Starting phenix.real_space_refine on Sun Jun 15 22:32:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jka_61549/06_2025/9jka_61549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jka_61549/06_2025/9jka_61549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jka_61549/06_2025/9jka_61549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jka_61549/06_2025/9jka_61549.map" model { file = "/net/cci-nas-00/data/ceres_data/9jka_61549/06_2025/9jka_61549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jka_61549/06_2025/9jka_61549.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 11706 2.51 5 N 3084 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17820 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2970 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.12, per 1000 atoms: 0.40 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 C 141 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 141 " - pdb=" SG CYS E 145 " distance=2.03 Simple disulfide: pdb=" SG CYS D 141 " - pdb=" SG CYS D 145 " distance=2.03 Simple disulfide: pdb=" SG CYS F 141 " - pdb=" SG CYS F 145 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.4 seconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4212 Finding SS restraints... Secondary structure from input PDB file: 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: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 109 through 134 Proline residue: A 123 - end of helix Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 142 through 168 removed outlier: 4.048A pdb=" N GLU A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 204 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS A 509 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 134 Proline residue: B 123 - end of helix Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 168 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 204 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 336 Processing helix chain 'B' and resid 339 through 368 removed outlier: 3.598A pdb=" N TYR B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 416 through 430 Processing helix chain 'B' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 456 through 459 Processing helix chain 'B' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS B 509 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 Proline residue: C 123 - end of helix Proline residue: C 130 - end of helix Processing helix chain 'C' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 204 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA C 396 " --> pdb=" O GLN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 416 through 430 Processing helix chain 'C' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR C 441 " --> pdb=" O PHE C 437 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 456 through 459 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS C 509 " --> pdb=" O PRO C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 134 Proline residue: D 123 - end of helix Proline residue: D 130 - end of helix Processing helix chain 'D' and resid 142 through 168 removed outlier: 4.048A pdb=" N GLU D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 204 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 336 Processing helix chain 'D' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA D 396 " --> pdb=" O GLN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 416 through 430 Processing helix chain 'D' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 456 through 459 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS D 509 " --> pdb=" O PRO D 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 134 Proline residue: E 123 - end of helix Proline residue: E 130 - end of helix Processing helix chain 'E' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 168 " --> pdb=" O TRP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 204 Processing helix chain 'E' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 Processing helix chain 'E' and resid 339 through 368 removed outlier: 3.598A pdb=" N TYR E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 396 removed outlier: 4.115A pdb=" N ALA E 396 " --> pdb=" O GLN E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 409 Processing helix chain 'E' and resid 416 through 430 Processing helix chain 'E' and resid 433 through 443 removed outlier: 4.950A pdb=" N ARG E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR E 441 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 456 through 459 Processing helix chain 'E' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS E 509 " --> pdb=" O PRO E 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 134 Proline residue: F 123 - end of helix Proline residue: F 130 - end of helix Processing helix chain 'F' and resid 142 through 168 removed outlier: 4.049A pdb=" N GLU F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 168 " --> pdb=" O TRP F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 204 Processing helix chain 'F' and resid 211 through 238 removed outlier: 3.559A pdb=" N VAL F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 removed outlier: 3.585A pdb=" N TYR F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 336 Processing helix chain 'F' and resid 339 through 368 removed outlier: 3.597A pdb=" N TYR F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 396 removed outlier: 4.116A pdb=" N ALA F 396 " --> pdb=" O GLN F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 409 Processing helix chain 'F' and resid 416 through 430 Processing helix chain 'F' and resid 433 through 443 removed outlier: 4.951A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR F 441 " --> pdb=" O PHE F 437 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA F 443 " --> pdb=" O GLU F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 450 Processing helix chain 'F' and resid 456 through 459 Processing helix chain 'F' and resid 505 through 509 removed outlier: 3.843A pdb=" N HIS F 509 " --> pdb=" O PRO F 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.920A pdb=" N TRP A 460 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.586A pdb=" N LYS A 371 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 173 through 174 removed outlier: 6.487A pdb=" N PHE A 497 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS A 498 " --> pdb=" O TRP C 460 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU C 462 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER A 500 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 512 removed outlier: 3.595A pdb=" N LYS B 371 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.755A pdb=" N TRP B 460 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AA7, first strand: chain 'D' and resid 173 through 174 removed outlier: 3.678A pdb=" N TRP D 460 " --> pdb=" O LYS E 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 371 through 372 Processing sheet with id=AA9, first strand: chain 'F' and resid 173 through 174 removed outlier: 6.627A pdb=" N PHE D 497 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS D 498 " --> pdb=" O TRP F 460 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU F 462 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER D 500 " --> pdb=" O LEU F 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 511 through 512 removed outlier: 3.511A pdb=" N LYS E 371 " --> pdb=" O VAL D 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.869A pdb=" N TRP E 460 " --> pdb=" O LYS F 498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 511 through 512 1086 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 5.52 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.360 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.590 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 2136 helix: -1.44 (0.12), residues: 1200 sheet: 1.47 (0.38), residues: 168 loop : -2.01 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 164 HIS 0.012 0.002 HIS E 423 PHE 0.045 0.006 PHE B 260 TYR 0.020 0.003 TYR D 279 ARG 0.012 0.001 ARG E 252 Details of bonding type rmsd hydrogen bonds : bond 0.11301 ( 1086) hydrogen bonds : angle 6.21183 ( 3159) SS BOND : bond 0.00100 ( 6) SS BOND : angle 0.67318 ( 12) covalent geometry : bond 0.00663 (18270) covalent geometry : angle 0.90196 (24762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8567 (tp) cc_final: 0.8272 (tm) REVERT: A 217 GLN cc_start: 0.7433 (mt0) cc_final: 0.7162 (mt0) REVERT: A 222 LEU cc_start: 0.7935 (tp) cc_final: 0.7684 (tp) REVERT: A 344 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 350 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6844 (ttm110) REVERT: A 418 GLU cc_start: 0.7634 (tp30) cc_final: 0.7292 (tp30) REVERT: A 422 GLN cc_start: 0.7628 (mt0) cc_final: 0.7003 (mt0) REVERT: B 135 ARG cc_start: 0.7199 (ttt180) cc_final: 0.6944 (tpt-90) REVERT: B 341 TYR cc_start: 0.8206 (t80) cc_final: 0.7774 (t80) REVERT: B 350 ARG cc_start: 0.7348 (ttm110) cc_final: 0.7093 (ttm110) REVERT: B 385 MET cc_start: 0.8593 (ttp) cc_final: 0.8149 (ttp) REVERT: B 403 GLN cc_start: 0.7952 (tt0) cc_final: 0.7748 (tt0) REVERT: B 418 GLU cc_start: 0.7989 (tp30) cc_final: 0.7607 (tp30) REVERT: B 422 GLN cc_start: 0.7766 (mt0) cc_final: 0.7464 (mm110) REVERT: B 435 LYS cc_start: 0.7679 (ttmp) cc_final: 0.7282 (tptp) REVERT: C 172 LYS cc_start: 0.8251 (pttp) cc_final: 0.7510 (mtpp) REVERT: C 344 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 385 MET cc_start: 0.8820 (ttp) cc_final: 0.8539 (ttp) REVERT: C 404 LYS cc_start: 0.8378 (mttm) cc_final: 0.8106 (mttm) REVERT: C 418 GLU cc_start: 0.7942 (tp30) cc_final: 0.7430 (tp30) REVERT: C 422 GLN cc_start: 0.7615 (mt0) cc_final: 0.7255 (mt0) REVERT: C 513 MET cc_start: 0.7389 (tpp) cc_final: 0.7088 (tpp) REVERT: D 213 GLN cc_start: 0.7984 (tt0) cc_final: 0.7593 (tm-30) REVERT: D 217 GLN cc_start: 0.7458 (mt0) cc_final: 0.7225 (mt0) REVERT: D 341 TYR cc_start: 0.7997 (t80) cc_final: 0.7623 (t80) REVERT: D 344 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7275 (mt-10) REVERT: D 347 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7494 (mt-10) REVERT: D 349 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 350 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6867 (ttm110) REVERT: D 385 MET cc_start: 0.8741 (ttp) cc_final: 0.8512 (ttp) REVERT: D 418 GLU cc_start: 0.7816 (tp30) cc_final: 0.7598 (tp30) REVERT: D 422 GLN cc_start: 0.7701 (mt0) cc_final: 0.7182 (mm-40) REVERT: D 435 LYS cc_start: 0.7833 (ttmp) cc_final: 0.7425 (tptp) REVERT: E 117 LEU cc_start: 0.8819 (tp) cc_final: 0.8616 (tm) REVERT: E 120 PHE cc_start: 0.7504 (t80) cc_final: 0.7018 (m-80) REVERT: E 170 ARG cc_start: 0.7369 (mtt180) cc_final: 0.7155 (mmp80) REVERT: E 172 LYS cc_start: 0.8306 (pttp) cc_final: 0.7542 (mtpp) REVERT: E 341 TYR cc_start: 0.8426 (t80) cc_final: 0.8029 (t80) REVERT: E 344 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 350 ARG cc_start: 0.7181 (ttm110) cc_final: 0.6852 (ttm110) REVERT: E 404 LYS cc_start: 0.8502 (mttm) cc_final: 0.8300 (mtmm) REVERT: E 418 GLU cc_start: 0.7950 (tp30) cc_final: 0.7457 (tp30) REVERT: E 435 LYS cc_start: 0.7614 (ttmp) cc_final: 0.7298 (tptp) REVERT: F 120 PHE cc_start: 0.7384 (t80) cc_final: 0.7172 (m-80) REVERT: F 172 LYS cc_start: 0.8230 (pttp) cc_final: 0.7474 (mtpp) REVERT: F 344 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7397 (mt-10) REVERT: F 385 MET cc_start: 0.8804 (ttp) cc_final: 0.8544 (ttp) REVERT: F 404 LYS cc_start: 0.8380 (mttm) cc_final: 0.8110 (mttm) REVERT: F 418 GLU cc_start: 0.7944 (tp30) cc_final: 0.7412 (tp30) REVERT: F 422 GLN cc_start: 0.7624 (mt0) cc_final: 0.7251 (mt0) REVERT: F 513 MET cc_start: 0.7402 (tpp) cc_final: 0.7199 (tpp) outliers start: 0 outliers final: 1 residues processed: 489 average time/residue: 1.7402 time to fit residues: 924.2610 Evaluate side-chains 301 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 282 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 411 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN B 411 GLN B 449 GLN C 412 GLN C 415 HIS C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN D 451 HIS E 411 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 GLN F 415 HIS F 449 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100901 restraints weight = 21289.006| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.04 r_work: 0.3097 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2407 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= 0.156 Angle : 0.553 7.294 24774 Z= 0.289 Chirality : 0.040 0.143 2808 Planarity : 0.005 0.043 3072 Dihedral : 4.464 48.977 2420 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.69 % Allowed : 11.55 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2136 helix: 1.10 (0.14), residues: 1212 sheet: 1.74 (0.39), residues: 168 loop : -1.28 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 164 HIS 0.005 0.001 HIS E 423 PHE 0.025 0.003 PHE B 149 TYR 0.010 0.002 TYR C 280 ARG 0.006 0.001 ARG E 210 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 1086) hydrogen bonds : angle 4.26940 ( 3159) SS BOND : bond 0.00118 ( 6) SS BOND : angle 0.57773 ( 12) covalent geometry : bond 0.00364 (18270) covalent geometry : angle 0.55336 (24762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 323 time to evaluate : 2.024 Fit side-chains revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.5407 (mmp-170) REVERT: A 182 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7144 (ttp80) REVERT: A 217 GLN cc_start: 0.7499 (mt0) cc_final: 0.7220 (mt0) REVERT: A 344 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7966 (mt-10) REVERT: A 350 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7010 (ttm110) REVERT: A 364 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7962 (mt-10) REVERT: A 418 GLU cc_start: 0.8589 (tp30) cc_final: 0.8206 (tp30) REVERT: A 422 GLN cc_start: 0.8163 (mt0) cc_final: 0.7732 (mt0) REVERT: B 172 LYS cc_start: 0.8374 (pttt) cc_final: 0.8161 (pttm) REVERT: B 182 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7014 (ttm170) REVERT: B 213 GLN cc_start: 0.7830 (tt0) cc_final: 0.7480 (tm-30) REVERT: B 341 TYR cc_start: 0.8598 (t80) cc_final: 0.8186 (t80) REVERT: B 350 ARG cc_start: 0.7736 (ttm110) cc_final: 0.7299 (ttm110) REVERT: B 418 GLU cc_start: 0.8760 (tp30) cc_final: 0.8215 (tp30) REVERT: B 422 GLN cc_start: 0.8321 (mt0) cc_final: 0.8009 (mt0) REVERT: B 435 LYS cc_start: 0.8269 (ttmp) cc_final: 0.7559 (tptt) REVERT: C 172 LYS cc_start: 0.8440 (pttp) cc_final: 0.7484 (mmmt) REVERT: C 190 PHE cc_start: 0.8145 (t80) cc_final: 0.7868 (t80) REVERT: C 344 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7761 (mt-10) REVERT: C 364 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: C 400 ARG cc_start: 0.8086 (tpm-80) cc_final: 0.7518 (tpp-160) REVERT: C 418 GLU cc_start: 0.8786 (tp30) cc_final: 0.8154 (tp30) REVERT: C 422 GLN cc_start: 0.8137 (mt0) cc_final: 0.7785 (mt0) REVERT: C 513 MET cc_start: 0.7562 (tpp) cc_final: 0.7092 (tpp) REVERT: D 120 PHE cc_start: 0.6718 (m-80) cc_final: 0.6223 (t80) REVERT: D 344 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7900 (mt-10) REVERT: D 347 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7791 (mt-10) REVERT: D 350 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7198 (ttm110) REVERT: D 364 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7786 (mt-10) REVERT: D 418 GLU cc_start: 0.8649 (tp30) cc_final: 0.8300 (tp30) REVERT: E 120 PHE cc_start: 0.7473 (t80) cc_final: 0.7017 (m-80) REVERT: E 170 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6936 (mmp80) REVERT: E 195 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8090 (p) REVERT: E 217 GLN cc_start: 0.7869 (mt0) cc_final: 0.7531 (mm-40) REVERT: E 341 TYR cc_start: 0.8671 (t80) cc_final: 0.8250 (t80) REVERT: E 344 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7902 (mt-10) REVERT: E 350 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7288 (ttm110) REVERT: E 412 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7598 (mp10) REVERT: E 418 GLU cc_start: 0.8668 (tp30) cc_final: 0.8187 (tp30) REVERT: F 120 PHE cc_start: 0.7374 (t80) cc_final: 0.7081 (m-80) REVERT: F 172 LYS cc_start: 0.8454 (pttp) cc_final: 0.7479 (mtpp) REVERT: F 190 PHE cc_start: 0.8146 (t80) cc_final: 0.7837 (t80) REVERT: F 344 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7808 (mt-10) REVERT: F 364 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: F 400 ARG cc_start: 0.8075 (tpm-80) cc_final: 0.7515 (tpp-160) REVERT: F 418 GLU cc_start: 0.8789 (tp30) cc_final: 0.8170 (tp30) REVERT: F 422 GLN cc_start: 0.8150 (mt0) cc_final: 0.7800 (mt0) REVERT: F 513 MET cc_start: 0.7271 (tpp) cc_final: 0.6874 (tpp) outliers start: 51 outliers final: 8 residues processed: 346 average time/residue: 1.5840 time to fit residues: 600.3973 Evaluate side-chains 299 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 287 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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 112 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 67 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 412 GLN E 449 GLN F 449 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100068 restraints weight = 21221.067| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.05 r_work: 0.3087 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2844 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= 0.135 Angle : 0.535 8.762 24774 Z= 0.269 Chirality : 0.039 0.137 2808 Planarity : 0.004 0.038 3072 Dihedral : 4.071 13.962 2418 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.80 % Allowed : 13.55 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.18), residues: 2136 helix: 2.07 (0.14), residues: 1212 sheet: 1.89 (0.40), residues: 168 loop : -0.92 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.004 0.001 HIS E 423 PHE 0.024 0.002 PHE B 149 TYR 0.013 0.001 TYR A 341 ARG 0.005 0.001 ARG E 482 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 1086) hydrogen bonds : angle 4.07371 ( 3159) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.61016 ( 12) covalent geometry : bond 0.00314 (18270) covalent geometry : angle 0.53456 (24762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: A 170 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.5665 (mmp-170) REVERT: A 182 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7140 (ttp80) REVERT: A 217 GLN cc_start: 0.7504 (mt0) cc_final: 0.7217 (mt0) REVERT: A 344 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7971 (mt-10) REVERT: A 350 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7048 (ttm110) REVERT: A 364 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7799 (mt-10) REVERT: A 418 GLU cc_start: 0.8681 (tp30) cc_final: 0.8357 (tp30) REVERT: B 182 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7035 (ttp-110) REVERT: B 213 GLN cc_start: 0.7860 (tt0) cc_final: 0.7643 (tm-30) REVERT: B 341 TYR cc_start: 0.8643 (t80) cc_final: 0.8246 (t80) REVERT: B 350 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7377 (ttm110) REVERT: B 418 GLU cc_start: 0.8750 (tp30) cc_final: 0.8178 (tp30) REVERT: B 422 GLN cc_start: 0.8287 (mt0) cc_final: 0.7953 (mt0) REVERT: C 172 LYS cc_start: 0.8488 (pttp) cc_final: 0.7515 (mtpt) REVERT: C 190 PHE cc_start: 0.8173 (t80) cc_final: 0.7921 (t80) REVERT: C 344 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7863 (mt-10) REVERT: C 364 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: C 400 ARG cc_start: 0.8127 (tpm-80) cc_final: 0.7522 (tpp-160) REVERT: C 418 GLU cc_start: 0.8802 (tp30) cc_final: 0.8185 (tp30) REVERT: C 422 GLN cc_start: 0.8142 (mt0) cc_final: 0.7794 (mt0) REVERT: C 513 MET cc_start: 0.7611 (tpp) cc_final: 0.7116 (tpp) REVERT: D 344 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7927 (mt-10) REVERT: D 347 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7707 (mt-10) REVERT: D 350 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7206 (ttm110) REVERT: D 364 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7765 (mt-10) REVERT: D 418 GLU cc_start: 0.8680 (tp30) cc_final: 0.8378 (tp30) REVERT: E 120 PHE cc_start: 0.7502 (t80) cc_final: 0.6993 (m-80) REVERT: E 170 ARG cc_start: 0.7920 (mtt180) cc_final: 0.6985 (mmp80) REVERT: E 186 MET cc_start: 0.8308 (mmt) cc_final: 0.7709 (mtp) REVERT: E 195 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.8052 (p) REVERT: E 217 GLN cc_start: 0.7605 (mt0) cc_final: 0.7343 (mm-40) REVERT: E 341 TYR cc_start: 0.8644 (t80) cc_final: 0.8281 (t80) REVERT: E 344 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7883 (mt-10) REVERT: E 350 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7277 (ttm110) REVERT: E 418 GLU cc_start: 0.8608 (tp30) cc_final: 0.8135 (tp30) REVERT: F 120 PHE cc_start: 0.7370 (t80) cc_final: 0.7041 (m-80) REVERT: F 172 LYS cc_start: 0.8444 (pttp) cc_final: 0.7549 (mtpt) REVERT: F 190 PHE cc_start: 0.8179 (t80) cc_final: 0.7915 (t80) REVERT: F 344 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7818 (mt-10) REVERT: F 364 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: F 400 ARG cc_start: 0.8120 (tpm-80) cc_final: 0.7527 (tpp-160) REVERT: F 418 GLU cc_start: 0.8799 (tp30) cc_final: 0.8221 (tp30) REVERT: F 422 GLN cc_start: 0.8144 (mt0) cc_final: 0.7815 (mt0) REVERT: F 513 MET cc_start: 0.7243 (tpp) cc_final: 0.6794 (tpp) outliers start: 53 outliers final: 12 residues processed: 320 average time/residue: 1.5852 time to fit residues: 558.2000 Evaluate side-chains 293 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 412 GLN 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 191 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 412 GLN Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.135744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097666 restraints weight = 21265.154| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.05 r_work: 0.3051 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18276 Z= 0.163 Angle : 0.539 8.276 24774 Z= 0.273 Chirality : 0.040 0.136 2808 Planarity : 0.004 0.036 3072 Dihedral : 4.085 14.124 2418 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.32 % Allowed : 14.93 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.18), residues: 2136 helix: 2.21 (0.14), residues: 1248 sheet: 1.48 (0.40), residues: 180 loop : -0.67 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.004 0.001 HIS B 423 PHE 0.027 0.002 PHE B 149 TYR 0.014 0.002 TYR A 280 ARG 0.004 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 1086) hydrogen bonds : angle 4.06022 ( 3159) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.57107 ( 12) covalent geometry : bond 0.00382 (18270) covalent geometry : angle 0.53857 (24762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5843 (mmp-170) REVERT: A 182 ARG cc_start: 0.7872 (ttm170) cc_final: 0.7161 (ttp80) REVERT: A 217 GLN cc_start: 0.7629 (mt0) cc_final: 0.7350 (mt0) REVERT: A 344 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7960 (mt-10) REVERT: A 350 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7092 (ttm110) REVERT: A 364 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7799 (mt-10) REVERT: A 418 GLU cc_start: 0.8750 (tp30) cc_final: 0.8383 (tp30) REVERT: B 117 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8149 (tm) REVERT: B 121 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7501 (mm) REVERT: B 172 LYS cc_start: 0.8192 (pttt) cc_final: 0.7941 (pttt) REVERT: B 182 ARG cc_start: 0.7899 (ttm170) cc_final: 0.6994 (ttm170) REVERT: B 186 MET cc_start: 0.8328 (mmt) cc_final: 0.7689 (mtp) REVERT: B 213 GLN cc_start: 0.7811 (tt0) cc_final: 0.7508 (tm-30) REVERT: B 350 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7305 (ttm110) REVERT: B 371 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8336 (ttpp) REVERT: B 418 GLU cc_start: 0.8769 (tp30) cc_final: 0.8209 (tp30) REVERT: B 422 GLN cc_start: 0.8290 (mt0) cc_final: 0.7969 (mt0) REVERT: C 172 LYS cc_start: 0.8492 (pttp) cc_final: 0.7521 (mtpt) REVERT: C 186 MET cc_start: 0.8316 (mmt) cc_final: 0.7554 (mtp) REVERT: C 344 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 364 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 371 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8159 (ptmm) REVERT: C 418 GLU cc_start: 0.8790 (tp30) cc_final: 0.8215 (tp30) REVERT: C 422 GLN cc_start: 0.8167 (mt0) cc_final: 0.7728 (mt0) REVERT: C 513 MET cc_start: 0.7674 (tpp) cc_final: 0.7201 (tpp) REVERT: D 170 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5898 (mmp-170) REVERT: D 344 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7921 (mt-10) REVERT: D 350 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7125 (ttm110) REVERT: D 364 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7776 (mt-10) REVERT: D 418 GLU cc_start: 0.8742 (tp30) cc_final: 0.8423 (tp30) REVERT: E 120 PHE cc_start: 0.7663 (t80) cc_final: 0.7060 (m-80) REVERT: E 170 ARG cc_start: 0.7940 (mtt180) cc_final: 0.6985 (mmp80) REVERT: E 172 LYS cc_start: 0.8314 (pttt) cc_final: 0.8103 (pttt) REVERT: E 186 MET cc_start: 0.8303 (mmt) cc_final: 0.7740 (mtp) REVERT: E 195 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.8094 (p) REVERT: E 217 GLN cc_start: 0.7612 (mt0) cc_final: 0.7322 (mm-40) REVERT: E 344 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7914 (mt-10) REVERT: E 350 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7310 (ttm110) REVERT: E 364 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: E 418 GLU cc_start: 0.8660 (tp30) cc_final: 0.8233 (tp30) REVERT: E 422 GLN cc_start: 0.8177 (mt0) cc_final: 0.7780 (mt0) REVERT: F 120 PHE cc_start: 0.7430 (t80) cc_final: 0.7070 (m-80) REVERT: F 172 LYS cc_start: 0.8446 (pttp) cc_final: 0.7549 (mtpt) REVERT: F 186 MET cc_start: 0.8336 (mmt) cc_final: 0.7590 (mtp) REVERT: F 344 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7808 (mt-10) REVERT: F 364 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: F 371 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8203 (ptmm) REVERT: F 418 GLU cc_start: 0.8786 (tp30) cc_final: 0.8213 (tp30) REVERT: F 422 GLN cc_start: 0.8160 (mt0) cc_final: 0.7721 (mt0) REVERT: F 513 MET cc_start: 0.7281 (tpp) cc_final: 0.6753 (tpp) outliers start: 44 outliers final: 17 residues processed: 302 average time/residue: 1.5573 time to fit residues: 517.5142 Evaluate side-chains 296 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 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 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 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 415 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095056 restraints weight = 21392.505| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.04 r_work: 0.3012 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18276 Z= 0.213 Angle : 0.576 6.678 24774 Z= 0.292 Chirality : 0.041 0.138 2808 Planarity : 0.005 0.050 3072 Dihedral : 4.260 15.539 2418 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.37 % Allowed : 16.03 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2136 helix: 2.17 (0.14), residues: 1248 sheet: 1.52 (0.40), residues: 180 loop : -0.53 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 134 HIS 0.005 0.001 HIS F 423 PHE 0.024 0.003 PHE B 149 TYR 0.024 0.002 TYR A 280 ARG 0.008 0.001 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1086) hydrogen bonds : angle 4.16896 ( 3159) SS BOND : bond 0.00241 ( 6) SS BOND : angle 0.78752 ( 12) covalent geometry : bond 0.00505 (18270) covalent geometry : angle 0.57625 (24762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5735 (mmt180) REVERT: A 217 GLN cc_start: 0.7625 (mt0) cc_final: 0.7339 (mt0) REVERT: A 344 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7972 (mt-10) REVERT: A 350 ARG cc_start: 0.7540 (ttm110) cc_final: 0.7124 (ttm110) REVERT: A 418 GLU cc_start: 0.8738 (tp30) cc_final: 0.8385 (tp30) REVERT: B 170 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6007 (mmt-90) REVERT: B 186 MET cc_start: 0.8286 (mmt) cc_final: 0.7737 (mtp) REVERT: B 350 ARG cc_start: 0.7637 (ttm110) cc_final: 0.7260 (ttm110) REVERT: B 412 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7788 (mp10) REVERT: B 418 GLU cc_start: 0.8762 (tp30) cc_final: 0.8223 (tp30) REVERT: B 422 GLN cc_start: 0.8262 (mt0) cc_final: 0.7875 (mt0) REVERT: C 172 LYS cc_start: 0.8438 (pttp) cc_final: 0.7506 (mtpt) REVERT: C 186 MET cc_start: 0.8256 (mmt) cc_final: 0.7546 (mtp) REVERT: C 344 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7852 (mt-10) REVERT: C 364 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 371 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8274 (ptmm) REVERT: C 418 GLU cc_start: 0.8782 (tp30) cc_final: 0.8347 (tp30) REVERT: C 422 GLN cc_start: 0.8174 (mt0) cc_final: 0.7810 (mt0) REVERT: C 459 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7469 (mt0) REVERT: C 513 MET cc_start: 0.7717 (tpp) cc_final: 0.7161 (tpp) REVERT: D 121 LEU cc_start: 0.7788 (mt) cc_final: 0.7569 (mt) REVERT: D 170 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5804 (mmt180) REVERT: D 344 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7984 (mt-10) REVERT: D 350 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7197 (ttm110) REVERT: D 364 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7791 (mt-10) REVERT: D 418 GLU cc_start: 0.8777 (tp30) cc_final: 0.8444 (tp30) REVERT: E 120 PHE cc_start: 0.7676 (t80) cc_final: 0.7106 (m-80) REVERT: E 148 LEU cc_start: 0.7982 (mt) cc_final: 0.7777 (mt) REVERT: E 170 ARG cc_start: 0.7973 (mtt180) cc_final: 0.6978 (mmp80) REVERT: E 186 MET cc_start: 0.8294 (mmt) cc_final: 0.7769 (mtp) REVERT: E 217 GLN cc_start: 0.7561 (mt0) cc_final: 0.7258 (mm-40) REVERT: E 344 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7950 (mt-10) REVERT: E 350 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7306 (ttm110) REVERT: E 364 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: E 418 GLU cc_start: 0.8653 (tp30) cc_final: 0.8209 (tp30) REVERT: F 120 PHE cc_start: 0.7558 (t80) cc_final: 0.7152 (m-80) REVERT: F 172 LYS cc_start: 0.8453 (pttp) cc_final: 0.7482 (mtpp) REVERT: F 186 MET cc_start: 0.8292 (mmt) cc_final: 0.7583 (mtp) REVERT: F 344 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7838 (mt-10) REVERT: F 364 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: F 371 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8292 (ptmm) REVERT: F 418 GLU cc_start: 0.8783 (tp30) cc_final: 0.8346 (tp30) REVERT: F 422 GLN cc_start: 0.8161 (mt0) cc_final: 0.7794 (mt0) REVERT: F 459 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: F 513 MET cc_start: 0.7457 (tpp) cc_final: 0.6853 (tpp) outliers start: 45 outliers final: 22 residues processed: 296 average time/residue: 1.5863 time to fit residues: 517.0486 Evaluate side-chains 300 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 282 ASP 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 435 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 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 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 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 111 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 65 optimal weight: 0.0570 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN C 451 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN F 451 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097958 restraints weight = 21239.239| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.05 r_work: 0.3059 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3416 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= 0.127 Angle : 0.512 6.571 24774 Z= 0.260 Chirality : 0.038 0.136 2808 Planarity : 0.004 0.038 3072 Dihedral : 3.970 14.316 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.06 % Allowed : 17.46 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.18), residues: 2136 helix: 2.43 (0.14), residues: 1248 sheet: 1.45 (0.40), residues: 180 loop : -0.32 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 274 HIS 0.003 0.001 HIS B 281 PHE 0.028 0.002 PHE B 149 TYR 0.012 0.001 TYR A 280 ARG 0.005 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 1086) hydrogen bonds : angle 4.04148 ( 3159) SS BOND : bond 0.00174 ( 6) SS BOND : angle 0.57340 ( 12) covalent geometry : bond 0.00294 (18270) covalent geometry : angle 0.51233 (24762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5894 (mmp-170) REVERT: A 210 ARG cc_start: 0.6920 (mpp80) cc_final: 0.6682 (mpt-90) REVERT: A 217 GLN cc_start: 0.7700 (mt0) cc_final: 0.7415 (mt0) REVERT: A 344 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 350 ARG cc_start: 0.7593 (ttm110) cc_final: 0.7197 (ttm110) REVERT: A 402 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8771 (tpp) REVERT: A 418 GLU cc_start: 0.8733 (tp30) cc_final: 0.8271 (tp30) REVERT: A 422 GLN cc_start: 0.8129 (mt0) cc_final: 0.7670 (mt0) REVERT: B 186 MET cc_start: 0.8314 (mmt) cc_final: 0.7785 (mtp) REVERT: B 350 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7285 (ttm110) REVERT: B 371 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8243 (ttpp) REVERT: B 412 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7775 (mp10) REVERT: B 418 GLU cc_start: 0.8736 (tp30) cc_final: 0.8184 (tp30) REVERT: B 422 GLN cc_start: 0.8262 (mt0) cc_final: 0.7961 (mt0) REVERT: C 118 LEU cc_start: 0.8219 (tp) cc_final: 0.7895 (tp) REVERT: C 172 LYS cc_start: 0.8446 (pttp) cc_final: 0.7528 (mtpt) REVERT: C 186 MET cc_start: 0.8220 (mmt) cc_final: 0.7549 (mtp) REVERT: C 243 GLN cc_start: 0.8971 (tt0) cc_final: 0.8626 (tt0) REVERT: C 344 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7874 (mt-10) REVERT: C 364 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: C 371 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8254 (ptmm) REVERT: C 418 GLU cc_start: 0.8815 (tp30) cc_final: 0.8303 (tp30) REVERT: C 422 GLN cc_start: 0.8129 (mt0) cc_final: 0.7700 (mt0) REVERT: C 513 MET cc_start: 0.7653 (tpp) cc_final: 0.7179 (tpp) REVERT: D 170 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.5984 (mmp-170) REVERT: D 344 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7962 (mt-10) REVERT: D 350 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7247 (ttm110) REVERT: D 364 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7747 (mt-10) REVERT: D 418 GLU cc_start: 0.8773 (tp30) cc_final: 0.8439 (tp30) REVERT: E 120 PHE cc_start: 0.7619 (t80) cc_final: 0.7002 (m-80) REVERT: E 170 ARG cc_start: 0.7951 (mtt180) cc_final: 0.6970 (mmp80) REVERT: E 186 MET cc_start: 0.8335 (mmt) cc_final: 0.7749 (mtp) REVERT: E 195 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.8062 (p) REVERT: E 217 GLN cc_start: 0.7548 (mt0) cc_final: 0.7305 (mt0) REVERT: E 344 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7915 (mt-10) REVERT: E 350 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7370 (ttm110) REVERT: E 418 GLU cc_start: 0.8638 (tp30) cc_final: 0.8169 (tp30) REVERT: F 120 PHE cc_start: 0.7500 (t80) cc_final: 0.7059 (m-80) REVERT: F 172 LYS cc_start: 0.8440 (pttp) cc_final: 0.7501 (mtpp) REVERT: F 186 MET cc_start: 0.8247 (mmt) cc_final: 0.7587 (mtp) REVERT: F 243 GLN cc_start: 0.8993 (tt0) cc_final: 0.8644 (tt0) REVERT: F 344 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7873 (mt-10) REVERT: F 364 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: F 371 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8301 (ptmm) REVERT: F 418 GLU cc_start: 0.8802 (tp30) cc_final: 0.8291 (tp30) REVERT: F 422 GLN cc_start: 0.8123 (mt0) cc_final: 0.7693 (mt0) REVERT: F 513 MET cc_start: 0.7440 (tpp) cc_final: 0.6856 (tpp) outliers start: 39 outliers final: 16 residues processed: 301 average time/residue: 1.6359 time to fit residues: 543.8816 Evaluate side-chains 292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain 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 435 LYS Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 195 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN F 459 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096887 restraints weight = 21193.485| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.05 r_work: 0.3041 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 18276 Z= 0.153 Angle : 0.534 9.504 24774 Z= 0.269 Chirality : 0.039 0.133 2808 Planarity : 0.004 0.038 3072 Dihedral : 4.016 15.098 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.06 % Allowed : 17.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.18), residues: 2136 helix: 2.42 (0.14), residues: 1248 sheet: 1.46 (0.40), residues: 180 loop : -0.24 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 134 HIS 0.003 0.001 HIS F 423 PHE 0.029 0.002 PHE B 149 TYR 0.016 0.002 TYR D 280 ARG 0.005 0.000 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 1086) hydrogen bonds : angle 4.05661 ( 3159) SS BOND : bond 0.00134 ( 6) SS BOND : angle 0.57453 ( 12) covalent geometry : bond 0.00358 (18270) covalent geometry : angle 0.53413 (24762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 270 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.5972 (mmp-170) REVERT: A 217 GLN cc_start: 0.7666 (mt0) cc_final: 0.7407 (mt0) REVERT: A 344 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 350 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7236 (ttm110) REVERT: A 364 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: A 402 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8770 (tpp) REVERT: A 418 GLU cc_start: 0.8723 (tp30) cc_final: 0.8369 (tp30) REVERT: B 170 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.5918 (mmt-90) REVERT: B 186 MET cc_start: 0.8415 (mmt) cc_final: 0.7772 (mtp) REVERT: B 350 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7326 (ttm110) REVERT: B 371 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8163 (ttpp) REVERT: B 412 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7777 (mp10) REVERT: B 418 GLU cc_start: 0.8761 (tp30) cc_final: 0.8215 (tp30) REVERT: B 422 GLN cc_start: 0.8261 (mt0) cc_final: 0.7890 (mt0) REVERT: C 118 LEU cc_start: 0.8205 (tp) cc_final: 0.7865 (tp) REVERT: C 172 LYS cc_start: 0.8435 (pttp) cc_final: 0.7484 (mtmt) REVERT: C 186 MET cc_start: 0.8224 (mmt) cc_final: 0.7554 (mtp) REVERT: C 243 GLN cc_start: 0.8987 (tt0) cc_final: 0.8634 (tt0) REVERT: C 344 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7875 (mt-10) REVERT: C 364 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: C 371 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8320 (ptmm) REVERT: C 418 GLU cc_start: 0.8777 (tp30) cc_final: 0.8191 (tp30) REVERT: C 422 GLN cc_start: 0.8147 (mt0) cc_final: 0.7732 (mt0) REVERT: C 513 MET cc_start: 0.7662 (tpp) cc_final: 0.7115 (tpp) REVERT: D 149 PHE cc_start: 0.8252 (m-80) cc_final: 0.7670 (m-80) REVERT: D 170 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6019 (mmp-170) REVERT: D 344 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7974 (mt-10) REVERT: D 350 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7247 (ttm110) REVERT: D 364 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7727 (mt-10) REVERT: D 371 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8303 (mtmm) REVERT: D 402 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8745 (tpp) REVERT: D 418 GLU cc_start: 0.8782 (tp30) cc_final: 0.8432 (tp30) REVERT: E 120 PHE cc_start: 0.7554 (t80) cc_final: 0.6968 (m-80) REVERT: E 170 ARG cc_start: 0.7964 (mtt180) cc_final: 0.6961 (mmp80) REVERT: E 186 MET cc_start: 0.8314 (mmt) cc_final: 0.7788 (mtp) REVERT: E 195 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.8090 (p) REVERT: E 217 GLN cc_start: 0.7541 (mt0) cc_final: 0.7252 (mt0) REVERT: E 344 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7951 (mt-10) REVERT: E 350 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7368 (ttm110) REVERT: E 418 GLU cc_start: 0.8639 (tp30) cc_final: 0.8175 (tp30) REVERT: F 120 PHE cc_start: 0.7593 (t80) cc_final: 0.7090 (m-80) REVERT: F 172 LYS cc_start: 0.8457 (pttp) cc_final: 0.7488 (mtpp) REVERT: F 186 MET cc_start: 0.8256 (mmt) cc_final: 0.7591 (mtp) REVERT: F 344 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7890 (mt-10) REVERT: F 364 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: F 392 GLN cc_start: 0.8347 (mt0) cc_final: 0.8072 (mt0) REVERT: F 418 GLU cc_start: 0.8766 (tp30) cc_final: 0.8176 (tp30) REVERT: F 422 GLN cc_start: 0.8134 (mt0) cc_final: 0.7715 (mt0) REVERT: F 513 MET cc_start: 0.7373 (tpp) cc_final: 0.6741 (tpp) outliers start: 39 outliers final: 17 residues processed: 282 average time/residue: 1.5665 time to fit residues: 486.4949 Evaluate side-chains 291 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 265 time to evaluate : 2.230 ------------------------------------------------------------------------------- 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 402 MET 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 435 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 402 MET 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 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 164 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 0.0060 chunk 89 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN D 243 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN E 451 HIS ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.097773 restraints weight = 21188.541| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.05 r_work: 0.3056 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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= 0.134 Angle : 0.520 8.038 24774 Z= 0.263 Chirality : 0.039 0.133 2808 Planarity : 0.004 0.038 3072 Dihedral : 3.935 14.910 2418 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.16 % Allowed : 18.14 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.18), residues: 2136 helix: 2.48 (0.14), residues: 1248 sheet: 1.38 (0.39), residues: 180 loop : -0.15 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 274 HIS 0.003 0.001 HIS E 230 PHE 0.031 0.002 PHE B 149 TYR 0.014 0.001 TYR A 280 ARG 0.005 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 1086) hydrogen bonds : angle 4.02891 ( 3159) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.53794 ( 12) covalent geometry : bond 0.00310 (18270) covalent geometry : angle 0.51967 (24762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8276 (m-80) cc_final: 0.7717 (m-80) REVERT: A 170 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.5964 (mmp-170) REVERT: A 217 GLN cc_start: 0.7692 (mt0) cc_final: 0.7402 (mt0) REVERT: A 344 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 350 ARG cc_start: 0.7651 (ttm110) cc_final: 0.7234 (ttm110) REVERT: A 364 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 402 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8776 (tpp) REVERT: A 418 GLU cc_start: 0.8777 (tp30) cc_final: 0.8437 (tp30) REVERT: B 170 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5891 (mmt-90) REVERT: B 186 MET cc_start: 0.8403 (mmt) cc_final: 0.7776 (mtp) REVERT: B 341 TYR cc_start: 0.8649 (t80) cc_final: 0.8327 (t80) REVERT: B 350 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7361 (ttm110) REVERT: B 371 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8188 (ttpp) REVERT: B 412 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7738 (mp10) REVERT: B 418 GLU cc_start: 0.8752 (tp30) cc_final: 0.8210 (tp30) REVERT: B 422 GLN cc_start: 0.8261 (mt0) cc_final: 0.7895 (mt0) REVERT: C 118 LEU cc_start: 0.8176 (tp) cc_final: 0.7860 (tp) REVERT: C 172 LYS cc_start: 0.8432 (pttp) cc_final: 0.7486 (mtmt) REVERT: C 186 MET cc_start: 0.8220 (mmt) cc_final: 0.7560 (mtp) REVERT: C 243 GLN cc_start: 0.8980 (tt0) cc_final: 0.8617 (tt0) REVERT: C 344 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7868 (mt-10) REVERT: C 364 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: C 371 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8254 (ptmm) REVERT: C 418 GLU cc_start: 0.8743 (tp30) cc_final: 0.8116 (tp30) REVERT: C 422 GLN cc_start: 0.8131 (mt0) cc_final: 0.7696 (mt0) REVERT: C 513 MET cc_start: 0.7675 (tpp) cc_final: 0.7131 (tpp) REVERT: D 149 PHE cc_start: 0.8187 (m-80) cc_final: 0.7599 (m-80) REVERT: D 170 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5899 (mmp-170) REVERT: D 344 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 350 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7257 (ttm110) REVERT: D 364 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7706 (mt-10) REVERT: D 371 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8339 (mtmm) REVERT: D 418 GLU cc_start: 0.8777 (tp30) cc_final: 0.8441 (tp30) REVERT: E 120 PHE cc_start: 0.7600 (t80) cc_final: 0.7005 (m-80) REVERT: E 170 ARG cc_start: 0.7955 (mtt180) cc_final: 0.6960 (mmp80) REVERT: E 186 MET cc_start: 0.8302 (mmt) cc_final: 0.7783 (mtp) REVERT: E 195 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8120 (p) REVERT: E 217 GLN cc_start: 0.7518 (mt0) cc_final: 0.7287 (mt0) REVERT: E 344 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7824 (mt-10) REVERT: E 350 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7364 (ttm110) REVERT: E 418 GLU cc_start: 0.8635 (tp30) cc_final: 0.8200 (tp30) REVERT: F 120 PHE cc_start: 0.7702 (t80) cc_final: 0.7120 (m-80) REVERT: F 172 LYS cc_start: 0.8447 (pttp) cc_final: 0.7482 (mtpp) REVERT: F 186 MET cc_start: 0.8256 (mmt) cc_final: 0.7582 (mtp) REVERT: F 243 GLN cc_start: 0.9009 (tt0) cc_final: 0.8693 (tt0) REVERT: F 344 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7867 (mt-10) REVERT: F 364 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: F 371 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8245 (ptmm) REVERT: F 418 GLU cc_start: 0.8742 (tp30) cc_final: 0.8112 (tp30) REVERT: F 422 GLN cc_start: 0.8125 (mt0) cc_final: 0.7687 (mt0) REVERT: F 513 MET cc_start: 0.7470 (tpp) cc_final: 0.6845 (tpp) outliers start: 41 outliers final: 16 residues processed: 291 average time/residue: 2.3192 time to fit residues: 753.9200 Evaluate side-chains 292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 2.976 ------------------------------------------------------------------------------- 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 402 MET 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 435 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 132 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 209 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 178 optimal weight: 0.0670 chunk 26 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099257 restraints weight = 21328.967| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.06 r_work: 0.3077 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.024 18276 Z= 0.115 Angle : 0.516 8.976 24774 Z= 0.258 Chirality : 0.038 0.161 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.830 14.121 2418 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.42 % Allowed : 18.88 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 2136 helix: 2.60 (0.14), residues: 1242 sheet: 1.33 (0.39), residues: 180 loop : -0.15 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 274 HIS 0.002 0.001 HIS E 230 PHE 0.034 0.002 PHE E 149 TYR 0.012 0.001 TYR A 280 ARG 0.005 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 1086) hydrogen bonds : angle 3.98355 ( 3159) SS BOND : bond 0.00118 ( 6) SS BOND : angle 0.52742 ( 12) covalent geometry : bond 0.00263 (18270) covalent geometry : angle 0.51584 (24762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8243 (m-80) cc_final: 0.7694 (m-80) REVERT: A 170 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6002 (mmp-170) REVERT: A 217 GLN cc_start: 0.7697 (mt0) cc_final: 0.7407 (mt0) REVERT: A 344 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 350 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7250 (ttm110) REVERT: A 364 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: A 402 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8815 (tpp) REVERT: A 418 GLU cc_start: 0.8778 (tp30) cc_final: 0.8281 (tp30) REVERT: A 422 GLN cc_start: 0.8128 (mt0) cc_final: 0.7639 (mt0) REVERT: B 186 MET cc_start: 0.8393 (mmt) cc_final: 0.7735 (mtp) REVERT: B 341 TYR cc_start: 0.8632 (t80) cc_final: 0.8276 (t80) REVERT: B 350 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7347 (ttm110) REVERT: B 371 LYS cc_start: 0.8772 (ttpp) cc_final: 0.8279 (ttpp) REVERT: B 412 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7757 (mp10) REVERT: B 418 GLU cc_start: 0.8760 (tp30) cc_final: 0.8221 (tp30) REVERT: B 422 GLN cc_start: 0.8253 (mt0) cc_final: 0.7884 (mt0) REVERT: C 118 LEU cc_start: 0.8156 (tp) cc_final: 0.7851 (tp) REVERT: C 172 LYS cc_start: 0.8427 (pttp) cc_final: 0.7462 (mtpp) REVERT: C 186 MET cc_start: 0.8254 (mmt) cc_final: 0.7561 (mtp) REVERT: C 344 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7862 (mt-10) REVERT: C 364 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: C 407 ARG cc_start: 0.8352 (mtm110) cc_final: 0.8081 (ttp80) REVERT: C 412 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7915 (tp40) REVERT: C 418 GLU cc_start: 0.8759 (tp30) cc_final: 0.8159 (tp30) REVERT: C 422 GLN cc_start: 0.8124 (mt0) cc_final: 0.7698 (mt0) REVERT: C 513 MET cc_start: 0.7609 (tpp) cc_final: 0.7092 (tpp) REVERT: D 149 PHE cc_start: 0.8158 (m-80) cc_final: 0.7532 (m-80) REVERT: D 170 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5889 (mmp-170) REVERT: D 344 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7980 (mt-10) REVERT: D 350 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7195 (ttm110) REVERT: D 364 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7687 (mt-10) REVERT: D 371 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8359 (mtmm) REVERT: D 402 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8757 (tpp) REVERT: D 418 GLU cc_start: 0.8780 (tp30) cc_final: 0.8330 (tp30) REVERT: D 422 GLN cc_start: 0.8119 (mt0) cc_final: 0.7671 (mt0) REVERT: E 120 PHE cc_start: 0.7580 (t80) cc_final: 0.6913 (m-80) REVERT: E 170 ARG cc_start: 0.7984 (mtt180) cc_final: 0.6949 (mmp80) REVERT: E 186 MET cc_start: 0.8313 (mmt) cc_final: 0.7810 (mtp) REVERT: E 195 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.8104 (p) REVERT: E 217 GLN cc_start: 0.7552 (mt0) cc_final: 0.7314 (mt0) REVERT: E 341 TYR cc_start: 0.8601 (t80) cc_final: 0.8257 (t80) REVERT: E 344 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7874 (mt-10) REVERT: E 350 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7360 (ttm110) REVERT: F 120 PHE cc_start: 0.7449 (t80) cc_final: 0.7018 (m-80) REVERT: F 172 LYS cc_start: 0.8459 (pttp) cc_final: 0.7502 (mtpp) REVERT: F 186 MET cc_start: 0.8246 (mmt) cc_final: 0.7576 (mtp) REVERT: F 243 GLN cc_start: 0.8969 (tt0) cc_final: 0.8630 (tt0) REVERT: F 344 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F 364 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: F 371 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8157 (ptmm) REVERT: F 407 ARG cc_start: 0.8344 (mtm110) cc_final: 0.8086 (ttp80) REVERT: F 412 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7858 (tp40) REVERT: F 418 GLU cc_start: 0.8744 (tp30) cc_final: 0.8114 (tp30) REVERT: F 422 GLN cc_start: 0.8112 (mt0) cc_final: 0.7672 (mt0) REVERT: F 513 MET cc_start: 0.7449 (tpp) cc_final: 0.6829 (tpp) outliers start: 27 outliers final: 14 residues processed: 286 average time/residue: 1.7905 time to fit residues: 568.2409 Evaluate side-chains 292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 3.626 ------------------------------------------------------------------------------- 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 402 MET 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 435 LYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 402 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096995 restraints weight = 21270.757| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.06 r_work: 0.3044 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 18276 Z= 0.154 Angle : 0.541 9.454 24774 Z= 0.271 Chirality : 0.040 0.132 2808 Planarity : 0.004 0.038 3072 Dihedral : 3.976 15.404 2418 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.53 % Allowed : 19.15 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.18), residues: 2136 helix: 2.44 (0.14), residues: 1248 sheet: 1.36 (0.39), residues: 180 loop : -0.07 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 134 HIS 0.003 0.001 HIS A 281 PHE 0.039 0.002 PHE E 149 TYR 0.015 0.002 TYR D 280 ARG 0.008 0.000 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 1086) hydrogen bonds : angle 4.04767 ( 3159) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.56080 ( 12) covalent geometry : bond 0.00361 (18270) covalent geometry : angle 0.54092 (24762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8296 (m-80) cc_final: 0.7729 (m-80) REVERT: A 170 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5957 (mmt180) REVERT: A 217 GLN cc_start: 0.7681 (mt0) cc_final: 0.7430 (mt0) REVERT: A 344 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7963 (mt-10) REVERT: A 350 ARG cc_start: 0.7620 (ttm110) cc_final: 0.7165 (ttm110) REVERT: A 364 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: A 402 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8776 (tpp) REVERT: A 418 GLU cc_start: 0.8784 (tp30) cc_final: 0.8425 (tp30) REVERT: B 170 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5873 (mmt-90) REVERT: B 186 MET cc_start: 0.8407 (mmt) cc_final: 0.7771 (mtp) REVERT: B 341 TYR cc_start: 0.8658 (t80) cc_final: 0.8354 (t80) REVERT: B 350 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7314 (ttm110) REVERT: B 371 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8259 (ttpp) REVERT: B 412 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7750 (mp10) REVERT: B 418 GLU cc_start: 0.8748 (tp30) cc_final: 0.8198 (tp30) REVERT: B 422 GLN cc_start: 0.8257 (mt0) cc_final: 0.7888 (mt0) REVERT: C 172 LYS cc_start: 0.8465 (pttp) cc_final: 0.7494 (mtmt) REVERT: C 186 MET cc_start: 0.8216 (mmt) cc_final: 0.7550 (mtp) REVERT: C 243 GLN cc_start: 0.8971 (tt0) cc_final: 0.8665 (tt0) REVERT: C 344 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7888 (mt-10) REVERT: C 364 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: C 371 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8249 (ptmm) REVERT: C 412 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7916 (tp40) REVERT: C 418 GLU cc_start: 0.8740 (tp30) cc_final: 0.8205 (tp30) REVERT: C 422 GLN cc_start: 0.8139 (mt0) cc_final: 0.7744 (mt0) REVERT: C 513 MET cc_start: 0.7641 (tpp) cc_final: 0.7104 (tpp) REVERT: D 149 PHE cc_start: 0.8175 (m-80) cc_final: 0.7529 (m-80) REVERT: D 170 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5871 (mmt180) REVERT: D 344 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7987 (mt-10) REVERT: D 350 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7148 (ttm110) REVERT: D 364 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7733 (mt-10) REVERT: D 402 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8745 (tpp) REVERT: D 418 GLU cc_start: 0.8785 (tp30) cc_final: 0.8442 (tp30) REVERT: E 120 PHE cc_start: 0.7621 (t80) cc_final: 0.6926 (m-80) REVERT: E 170 ARG cc_start: 0.8000 (mtt180) cc_final: 0.6972 (mmp80) REVERT: E 186 MET cc_start: 0.8319 (mmt) cc_final: 0.7765 (mtp) REVERT: E 195 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.8115 (p) REVERT: E 217 GLN cc_start: 0.7505 (mt0) cc_final: 0.7286 (mt0) REVERT: E 344 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7872 (mt-10) REVERT: E 350 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7379 (ttm110) REVERT: E 412 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7774 (mp10) REVERT: E 418 GLU cc_start: 0.8665 (tp30) cc_final: 0.8258 (tp30) REVERT: F 120 PHE cc_start: 0.7717 (t80) cc_final: 0.7118 (m-80) REVERT: F 172 LYS cc_start: 0.8447 (pttp) cc_final: 0.7472 (mtpp) REVERT: F 186 MET cc_start: 0.8260 (mmt) cc_final: 0.7586 (mtp) REVERT: F 243 GLN cc_start: 0.8985 (tt0) cc_final: 0.8631 (tt0) REVERT: F 344 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7887 (mt-10) REVERT: F 364 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: F 371 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8236 (ptmm) REVERT: F 412 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7960 (tp40) REVERT: F 418 GLU cc_start: 0.8729 (tp30) cc_final: 0.8197 (tp30) REVERT: F 422 GLN cc_start: 0.8139 (mt0) cc_final: 0.7749 (mt0) REVERT: F 513 MET cc_start: 0.7474 (tpp) cc_final: 0.6846 (tpp) outliers start: 29 outliers final: 13 residues processed: 278 average time/residue: 1.4905 time to fit residues: 457.1456 Evaluate side-chains 286 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 402 MET 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 435 LYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 402 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095385 restraints weight = 21250.519| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.04 r_work: 0.3022 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18276 Z= 0.190 Angle : 0.570 9.406 24774 Z= 0.286 Chirality : 0.041 0.134 2808 Planarity : 0.004 0.041 3072 Dihedral : 4.147 17.280 2418 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.48 % Allowed : 19.30 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.18), residues: 2136 helix: 2.32 (0.14), residues: 1248 sheet: 1.38 (0.40), residues: 180 loop : -0.09 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 134 HIS 0.004 0.001 HIS D 281 PHE 0.039 0.002 PHE E 149 TYR 0.018 0.002 TYR A 280 ARG 0.007 0.001 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1086) hydrogen bonds : angle 4.14561 ( 3159) SS BOND : bond 0.00134 ( 6) SS BOND : angle 0.57279 ( 12) covalent geometry : bond 0.00448 (18270) covalent geometry : angle 0.57022 (24762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17305.49 seconds wall clock time: 300 minutes 1.81 seconds (18001.81 seconds total)