 0.8772 (tp30) cc_final: 0.8225 (tp30) REVERT: C 422 GLN cc_start: 0.8116 (mt0) cc_final: 0.7773 (mt0) REVERT: D 170 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.5709 (mmp-170) REVERT: D 344 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7963 (mt-10) REVERT: D 350 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7249 (ttm110) REVERT: D 418 GLU cc_start: 0.8680 (tp30) cc_final: 0.8368 (tp30) REVERT: E 120 PHE cc_start: 0.7467 (t80) cc_final: 0.6938 (m-80) REVERT: E 170 ARG cc_start: 0.7940 (mtt180) cc_final: 0.6967 (mmp80) REVERT: E 172 LYS cc_start: 0.8341 (pttt) cc_final: 0.8129 (pttt) REVERT: E 186 MET cc_start: 0.8292 (mmt) cc_final: 0.7677 (mtp) REVERT: E 195 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8144 (p) REVERT: E 217 GLN cc_start: 0.7615 (mt0) cc_final: 0.7316 (mm-40) REVERT: E 341 TYR cc_start: 0.8589 (t80) cc_final: 0.8248 (t80) REVERT: E 344 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7857 (mt-10) REVERT: E 350 ARG cc_start: 0.7625 (ttm110) cc_final: 0.7136 (ttm110) REVERT: E 364 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: E 418 GLU cc_start: 0.8639 (tp30) cc_final: 0.8195 (tp30) REVERT: F 118 LEU cc_start: 0.8015 (tp) cc_final: 0.7737 (tt) REVERT: F 120 PHE cc_start: 0.7338 (t80) cc_final: 0.7035 (m-80) REVERT: F 172 LYS cc_start: 0.8443 (pttp) cc_final: 0.7552 (mtpt) REVERT: F 190 PHE cc_start: 0.8103 (t80) cc_final: 0.7851 (t80) REVERT: F 344 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7859 (mt-10) REVERT: F 364 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: F 371 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8123 (ptmm) REVERT: F 418 GLU cc_start: 0.8768 (tp30) cc_final: 0.8225 (tp30) REVERT: F 422 GLN cc_start: 0.8111 (mt0) cc_final: 0.7767 (mt0) REVERT: F 513 MET cc_start: 0.7312 (tpp) cc_final: 0.6822 (tpp) outliers start: 41 outliers final: 9 residues processed: 319 average time/residue: 0.7717 time to fit residues: 269.4150 Evaluate side-chains 293 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 9 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS E 415 HIS F 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097201 restraints weight = 21202.204| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.04 r_work: 0.3044 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18276 Z= 0.183 Angle : 0.556 7.950 24774 Z= 0.279 Chirality : 0.040 0.137 2808 Planarity : 0.004 0.039 3072 Dihedral : 4.072 14.333 2418 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.32 % Allowed : 16.24 % Favored : 81.43 % 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: 2.06 (0.18), residues: 2136 helix: 2.37 (0.14), residues: 1248 sheet: 1.48 (0.40), residues: 180 loop : -0.53 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 170 TYR 0.015 0.002 TYR A 280 PHE 0.024 0.002 PHE E 149 TRP 0.019 0.002 TRP B 134 HIS 0.006 0.001 HIS B 423 Details of bonding type rmsd covalent geometry : bond 0.00430 (18270) covalent geometry : angle 0.55558 (24762) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.61452 ( 12) hydrogen bonds : bond 0.03465 ( 1086) hydrogen bonds : angle 4.03885 ( 3159) *********************** 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 327 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.5886 (mmp-170) REVERT: A 217 GLN cc_start: 0.7644 (mt0) cc_final: 0.7354 (mt0) REVERT: A 344 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7972 (mt-10) REVERT: A 350 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7059 (ttm110) REVERT: A 418 GLU cc_start: 0.8763 (tp30) cc_final: 0.8434 (tp30) REVERT: B 186 MET cc_start: 0.8314 (mmt) cc_final: 0.7740 (mtp) REVERT: B 341 TYR cc_start: 0.8686 (t80) cc_final: 0.8261 (t80) REVERT: B 350 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7344 (ttm110) REVERT: B 418 GLU cc_start: 0.8771 (tp30) cc_final: 0.8228 (tp30) REVERT: B 422 GLN cc_start: 0.8288 (mt0) cc_final: 0.7960 (mt0) REVERT: B 503 PHE cc_start: 0.8163 (t80) cc_final: 0.7898 (t80) REVERT: C 172 LYS cc_start: 0.8486 (pttp) cc_final: 0.7548 (mtpt) REVERT: C 186 MET cc_start: 0.8293 (mmt) cc_final: 0.7562 (mtp) REVERT: C 344 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7834 (mt-10) REVERT: C 364 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: C 371 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8275 (ptmm) REVERT: C 400 ARG cc_start: 0.8090 (tpm-80) cc_final: 0.7802 (tpm-80) REVERT: C 418 GLU cc_start: 0.8780 (tp30) cc_final: 0.8218 (tp30) REVERT: C 422 GLN cc_start: 0.8161 (mt0) cc_final: 0.7738 (mt0) REVERT: C 459 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: D 170 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.5895 (mmp-170) REVERT: D 344 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8002 (mt-10) REVERT: D 350 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7114 (ttm110) REVERT: D 418 GLU cc_start: 0.8757 (tp30) cc_final: 0.8450 (tp30) REVERT: E 120 PHE cc_start: 0.7605 (t80) cc_final: 0.6999 (m-80) REVERT: E 170 ARG cc_start: 0.7964 (mtt180) cc_final: 0.6972 (mmp80) REVERT: E 172 LYS cc_start: 0.8321 (pttt) cc_final: 0.8107 (pttt) REVERT: E 186 MET cc_start: 0.8288 (mmt) cc_final: 0.7759 (mtp) REVERT: E 195 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.8079 (p) REVERT: E 217 GLN cc_start: 0.7553 (mt0) cc_final: 0.7229 (mm-40) REVERT: E 344 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7949 (mt-10) REVERT: E 350 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7291 (ttm110) REVERT: E 364 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: E 417 MET cc_start: 0.8139 (ttp) cc_final: 0.7931 (ttm) REVERT: E 418 GLU cc_start: 0.8669 (tp30) cc_final: 0.8201 (tp30) REVERT: F 120 PHE cc_start: 0.7441 (t80) cc_final: 0.7087 (m-80) REVERT: F 172 LYS cc_start: 0.8442 (pttp) cc_final: 0.7548 (mtpt) REVERT: F 186 MET cc_start: 0.8307 (mmt) cc_final: 0.7576 (mtp) REVERT: F 243 GLN cc_start: 0.8939 (tt0) cc_final: 0.8573 (tt0) REVERT: F 344 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7830 (mt-10) REVERT: F 364 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: F 418 GLU cc_start: 0.8764 (tp30) cc_final: 0.8200 (tp30) REVERT: F 422 GLN cc_start: 0.8162 (mt0) cc_final: 0.7740 (mt0) REVERT: F 459 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: F 513 MET cc_start: 0.7397 (tpp) cc_final: 0.6851 (tpp) outliers start: 44 outliers final: 18 residues processed: 299 average time/residue: 0.7980 time to fit residues: 261.3078 Evaluate side-chains 297 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 439 GLU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 459 GLN Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 59 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097150 restraints weight = 21166.473| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.05 r_work: 0.3046 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18276 Z= 0.163 Angle : 0.537 7.054 24774 Z= 0.271 Chirality : 0.040 0.135 2808 Planarity : 0.004 0.037 3072 Dihedral : 4.034 13.881 2418 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.27 % Allowed : 17.30 % Favored : 80.43 % 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: 2.15 (0.18), residues: 2136 helix: 2.42 (0.14), residues: 1248 sheet: 1.42 (0.39), residues: 180 loop : -0.39 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 170 TYR 0.014 0.002 TYR F 280 PHE 0.025 0.002 PHE E 149 TRP 0.020 0.001 TRP B 134 HIS 0.004 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00383 (18270) covalent geometry : angle 0.53735 (24762) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.61901 ( 12) hydrogen bonds : bond 0.03356 ( 1086) hydrogen bonds : angle 4.04261 ( 3159) *********************** 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 318 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5956 (mmp-170) REVERT: A 217 GLN cc_start: 0.7659 (mt0) cc_final: 0.7441 (mt0) REVERT: A 344 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 350 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7062 (ttm110) REVERT: A 364 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: A 418 GLU cc_start: 0.8768 (tp30) cc_final: 0.8446 (tp30) REVERT: B 186 MET cc_start: 0.8315 (mmt) cc_final: 0.7788 (mtp) REVERT: B 350 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7241 (ttm110) REVERT: B 371 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8375 (ttpp) REVERT: B 418 GLU cc_start: 0.8760 (tp30) cc_final: 0.8212 (tp30) REVERT: B 422 GLN cc_start: 0.8276 (mt0) cc_final: 0.7968 (mt0) REVERT: B 503 PHE cc_start: 0.8125 (t80) cc_final: 0.7895 (t80) REVERT: C 118 LEU cc_start: 0.8180 (tp) cc_final: 0.7864 (tp) REVERT: C 172 LYS cc_start: 0.8418 (pttp) cc_final: 0.7480 (mtpt) REVERT: C 186 MET cc_start: 0.8257 (mmt) cc_final: 0.7534 (mtp) REVERT: C 243 GLN cc_start: 0.8982 (tt0) cc_final: 0.8628 (tt0) REVERT: C 344 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7874 (mt-10) REVERT: C 364 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: C 371 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8287 (ptmm) REVERT: C 400 ARG cc_start: 0.8095 (tpm-80) cc_final: 0.7773 (tpm-80) REVERT: C 418 GLU cc_start: 0.8754 (tp30) cc_final: 0.8127 (tp30) REVERT: C 422 GLN cc_start: 0.8154 (mt0) cc_final: 0.7710 (mt0) REVERT: D 170 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5927 (mmp-170) REVERT: D 344 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7978 (mt-10) REVERT: D 350 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7106 (ttm110) REVERT: D 371 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8334 (mtmm) REVERT: D 418 GLU cc_start: 0.8784 (tp30) cc_final: 0.8443 (tp30) REVERT: E 120 PHE cc_start: 0.7613 (t80) cc_final: 0.7001 (m-80) REVERT: E 170 ARG cc_start: 0.7965 (mtt180) cc_final: 0.6964 (mmp80) REVERT: E 172 LYS cc_start: 0.8340 (pttt) cc_final: 0.8117 (pttt) REVERT: E 186 MET cc_start: 0.8320 (mmt) cc_final: 0.7758 (mtp) REVERT: E 195 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8117 (p) REVERT: E 344 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7932 (mt-10) REVERT: E 350 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7356 (ttm110) REVERT: E 418 GLU cc_start: 0.8676 (tp30) cc_final: 0.8288 (tp30) REVERT: E 422 GLN cc_start: 0.8193 (mt0) cc_final: 0.7871 (mt0) REVERT: F 120 PHE cc_start: 0.7523 (t80) cc_final: 0.7099 (m-80) REVERT: F 172 LYS cc_start: 0.8481 (pttp) cc_final: 0.7515 (mtpp) REVERT: F 186 MET cc_start: 0.8270 (mmt) cc_final: 0.7555 (mtp) REVERT: F 344 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7881 (mt-10) REVERT: F 364 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: F 371 LYS cc_start: 0.8772 (ttpp) cc_final: 0.8277 (ptmm) REVERT: F 418 GLU cc_start: 0.8741 (tp30) cc_final: 0.8200 (tp30) REVERT: F 422 GLN cc_start: 0.8152 (mt0) cc_final: 0.7747 (mt0) REVERT: F 513 MET cc_start: 0.7415 (tpp) cc_final: 0.6802 (tpp) outliers start: 43 outliers final: 19 residues processed: 295 average time/residue: 0.8023 time to fit residues: 258.6528 Evaluate side-chains 293 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 439 GLU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 157 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 171 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098071 restraints weight = 21356.101| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.06 r_work: 0.3059 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18276 Z= 0.140 Angle : 0.525 9.830 24774 Z= 0.263 Chirality : 0.039 0.133 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.945 13.570 2418 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.90 % Allowed : 17.72 % Favored : 80.38 % 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: 2.27 (0.18), residues: 2136 helix: 2.50 (0.14), residues: 1248 sheet: 1.42 (0.39), residues: 180 loop : -0.29 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.012 0.001 TYR F 280 PHE 0.029 0.002 PHE E 149 TRP 0.023 0.001 TRP B 134 HIS 0.003 0.001 HIS E 423 Details of bonding type rmsd covalent geometry : bond 0.00326 (18270) covalent geometry : angle 0.52450 (24762) SS BOND : bond 0.00118 ( 6) SS BOND : angle 0.54656 ( 12) hydrogen bonds : bond 0.03244 ( 1086) hydrogen bonds : angle 4.00443 ( 3159) *********************** 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 317 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 281 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8236 (m-80) cc_final: 0.7670 (m-80) REVERT: A 170 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.5957 (mmp-170) REVERT: A 217 GLN cc_start: 0.7639 (mt0) cc_final: 0.7424 (mt0) REVERT: A 344 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 350 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7118 (ttm110) REVERT: A 364 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 418 GLU cc_start: 0.8781 (tp30) cc_final: 0.8431 (tp30) REVERT: B 170 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.5858 (mmt-90) REVERT: B 186 MET cc_start: 0.8320 (mmt) cc_final: 0.7769 (mtp) REVERT: B 341 TYR cc_start: 0.8635 (t80) cc_final: 0.8291 (t80) REVERT: B 350 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7254 (ttm110) REVERT: B 371 LYS cc_start: 0.8867 (ttpp) cc_final: 0.8378 (ttpp) REVERT: B 418 GLU cc_start: 0.8755 (tp30) cc_final: 0.8209 (tp30) REVERT: B 422 GLN cc_start: 0.8265 (mt0) cc_final: 0.7960 (mt0) REVERT: B 503 PHE cc_start: 0.8119 (t80) cc_final: 0.7899 (t80) REVERT: C 118 LEU cc_start: 0.8185 (tp) cc_final: 0.7868 (tp) REVERT: C 172 LYS cc_start: 0.8416 (pttp) cc_final: 0.7482 (mtpt) REVERT: C 186 MET cc_start: 0.8240 (mmt) cc_final: 0.7531 (mtp) REVERT: C 243 GLN cc_start: 0.8973 (tt0) cc_final: 0.8595 (tt0) REVERT: C 344 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 364 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: C 371 LYS cc_start: 0.8823 (ttpp) cc_final: 0.8274 (ptmm) REVERT: C 418 GLU cc_start: 0.8781 (tp30) cc_final: 0.8188 (tp30) REVERT: C 422 GLN cc_start: 0.8151 (mt0) cc_final: 0.7723 (mt0) REVERT: D 170 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5988 (mmp-170) REVERT: D 344 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7976 (mt-10) REVERT: D 350 ARG cc_start: 0.7607 (ttm110) cc_final: 0.7303 (ttm110) REVERT: D 371 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8358 (mtmm) REVERT: D 418 GLU cc_start: 0.8797 (tp30) cc_final: 0.8461 (tp30) REVERT: E 120 PHE cc_start: 0.7535 (t80) cc_final: 0.6961 (m-80) REVERT: E 170 ARG cc_start: 0.7959 (mtt180) cc_final: 0.6965 (mmp80) REVERT: E 172 LYS cc_start: 0.8336 (pttt) cc_final: 0.8100 (pttt) REVERT: E 186 MET cc_start: 0.8306 (mmt) cc_final: 0.7779 (mtp) REVERT: E 195 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8116 (p) REVERT: E 341 TYR cc_start: 0.8583 (t80) cc_final: 0.8267 (t80) REVERT: E 344 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7913 (mt-10) REVERT: E 350 ARG cc_start: 0.7783 (ttm110) cc_final: 0.7370 (ttm110) REVERT: E 418 GLU cc_start: 0.8668 (tp30) cc_final: 0.8207 (tp30) REVERT: F 118 LEU cc_start: 0.8176 (tp) cc_final: 0.7863 (tp) REVERT: F 120 PHE cc_start: 0.7506 (t80) cc_final: 0.7077 (m-80) REVERT: F 172 LYS cc_start: 0.8465 (pttp) cc_final: 0.7497 (mtpp) REVERT: F 186 MET cc_start: 0.8254 (mmt) cc_final: 0.7572 (mtp) REVERT: F 243 GLN cc_start: 0.8993 (tt0) cc_final: 0.8660 (tt0) REVERT: F 344 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7863 (mt-10) REVERT: F 364 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F 371 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8149 (ptmm) REVERT: F 418 GLU cc_start: 0.8767 (tp30) cc_final: 0.8204 (tp30) REVERT: F 422 GLN cc_start: 0.8143 (mt0) cc_final: 0.7735 (mt0) REVERT: F 513 MET cc_start: 0.7449 (tpp) cc_final: 0.6855 (tpp) outliers start: 36 outliers final: 15 residues processed: 294 average time/residue: 0.7306 time to fit residues: 236.3460 Evaluate side-chains 297 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 0.5980 chunk 77 optimal weight: 0.0870 chunk 117 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 109 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS E 451 HIS F 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100251 restraints weight = 21157.552| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.06 r_work: 0.3091 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18276 Z= 0.112 Angle : 0.499 6.914 24774 Z= 0.251 Chirality : 0.038 0.130 2808 Planarity : 0.003 0.035 3072 Dihedral : 3.790 13.082 2418 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.53 % Allowed : 17.77 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.42 (0.18), residues: 2136 helix: 2.66 (0.14), residues: 1242 sheet: 1.37 (0.39), residues: 180 loop : -0.27 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 400 TYR 0.010 0.001 TYR F 280 PHE 0.030 0.002 PHE E 149 TRP 0.020 0.001 TRP B 134 HIS 0.003 0.001 HIS E 423 Details of bonding type rmsd covalent geometry : bond 0.00255 (18270) covalent geometry : angle 0.49856 (24762) SS BOND : bond 0.00125 ( 6) SS BOND : angle 0.52460 ( 12) hydrogen bonds : bond 0.03032 ( 1086) hydrogen bonds : angle 3.92986 ( 3159) *********************** 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 309 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8213 (m-80) cc_final: 0.7662 (m-80) REVERT: A 170 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.5912 (mmt180) REVERT: A 217 GLN cc_start: 0.7676 (mt0) cc_final: 0.7429 (mt0) REVERT: A 344 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7955 (mt-10) REVERT: A 350 ARG cc_start: 0.7529 (ttm110) cc_final: 0.7116 (ttm110) REVERT: A 364 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: A 402 MET cc_start: 0.9048 (tpt) cc_final: 0.8829 (tpp) REVERT: A 418 GLU cc_start: 0.8765 (tp30) cc_final: 0.8238 (tp30) REVERT: A 422 GLN cc_start: 0.8163 (mt0) cc_final: 0.7659 (mt0) REVERT: B 186 MET cc_start: 0.8404 (mmt) cc_final: 0.7760 (mtp) REVERT: B 341 TYR cc_start: 0.8641 (t80) cc_final: 0.8280 (t80) REVERT: B 350 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7273 (ttm110) REVERT: B 371 LYS cc_start: 0.8812 (ttpp) cc_final: 0.8364 (ttpp) REVERT: B 418 GLU cc_start: 0.8762 (tp30) cc_final: 0.8195 (tp30) REVERT: B 422 GLN cc_start: 0.8258 (mt0) cc_final: 0.7939 (mt0) REVERT: B 498 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8396 (tptt) REVERT: B 503 PHE cc_start: 0.8122 (t80) cc_final: 0.7875 (t80) REVERT: C 118 LEU cc_start: 0.8154 (tp) cc_final: 0.7857 (tp) REVERT: C 172 LYS cc_start: 0.8407 (pttp) cc_final: 0.7477 (mtpt) REVERT: C 186 MET cc_start: 0.8245 (mmt) cc_final: 0.7575 (mtp) REVERT: C 243 GLN cc_start: 0.8957 (tt0) cc_final: 0.8590 (tt0) REVERT: C 344 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 364 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: C 400 ARG cc_start: 0.8189 (tpm-80) cc_final: 0.7423 (tpp-160) REVERT: C 418 GLU cc_start: 0.8767 (tp30) cc_final: 0.8172 (tp30) REVERT: C 422 GLN cc_start: 0.8128 (mt0) cc_final: 0.7701 (mt0) REVERT: D 149 PHE cc_start: 0.8232 (m-80) cc_final: 0.7687 (m-80) REVERT: D 170 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.5976 (mmp-170) REVERT: D 344 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8001 (mt-10) REVERT: D 350 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7311 (ttm110) REVERT: D 364 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7316 (mm-30) REVERT: D 371 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8381 (mtmm) REVERT: D 402 MET cc_start: 0.9029 (tpt) cc_final: 0.8754 (tpp) REVERT: D 418 GLU cc_start: 0.8728 (tp30) cc_final: 0.8307 (tp30) REVERT: D 422 GLN cc_start: 0.8137 (mt0) cc_final: 0.7682 (mt0) REVERT: E 120 PHE cc_start: 0.7485 (t80) cc_final: 0.6880 (m-80) REVERT: E 170 ARG cc_start: 0.7973 (mtt180) cc_final: 0.6971 (mmp80) REVERT: E 172 LYS cc_start: 0.8337 (pttt) cc_final: 0.8121 (pttt) REVERT: E 186 MET cc_start: 0.8383 (mmt) cc_final: 0.7821 (mtp) REVERT: E 195 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8149 (p) REVERT: E 341 TYR cc_start: 0.8588 (t80) cc_final: 0.8254 (t80) REVERT: E 344 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7791 (mt-10) REVERT: E 350 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7365 (ttm110) REVERT: E 418 GLU cc_start: 0.8655 (tp30) cc_final: 0.8216 (tp30) REVERT: E 422 GLN cc_start: 0.8206 (mt0) cc_final: 0.7903 (mt0) REVERT: F 118 LEU cc_start: 0.8161 (tp) cc_final: 0.7859 (tp) REVERT: F 120 PHE cc_start: 0.7448 (t80) cc_final: 0.7066 (m-80) REVERT: F 172 LYS cc_start: 0.8428 (pttp) cc_final: 0.7475 (mtpp) REVERT: F 186 MET cc_start: 0.8261 (mmt) cc_final: 0.7600 (mtp) REVERT: F 243 GLN cc_start: 0.8963 (tt0) cc_final: 0.8618 (tt0) REVERT: F 344 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7875 (mt-10) REVERT: F 364 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: F 371 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8157 (ptmm) REVERT: F 418 GLU cc_start: 0.8754 (tp30) cc_final: 0.8161 (tp30) REVERT: F 422 GLN cc_start: 0.8126 (mt0) cc_final: 0.7699 (mt0) REVERT: F 513 MET cc_start: 0.7430 (tpp) cc_final: 0.6844 (tpp) outliers start: 29 outliers final: 10 residues processed: 291 average time/residue: 0.6812 time to fit residues: 218.6129 Evaluate side-chains 292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 144 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 135 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN D 243 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098779 restraints weight = 21149.079| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.06 r_work: 0.3068 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18276 Z= 0.133 Angle : 0.522 9.108 24774 Z= 0.261 Chirality : 0.039 0.129 2808 Planarity : 0.004 0.036 3072 Dihedral : 3.868 13.549 2418 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.64 % Allowed : 18.35 % Favored : 80.01 % 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: 2.39 (0.18), residues: 2136 helix: 2.55 (0.14), residues: 1248 sheet: 1.36 (0.39), residues: 180 loop : -0.13 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 400 TYR 0.012 0.001 TYR F 280 PHE 0.035 0.002 PHE E 149 TRP 0.018 0.001 TRP B 134 HIS 0.003 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00309 (18270) covalent geometry : angle 0.52161 (24762) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.54548 ( 12) hydrogen bonds : bond 0.03183 ( 1086) hydrogen bonds : angle 3.97269 ( 3159) *********************** 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 304 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8172 (m-80) cc_final: 0.7619 (m-80) REVERT: A 170 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.5931 (mmp-170) REVERT: A 217 GLN cc_start: 0.7685 (mt0) cc_final: 0.7431 (mt0) REVERT: A 344 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7958 (mt-10) REVERT: A 350 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7130 (ttm110) REVERT: A 364 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 418 GLU cc_start: 0.8797 (tp30) cc_final: 0.8443 (tp30) REVERT: B 186 MET cc_start: 0.8316 (mmt) cc_final: 0.7799 (mtp) REVERT: B 341 TYR cc_start: 0.8630 (t80) cc_final: 0.8361 (t80) REVERT: B 350 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7252 (ttm110) REVERT: B 371 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8369 (ttpp) REVERT: B 418 GLU cc_start: 0.8758 (tp30) cc_final: 0.8196 (tp30) REVERT: B 422 GLN cc_start: 0.8262 (mt0) cc_final: 0.7939 (mt0) REVERT: B 503 PHE cc_start: 0.8103 (t80) cc_final: 0.7824 (t80) REVERT: C 118 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7820 (tp) REVERT: C 172 LYS cc_start: 0.8415 (pttp) cc_final: 0.7447 (mtpp) REVERT: C 186 MET cc_start: 0.8256 (mmt) cc_final: 0.7590 (mtp) REVERT: C 243 GLN cc_start: 0.8962 (tt0) cc_final: 0.8587 (tt0) REVERT: C 344 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 364 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: C 371 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8198 (ptmm) REVERT: C 418 GLU cc_start: 0.8744 (tp30) cc_final: 0.8216 (tp30) REVERT: C 422 GLN cc_start: 0.8140 (mt0) cc_final: 0.7749 (mt0) REVERT: D 149 PHE cc_start: 0.8237 (m-80) cc_final: 0.7655 (m-80) REVERT: D 170 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5864 (mmp-170) REVERT: D 344 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 350 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7303 (ttm110) REVERT: D 371 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8373 (mtmm) REVERT: D 418 GLU cc_start: 0.8765 (tp30) cc_final: 0.8451 (tp30) REVERT: E 120 PHE cc_start: 0.7559 (t80) cc_final: 0.6885 (m-80) REVERT: E 170 ARG cc_start: 0.7982 (mtt180) cc_final: 0.6962 (mmp80) REVERT: E 172 LYS cc_start: 0.8362 (pttt) cc_final: 0.8130 (pttt) REVERT: E 186 MET cc_start: 0.8409 (mmt) cc_final: 0.7832 (mtp) REVERT: E 195 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8145 (p) REVERT: E 341 TYR cc_start: 0.8602 (t80) cc_final: 0.8248 (t80) REVERT: E 344 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7826 (mt-10) REVERT: E 350 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7364 (ttm110) REVERT: E 418 GLU cc_start: 0.8683 (tp30) cc_final: 0.8215 (tp30) REVERT: F 118 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7887 (tp) REVERT: F 120 PHE cc_start: 0.7477 (t80) cc_final: 0.7035 (m-80) REVERT: F 172 LYS cc_start: 0.8449 (pttp) cc_final: 0.7530 (mtmt) REVERT: F 186 MET cc_start: 0.8264 (mmt) cc_final: 0.7611 (mtp) REVERT: F 243 GLN cc_start: 0.8960 (tt0) cc_final: 0.8589 (tt0) REVERT: F 344 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7879 (mt-10) REVERT: F 364 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: F 371 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8116 (ptmm) REVERT: F 418 GLU cc_start: 0.8736 (tp30) cc_final: 0.8213 (tp30) REVERT: F 422 GLN cc_start: 0.8142 (mt0) cc_final: 0.7755 (mt0) REVERT: F 513 MET cc_start: 0.7448 (tpp) cc_final: 0.6855 (tpp) outliers start: 31 outliers final: 12 residues processed: 285 average time/residue: 0.7075 time to fit residues: 221.6596 Evaluate side-chains 286 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 51 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.097395 restraints weight = 21129.566| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.05 r_work: 0.3049 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18276 Z= 0.159 Angle : 0.541 9.563 24774 Z= 0.271 Chirality : 0.040 0.131 2808 Planarity : 0.004 0.039 3072 Dihedral : 3.990 14.983 2418 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.58 % Allowed : 18.78 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.31 (0.18), residues: 2136 helix: 2.46 (0.14), residues: 1248 sheet: 1.34 (0.39), residues: 180 loop : -0.12 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 252 TYR 0.014 0.002 TYR A 343 PHE 0.038 0.002 PHE E 149 TRP 0.018 0.001 TRP B 134 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00374 (18270) covalent geometry : angle 0.54118 (24762) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.55340 ( 12) hydrogen bonds : bond 0.03344 ( 1086) hydrogen bonds : angle 4.03470 ( 3159) ********************** 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 295 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8140 (m-80) cc_final: 0.7561 (m-80) REVERT: A 170 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.5663 (mmt180) REVERT: A 217 GLN cc_start: 0.7723 (mt0) cc_final: 0.7497 (mt0) REVERT: A 344 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7975 (mt-10) REVERT: A 350 ARG cc_start: 0.7573 (ttm110) cc_final: 0.7130 (ttm110) REVERT: A 364 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: A 418 GLU cc_start: 0.8790 (tp30) cc_final: 0.8440 (tp30) REVERT: B 170 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5799 (mmt-90) REVERT: B 186 MET cc_start: 0.8408 (mmt) cc_final: 0.7777 (mtp) REVERT: B 341 TYR cc_start: 0.8659 (t80) cc_final: 0.8359 (t80) REVERT: B 350 ARG cc_start: 0.7678 (ttm110) cc_final: 0.7237 (ttm110) REVERT: B 371 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8335 (ttpp) REVERT: B 418 GLU cc_start: 0.8751 (tp30) cc_final: 0.8206 (tp30) REVERT: B 422 GLN cc_start: 0.8267 (mt0) cc_final: 0.7963 (mt0) REVERT: B 503 PHE cc_start: 0.8098 (t80) cc_final: 0.7850 (t80) REVERT: C 172 LYS cc_start: 0.8420 (pttp) cc_final: 0.7454 (mtpp) REVERT: C 186 MET cc_start: 0.8264 (mmt) cc_final: 0.7590 (mtp) REVERT: C 243 GLN cc_start: 0.8946 (tt0) cc_final: 0.8568 (tt0) REVERT: C 344 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7871 (mt-10) REVERT: C 364 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: C 371 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8172 (ptmm) REVERT: C 418 GLU cc_start: 0.8753 (tp30) cc_final: 0.8220 (tp30) REVERT: C 422 GLN cc_start: 0.8145 (mt0) cc_final: 0.7746 (mt0) REVERT: D 170 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5886 (mmp-170) REVERT: D 344 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7961 (mt-10) REVERT: D 350 ARG cc_start: 0.7651 (ttm110) cc_final: 0.7308 (ttm110) REVERT: D 371 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8313 (mtmm) REVERT: D 418 GLU cc_start: 0.8789 (tp30) cc_final: 0.8450 (tp30) REVERT: E 120 PHE cc_start: 0.7631 (t80) cc_final: 0.6912 (m-80) REVERT: E 170 ARG cc_start: 0.7985 (mtt180) cc_final: 0.6943 (mmp80) REVERT: E 172 LYS cc_start: 0.8349 (pttt) cc_final: 0.8102 (pttt) REVERT: E 186 MET cc_start: 0.8305 (mmt) cc_final: 0.7770 (mtp) REVERT: E 195 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.8113 (p) REVERT: E 341 TYR cc_start: 0.8583 (t80) cc_final: 0.8238 (t80) REVERT: E 344 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7863 (mt-10) REVERT: E 350 ARG cc_start: 0.7790 (ttm110) cc_final: 0.7338 (ttm110) REVERT: F 118 LEU cc_start: 0.8174 (tp) cc_final: 0.7891 (tp) REVERT: F 120 PHE cc_start: 0.7515 (t80) cc_final: 0.7042 (m-80) REVERT: F 172 LYS cc_start: 0.8399 (pttp) cc_final: 0.7484 (mtpt) REVERT: F 186 MET cc_start: 0.8250 (mmt) cc_final: 0.7585 (mtp) REVERT: F 243 GLN cc_start: 0.8979 (tt0) cc_final: 0.8606 (tt0) REVERT: F 344 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7865 (mt-10) REVERT: F 364 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: F 371 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8198 (ptmm) REVERT: F 418 GLU cc_start: 0.8743 (tp30) cc_final: 0.8211 (tp30) REVERT: F 422 GLN cc_start: 0.8152 (mt0) cc_final: 0.7758 (mt0) REVERT: F 513 MET cc_start: 0.7466 (tpp) cc_final: 0.6875 (tpp) outliers start: 30 outliers final: 13 residues processed: 274 average time/residue: 0.7621 time to fit residues: 229.0442 Evaluate side-chains 284 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 149 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098709 restraints weight = 21282.454| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.05 r_work: 0.3069 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18276 Z= 0.132 Angle : 0.523 8.797 24774 Z= 0.262 Chirality : 0.039 0.130 2808 Planarity : 0.004 0.035 3072 Dihedral : 3.895 14.659 2418 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.53 % Allowed : 18.88 % Favored : 79.59 % 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: 2.40 (0.18), residues: 2136 helix: 2.54 (0.14), residues: 1248 sheet: 1.31 (0.39), residues: 180 loop : -0.04 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 400 TYR 0.012 0.001 TYR D 280 PHE 0.040 0.002 PHE E 149 TRP 0.018 0.001 TRP D 134 HIS 0.003 0.001 HIS D 423 Details of bonding type rmsd covalent geometry : bond 0.00306 (18270) covalent geometry : angle 0.52259 (24762) SS BOND : bond 0.00103 ( 6) SS BOND : angle 0.52190 ( 12) hydrogen bonds : bond 0.03186 ( 1086) hydrogen bonds : angle 4.00251 ( 3159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7800.18 seconds wall clock time: 133 minutes 21.49 seconds (8001.49 seconds total)