Starting phenix.real_space_refine on Mon May 19 02:27:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jka_61549/05_2025/9jka_61549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jka_61549/05_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_61549/05_2025/9jka_61549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jka_61549/05_2025/9jka_61549.map" model { file = "/net/cci-nas-00/data/ceres_data/9jka_61549/05_2025/9jka_61549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jka_61549/05_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-5687/modules/chem_data/mon_lib" Total number of atoms: 17820 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2970 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.75, per 1000 atoms: 0.43 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: 4.23 Conformation dependent library (CDL) restraints added in 2.2 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: 1.79 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: 6.00 Time building geometry restraints manager: 5.02 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 37.320 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: 0.010 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.130 ------------------------------------------------------------------------------- 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 : 1.857 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: 1.7193 time to fit residues: 911.8367 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 : 1.914 ------------------------------------------------------------------------------- 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: 0.6980 chunk 102 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.138064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100487 restraints weight = 21289.590| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.04 r_work: 0.3092 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2415 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= 0.162 Angle : 0.560 7.284 24774 Z= 0.293 Chirality : 0.040 0.143 2808 Planarity : 0.005 0.044 3072 Dihedral : 4.488 49.282 2420 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.69 % Allowed : 11.71 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2136 helix: 1.05 (0.14), residues: 1212 sheet: 1.75 (0.39), residues: 168 loop : -1.29 (0.21), 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 0.024 0.003 PHE B 149 TYR 0.011 0.002 TYR F 450 ARG 0.006 0.001 ARG E 210 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 1086) hydrogen bonds : angle 4.28712 ( 3159) SS BOND : bond 0.00136 ( 6) SS BOND : angle 0.58666 ( 12) covalent geometry : bond 0.00378 (18270) covalent geometry : angle 0.55999 (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 376 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 325 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.5549 (mmp-170) REVERT: A 182 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7147 (ttp80) REVERT: A 217 GLN cc_start: 0.7502 (mt0) cc_final: 0.7226 (mt0) REVERT: A 344 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7971 (mt-10) REVERT: A 350 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7008 (ttm110) REVERT: A 364 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7979 (mt-10) REVERT: A 418 GLU cc_start: 0.8591 (tp30) cc_final: 0.8208 (tp30) REVERT: A 422 GLN cc_start: 0.8171 (mt0) cc_final: 0.7742 (mt0) REVERT: B 172 LYS cc_start: 0.8374 (pttt) cc_final: 0.8165 (pttm) REVERT: B 182 ARG cc_start: 0.7700 (ttm170) cc_final: 0.6965 (ttm170) REVERT: B 213 GLN cc_start: 0.7816 (tt0) cc_final: 0.7473 (tm-30) REVERT: B 341 TYR cc_start: 0.8598 (t80) cc_final: 0.8186 (t80) REVERT: B 350 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7297 (ttm110) REVERT: B 418 GLU cc_start: 0.8778 (tp30) cc_final: 0.8240 (tp30) REVERT: B 422 GLN cc_start: 0.8317 (mt0) cc_final: 0.8007 (mt0) REVERT: B 435 LYS cc_start: 0.8278 (ttmp) cc_final: 0.7567 (tptt) REVERT: C 172 LYS cc_start: 0.8441 (pttp) cc_final: 0.7486 (mmmt) REVERT: C 190 PHE cc_start: 0.8150 (t80) cc_final: 0.7871 (t80) REVERT: C 344 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 364 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: C 418 GLU cc_start: 0.8785 (tp30) cc_final: 0.8161 (tp30) REVERT: C 422 GLN cc_start: 0.8156 (mt0) cc_final: 0.7803 (mt0) REVERT: C 513 MET cc_start: 0.7588 (tpp) cc_final: 0.7123 (tpp) REVERT: D 344 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7898 (mt-10) REVERT: D 347 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7767 (mt-10) REVERT: D 350 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7200 (ttm110) REVERT: D 364 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7789 (mt-10) REVERT: D 418 GLU cc_start: 0.8648 (tp30) cc_final: 0.8301 (tp30) REVERT: E 120 PHE cc_start: 0.7471 (t80) cc_final: 0.7017 (m-80) REVERT: E 170 ARG cc_start: 0.7885 (mtt180) cc_final: 0.6936 (mmp80) REVERT: E 195 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8094 (p) REVERT: E 217 GLN cc_start: 0.7870 (mt0) cc_final: 0.7537 (mm-40) REVERT: E 341 TYR cc_start: 0.8660 (t80) cc_final: 0.8241 (t80) REVERT: E 344 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7900 (mt-10) REVERT: E 350 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7268 (ttm110) REVERT: E 412 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7605 (mp10) REVERT: E 418 GLU cc_start: 0.8664 (tp30) cc_final: 0.8184 (tp30) REVERT: F 120 PHE cc_start: 0.7373 (t80) cc_final: 0.7075 (m-80) REVERT: F 172 LYS cc_start: 0.8450 (pttp) cc_final: 0.7466 (mtpp) REVERT: F 190 PHE cc_start: 0.8147 (t80) cc_final: 0.7843 (t80) REVERT: F 344 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7804 (mt-10) REVERT: F 364 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: F 418 GLU cc_start: 0.8788 (tp30) cc_final: 0.8170 (tp30) REVERT: F 422 GLN cc_start: 0.8153 (mt0) cc_final: 0.7803 (mt0) REVERT: F 513 MET cc_start: 0.7274 (tpp) cc_final: 0.6878 (tpp) outliers start: 51 outliers final: 8 residues processed: 347 average time/residue: 1.5402 time to fit residues: 585.1232 Evaluate side-chains 294 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 282 time to evaluate : 1.881 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS E 449 GLN F 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097056 restraints weight = 21192.500| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.04 r_work: 0.3042 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18276 Z= 0.183 Angle : 0.571 9.110 24774 Z= 0.289 Chirality : 0.040 0.138 2808 Planarity : 0.004 0.038 3072 Dihedral : 4.265 14.909 2418 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.95 % Allowed : 13.34 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.18), residues: 2136 helix: 1.92 (0.14), residues: 1212 sheet: 1.94 (0.40), residues: 168 loop : -0.92 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 134 HIS 0.005 0.001 HIS B 423 PHE 0.024 0.003 PHE B 149 TYR 0.016 0.002 TYR A 280 ARG 0.007 0.001 ARG B 482 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1086) hydrogen bonds : angle 4.17128 ( 3159) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.54537 ( 12) covalent geometry : bond 0.00430 (18270) covalent geometry : angle 0.57112 (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 344 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5886 (mmp-170) REVERT: A 182 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7153 (ttp80) REVERT: A 217 GLN cc_start: 0.7629 (mt0) cc_final: 0.7317 (mt0) REVERT: A 344 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 350 ARG cc_start: 0.7523 (ttm110) cc_final: 0.7088 (ttm110) REVERT: A 364 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7808 (mt-10) REVERT: A 402 MET cc_start: 0.9098 (tpt) cc_final: 0.8869 (tpp) REVERT: A 418 GLU cc_start: 0.8692 (tp30) cc_final: 0.8344 (tp30) REVERT: A 459 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: B 182 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7029 (ttm170) REVERT: B 186 MET cc_start: 0.8329 (mmt) cc_final: 0.7684 (mtp) REVERT: B 350 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7351 (ttm110) REVERT: B 418 GLU cc_start: 0.8775 (tp30) cc_final: 0.8227 (tp30) REVERT: B 422 GLN cc_start: 0.8281 (mt0) cc_final: 0.7961 (mt0) REVERT: C 172 LYS cc_start: 0.8492 (pttp) cc_final: 0.7518 (mtpt) REVERT: C 186 MET cc_start: 0.8324 (mmt) cc_final: 0.7571 (mtp) REVERT: C 190 PHE cc_start: 0.8214 (t80) cc_final: 0.7995 (t80) REVERT: C 344 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7755 (mt-10) REVERT: C 364 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 418 GLU cc_start: 0.8785 (tp30) cc_final: 0.8179 (tp30) REVERT: C 422 GLN cc_start: 0.8162 (mt0) cc_final: 0.7722 (mt0) REVERT: C 513 MET cc_start: 0.7594 (tpp) cc_final: 0.7116 (tpp) REVERT: D 170 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6009 (mmp-170) REVERT: D 344 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7949 (mt-10) REVERT: D 347 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7780 (mt-10) REVERT: D 350 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7226 (ttm110) REVERT: D 364 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7810 (mt-10) REVERT: D 418 GLU cc_start: 0.8754 (tp30) cc_final: 0.8402 (tp30) REVERT: E 120 PHE cc_start: 0.7663 (t80) cc_final: 0.7103 (m-80) REVERT: E 170 ARG cc_start: 0.7944 (mtt180) cc_final: 0.6990 (mmp80) REVERT: E 186 MET cc_start: 0.8320 (mmt) cc_final: 0.7727 (mtp) REVERT: E 195 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.8074 (p) REVERT: E 217 GLN cc_start: 0.7585 (mt0) cc_final: 0.7332 (mm-40) REVERT: E 344 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7918 (mt-10) REVERT: E 350 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7349 (ttm110) REVERT: E 418 GLU cc_start: 0.8643 (tp30) cc_final: 0.8191 (tp30) REVERT: F 120 PHE cc_start: 0.7376 (t80) cc_final: 0.7045 (m-80) REVERT: F 172 LYS cc_start: 0.8445 (pttp) cc_final: 0.7550 (mtpt) REVERT: F 186 MET cc_start: 0.8337 (mmt) cc_final: 0.7589 (mtp) REVERT: F 190 PHE cc_start: 0.8204 (t80) cc_final: 0.7982 (t80) REVERT: F 344 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7764 (mt-10) REVERT: F 364 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: F 418 GLU cc_start: 0.8781 (tp30) cc_final: 0.8173 (tp30) REVERT: F 422 GLN cc_start: 0.8160 (mt0) cc_final: 0.7723 (mt0) REVERT: F 513 MET cc_start: 0.7271 (tpp) cc_final: 0.6755 (tpp) outliers start: 56 outliers final: 12 residues processed: 315 average time/residue: 1.5547 time to fit residues: 537.0263 Evaluate side-chains 293 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 2.197 ------------------------------------------------------------------------------- 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 459 GLN 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 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 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 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: 0.6980 chunk 185 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3711 r_free = 0.3711 target = 0.136201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098271 restraints weight = 21254.780| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.05 r_work: 0.3061 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18276 Z= 0.140 Angle : 0.527 8.244 24774 Z= 0.266 Chirality : 0.039 0.137 2808 Planarity : 0.004 0.038 3072 Dihedral : 4.030 13.789 2418 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.48 % Allowed : 15.03 % Favored : 82.49 % 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: 1.87 (0.18), residues: 2136 helix: 2.23 (0.14), residues: 1248 sheet: 1.47 (0.40), residues: 180 loop : -0.65 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 134 HIS 0.003 0.001 HIS E 423 PHE 0.024 0.002 PHE B 149 TYR 0.011 0.001 TYR C 280 ARG 0.004 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 1086) hydrogen bonds : angle 4.04146 ( 3159) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.65743 ( 12) covalent geometry : bond 0.00326 (18270) covalent geometry : angle 0.52716 (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 334 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 287 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5855 (mmp-170) REVERT: A 217 GLN cc_start: 0.7636 (mt0) cc_final: 0.7370 (mt0) REVERT: A 344 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7960 (mt-10) REVERT: A 347 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 350 ARG cc_start: 0.7489 (ttm110) cc_final: 0.7111 (ttm110) REVERT: A 364 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7757 (mt-10) REVERT: A 402 MET cc_start: 0.9072 (tpt) cc_final: 0.8868 (tpp) REVERT: A 418 GLU cc_start: 0.8763 (tp30) cc_final: 0.8403 (tp30) REVERT: B 172 LYS cc_start: 0.8205 (pttt) cc_final: 0.7947 (pttt) REVERT: B 186 MET cc_start: 0.8305 (mmt) cc_final: 0.7745 (mtp) REVERT: B 213 GLN cc_start: 0.7774 (tt0) cc_final: 0.7476 (tm-30) REVERT: B 350 ARG cc_start: 0.7651 (ttm110) cc_final: 0.7297 (ttm110) REVERT: B 371 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8194 (ttpp) REVERT: B 417 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7940 (ttm) REVERT: B 418 GLU cc_start: 0.8773 (tp30) cc_final: 0.8216 (tp30) REVERT: B 422 GLN cc_start: 0.8274 (mt0) cc_final: 0.7944 (mt0) REVERT: C 172 LYS cc_start: 0.8487 (pttp) cc_final: 0.7522 (mtpt) REVERT: C 186 MET cc_start: 0.8279 (mmt) cc_final: 0.7541 (mtp) REVERT: C 344 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7846 (mt-10) REVERT: C 364 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: C 371 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8195 (ptmm) REVERT: C 418 GLU cc_start: 0.8797 (tp30) cc_final: 0.8222 (tp30) REVERT: C 422 GLN cc_start: 0.8151 (mt0) cc_final: 0.7723 (mt0) REVERT: C 513 MET cc_start: 0.7665 (tpp) cc_final: 0.7189 (tpp) REVERT: D 149 PHE cc_start: 0.8289 (m-80) cc_final: 0.7628 (m-80) REVERT: D 344 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7947 (mt-10) REVERT: D 347 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7686 (mt-10) REVERT: D 350 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7212 (ttm110) REVERT: D 364 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7769 (mt-10) REVERT: D 418 GLU cc_start: 0.8763 (tp30) cc_final: 0.8303 (tp30) REVERT: D 422 GLN cc_start: 0.8166 (mt0) cc_final: 0.7691 (mt0) REVERT: E 120 PHE cc_start: 0.7656 (t80) cc_final: 0.7077 (m-80) REVERT: E 170 ARG cc_start: 0.7960 (mtt180) cc_final: 0.6983 (mmp80) REVERT: E 172 LYS cc_start: 0.8355 (pttt) cc_final: 0.8139 (pttt) REVERT: E 186 MET cc_start: 0.8299 (mmt) cc_final: 0.7746 (mtp) REVERT: E 195 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.8093 (p) REVERT: E 217 GLN cc_start: 0.7557 (mt0) cc_final: 0.7252 (mm-40) REVERT: E 344 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7897 (mt-10) REVERT: E 350 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7312 (ttm110) REVERT: E 364 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: E 418 GLU cc_start: 0.8628 (tp30) cc_final: 0.8148 (tp30) REVERT: F 120 PHE cc_start: 0.7412 (t80) cc_final: 0.7065 (m-80) REVERT: F 172 LYS cc_start: 0.8439 (pttp) cc_final: 0.7545 (mtpt) REVERT: F 186 MET cc_start: 0.8300 (mmt) cc_final: 0.7558 (mtp) REVERT: F 344 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7868 (mt-10) REVERT: F 364 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: F 371 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8199 (ptmm) REVERT: F 418 GLU cc_start: 0.8793 (tp30) cc_final: 0.8219 (tp30) REVERT: F 422 GLN cc_start: 0.8147 (mt0) cc_final: 0.7718 (mt0) REVERT: F 513 MET cc_start: 0.7281 (tpp) cc_final: 0.6750 (tpp) outliers start: 47 outliers final: 13 residues processed: 305 average time/residue: 1.5230 time to fit residues: 510.7839 Evaluate side-chains 292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 273 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 417 MET 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 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 484 ASP Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 23 optimal weight: 0.0060 chunk 61 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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** D 459 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.136202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098191 restraints weight = 21335.393| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.06 r_work: 0.3062 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3300 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= 0.135 Angle : 0.521 8.514 24774 Z= 0.263 Chirality : 0.039 0.134 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.953 13.459 2418 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.11 % Allowed : 16.61 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.18), residues: 2136 helix: 2.40 (0.14), residues: 1248 sheet: 1.45 (0.40), residues: 180 loop : -0.46 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 134 HIS 0.003 0.001 HIS E 423 PHE 0.028 0.002 PHE B 149 TYR 0.013 0.001 TYR F 280 ARG 0.007 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 1086) hydrogen bonds : angle 4.01183 ( 3159) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.57623 ( 12) covalent geometry : bond 0.00314 (18270) covalent geometry : angle 0.52101 (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 320 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5903 (mmp-170) REVERT: A 217 GLN cc_start: 0.7543 (mt0) cc_final: 0.7266 (mt0) REVERT: A 344 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7975 (mt-10) REVERT: A 350 ARG cc_start: 0.7511 (ttm110) cc_final: 0.7115 (ttm110) REVERT: A 364 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7773 (mt-10) REVERT: A 402 MET cc_start: 0.9073 (tpt) cc_final: 0.8869 (tpp) REVERT: A 418 GLU cc_start: 0.8761 (tp30) cc_final: 0.8416 (tp30) REVERT: B 172 LYS cc_start: 0.8302 (pttt) cc_final: 0.8072 (pttt) REVERT: B 186 MET cc_start: 0.8275 (mmt) cc_final: 0.7735 (mtp) REVERT: B 350 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7260 (ttm110) REVERT: B 371 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8203 (ttpp) REVERT: B 418 GLU cc_start: 0.8771 (tp30) cc_final: 0.8209 (tp30) REVERT: B 422 GLN cc_start: 0.8263 (mt0) cc_final: 0.7935 (mt0) REVERT: C 172 LYS cc_start: 0.8418 (pttp) cc_final: 0.7482 (mtpt) REVERT: C 186 MET cc_start: 0.8268 (mmt) cc_final: 0.7561 (mtp) REVERT: C 243 GLN cc_start: 0.8976 (tt0) cc_final: 0.8602 (tt0) REVERT: C 344 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7866 (mt-10) REVERT: C 364 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: C 371 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8277 (ptmm) REVERT: C 400 ARG cc_start: 0.8087 (tpm-80) cc_final: 0.7682 (tpm-80) REVERT: C 418 GLU cc_start: 0.8778 (tp30) cc_final: 0.8186 (tp30) REVERT: C 422 GLN cc_start: 0.8150 (mt0) cc_final: 0.7702 (mt0) REVERT: C 513 MET cc_start: 0.7597 (tpp) cc_final: 0.7116 (tpp) REVERT: D 170 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.5935 (mmp-170) REVERT: D 344 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7956 (mt-10) REVERT: D 347 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7779 (mt-10) REVERT: D 350 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7208 (ttm110) REVERT: D 364 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7771 (mt-10) REVERT: D 417 MET cc_start: 0.7964 (ttp) cc_final: 0.7758 (ttm) REVERT: D 418 GLU cc_start: 0.8758 (tp30) cc_final: 0.8409 (tp30) REVERT: E 120 PHE cc_start: 0.7657 (t80) cc_final: 0.7067 (m-80) REVERT: E 170 ARG cc_start: 0.7959 (mtt180) cc_final: 0.6971 (mmp80) REVERT: E 172 LYS cc_start: 0.8357 (pttt) cc_final: 0.8132 (pttt) REVERT: E 186 MET cc_start: 0.8320 (mmt) cc_final: 0.7754 (mtp) REVERT: E 195 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8074 (p) REVERT: E 217 GLN cc_start: 0.7541 (mt0) cc_final: 0.7258 (mm-40) REVERT: E 344 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7955 (mt-10) REVERT: E 350 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7393 (ttm110) REVERT: E 364 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: E 418 GLU cc_start: 0.8645 (tp30) cc_final: 0.8184 (tp30) REVERT: E 466 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: F 120 PHE cc_start: 0.7436 (t80) cc_final: 0.7080 (m-80) REVERT: F 172 LYS cc_start: 0.8438 (pttp) cc_final: 0.7545 (mtpt) REVERT: F 186 MET cc_start: 0.8252 (mmt) cc_final: 0.7577 (mtp) REVERT: F 344 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7859 (mt-10) REVERT: F 364 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: F 371 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8271 (ptmm) REVERT: F 400 ARG cc_start: 0.8069 (tpm-80) cc_final: 0.7664 (tpm-80) REVERT: F 418 GLU cc_start: 0.8782 (tp30) cc_final: 0.8191 (tp30) REVERT: F 422 GLN cc_start: 0.8142 (mt0) cc_final: 0.7695 (mt0) REVERT: F 459 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: F 513 MET cc_start: 0.7427 (tpp) cc_final: 0.6812 (tpp) outliers start: 40 outliers final: 16 residues processed: 298 average time/residue: 1.4929 time to fit residues: 489.1129 Evaluate side-chains 291 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 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 435 LYS Chi-restraints excluded: chain E residue 118 LEU 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 466 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 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: 0.9980 chunk 212 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097528 restraints weight = 21253.814| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.06 r_work: 0.3051 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3392 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= 0.145 Angle : 0.527 7.404 24774 Z= 0.266 Chirality : 0.039 0.133 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.966 14.094 2418 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.27 % Allowed : 17.51 % Favored : 80.22 % 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: 2.20 (0.18), residues: 2136 helix: 2.43 (0.14), residues: 1248 sheet: 1.46 (0.39), residues: 180 loop : -0.34 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 134 HIS 0.003 0.001 HIS E 423 PHE 0.029 0.002 PHE B 149 TYR 0.014 0.002 TYR A 280 ARG 0.006 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 1086) hydrogen bonds : angle 4.02392 ( 3159) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.55190 ( 12) covalent geometry : bond 0.00339 (18270) covalent geometry : angle 0.52736 (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 319 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.5918 (mmp-170) REVERT: A 210 ARG cc_start: 0.6966 (mpp80) cc_final: 0.6685 (mpt-90) REVERT: A 217 GLN cc_start: 0.7528 (mt0) cc_final: 0.7288 (mt0) REVERT: A 344 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7971 (mt-10) REVERT: A 350 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7154 (ttm110) REVERT: A 364 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7779 (mt-10) REVERT: A 402 MET cc_start: 0.9090 (tpt) cc_final: 0.8871 (tpp) REVERT: A 418 GLU cc_start: 0.8774 (tp30) cc_final: 0.8425 (tp30) REVERT: B 172 LYS cc_start: 0.8325 (pttt) cc_final: 0.8107 (pttt) REVERT: B 186 MET cc_start: 0.8396 (mmt) cc_final: 0.7767 (mtp) REVERT: B 350 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7279 (ttm110) REVERT: B 418 GLU cc_start: 0.8773 (tp30) cc_final: 0.8214 (tp30) REVERT: B 422 GLN cc_start: 0.8259 (mt0) cc_final: 0.7858 (mt0) REVERT: C 172 LYS cc_start: 0.8427 (pttp) cc_final: 0.7503 (mtpt) REVERT: C 186 MET cc_start: 0.8238 (mmt) cc_final: 0.7568 (mtp) REVERT: C 344 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7851 (mt-10) REVERT: C 364 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 371 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8269 (ptmm) REVERT: C 392 GLN cc_start: 0.8317 (mt0) cc_final: 0.8038 (mt0) REVERT: C 400 ARG cc_start: 0.8091 (tpm-80) cc_final: 0.7849 (tpm-80) REVERT: C 418 GLU cc_start: 0.8729 (tp30) cc_final: 0.8178 (tp30) REVERT: C 422 GLN cc_start: 0.8148 (mt0) cc_final: 0.7731 (mt0) REVERT: C 513 MET cc_start: 0.7645 (tpp) cc_final: 0.7169 (tpp) REVERT: D 149 PHE cc_start: 0.8246 (m-80) cc_final: 0.7600 (m-80) REVERT: D 170 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.5979 (mmp-170) REVERT: D 344 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7953 (mt-10) REVERT: D 350 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7206 (ttm110) REVERT: D 364 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7747 (mt-10) REVERT: D 371 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8358 (mtmm) REVERT: D 418 GLU cc_start: 0.8788 (tp30) cc_final: 0.8433 (tp30) REVERT: E 120 PHE cc_start: 0.7642 (t80) cc_final: 0.7054 (m-80) REVERT: E 170 ARG cc_start: 0.7964 (mtt180) cc_final: 0.6966 (mmp80) REVERT: E 172 LYS cc_start: 0.8353 (pttt) cc_final: 0.8116 (pttt) REVERT: E 186 MET cc_start: 0.8316 (mmt) cc_final: 0.7750 (mtp) REVERT: E 195 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.8072 (p) REVERT: E 217 GLN cc_start: 0.7572 (mt0) cc_final: 0.7358 (mt0) REVERT: E 344 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7925 (mt-10) REVERT: E 350 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7371 (ttm110) REVERT: E 418 GLU cc_start: 0.8651 (tp30) cc_final: 0.8182 (tp30) REVERT: E 466 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: F 120 PHE cc_start: 0.7598 (t80) cc_final: 0.7115 (m-80) REVERT: F 172 LYS cc_start: 0.8442 (pttp) cc_final: 0.7552 (mtpt) REVERT: F 186 MET cc_start: 0.8282 (mmt) cc_final: 0.7585 (mtp) REVERT: F 243 GLN cc_start: 0.8992 (tt0) cc_final: 0.8643 (tt0) REVERT: F 344 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7853 (mt-10) REVERT: F 364 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: F 371 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8258 (ptmm) REVERT: F 392 GLN cc_start: 0.8309 (mt0) cc_final: 0.8029 (mt0) REVERT: F 400 ARG cc_start: 0.8080 (tpm-80) cc_final: 0.7837 (tpm-80) REVERT: F 418 GLU cc_start: 0.8732 (tp30) cc_final: 0.8177 (tp30) REVERT: F 422 GLN cc_start: 0.8138 (mt0) cc_final: 0.7719 (mt0) REVERT: F 513 MET cc_start: 0.7319 (tpp) cc_final: 0.6704 (tpp) outliers start: 43 outliers final: 17 residues processed: 293 average time/residue: 1.5596 time to fit residues: 502.7905 Evaluate side-chains 292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 269 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 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 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 466 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 195 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096798 restraints weight = 21184.383| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.05 r_work: 0.3039 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18276 Z= 0.158 Angle : 0.532 7.102 24774 Z= 0.269 Chirality : 0.040 0.137 2808 Planarity : 0.004 0.037 3072 Dihedral : 4.012 15.217 2418 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.95 % Allowed : 18.04 % 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: 2.22 (0.18), residues: 2136 helix: 2.40 (0.14), residues: 1248 sheet: 1.46 (0.39), residues: 180 loop : -0.23 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 134 HIS 0.003 0.001 HIS D 281 PHE 0.029 0.002 PHE B 149 TYR 0.017 0.002 TYR A 280 ARG 0.005 0.001 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 1086) hydrogen bonds : angle 4.04994 ( 3159) SS BOND : bond 0.00136 ( 6) SS BOND : angle 0.53237 ( 12) covalent geometry : bond 0.00371 (18270) covalent geometry : angle 0.53224 (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 308 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8258 (m-80) cc_final: 0.7652 (m-80) REVERT: A 170 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.5792 (mmt180) REVERT: A 217 GLN cc_start: 0.7610 (mt0) cc_final: 0.7368 (mt0) REVERT: A 344 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 350 ARG cc_start: 0.7612 (ttm110) cc_final: 0.7199 (ttm110) REVERT: A 402 MET cc_start: 0.9104 (tpt) cc_final: 0.8855 (tpp) REVERT: A 418 GLU cc_start: 0.8776 (tp30) cc_final: 0.8430 (tp30) REVERT: B 172 LYS cc_start: 0.8312 (pttt) cc_final: 0.8083 (pttt) REVERT: B 186 MET cc_start: 0.8309 (mmt) cc_final: 0.7728 (mtp) REVERT: B 350 ARG cc_start: 0.7707 (ttm110) cc_final: 0.7309 (ttm110) REVERT: B 371 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8273 (ttpp) REVERT: B 418 GLU cc_start: 0.8768 (tp30) cc_final: 0.8218 (tp30) REVERT: B 422 GLN cc_start: 0.8266 (mt0) cc_final: 0.7878 (mt0) REVERT: C 172 LYS cc_start: 0.8426 (pttp) cc_final: 0.7503 (mtpt) REVERT: C 186 MET cc_start: 0.8238 (mmt) cc_final: 0.7575 (mtp) REVERT: C 243 GLN cc_start: 0.8979 (tt0) cc_final: 0.8657 (tt0) REVERT: C 344 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7878 (mt-10) REVERT: C 364 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: C 400 ARG cc_start: 0.8070 (tpm-80) cc_final: 0.7794 (tpm-80) REVERT: C 418 GLU cc_start: 0.8750 (tp30) cc_final: 0.8111 (tp30) REVERT: C 422 GLN cc_start: 0.8147 (mt0) cc_final: 0.7695 (mt0) REVERT: C 513 MET cc_start: 0.7661 (tpp) cc_final: 0.7122 (tpp) REVERT: D 170 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.5961 (mmp-170) REVERT: D 344 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7979 (mt-10) REVERT: D 350 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7203 (ttm110) REVERT: D 364 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7754 (mt-10) REVERT: D 418 GLU cc_start: 0.8789 (tp30) cc_final: 0.8436 (tp30) REVERT: E 120 PHE cc_start: 0.7650 (t80) cc_final: 0.7047 (m-80) REVERT: E 148 LEU cc_start: 0.7921 (mt) cc_final: 0.7696 (mt) REVERT: E 170 ARG cc_start: 0.7969 (mtt180) cc_final: 0.6965 (mmp80) REVERT: E 172 LYS cc_start: 0.8341 (pttt) cc_final: 0.8116 (pttt) REVERT: E 186 MET cc_start: 0.8315 (mmt) cc_final: 0.7756 (mtp) REVERT: E 217 GLN cc_start: 0.7564 (mt0) cc_final: 0.7338 (mt0) REVERT: E 344 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7925 (mt-10) REVERT: E 350 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7356 (ttm110) REVERT: E 418 GLU cc_start: 0.8660 (tp30) cc_final: 0.8215 (tp30) REVERT: E 466 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: F 120 PHE cc_start: 0.7658 (t80) cc_final: 0.7119 (m-80) REVERT: F 172 LYS cc_start: 0.8449 (pttp) cc_final: 0.7467 (mtpp) REVERT: F 186 MET cc_start: 0.8254 (mmt) cc_final: 0.7594 (mtp) REVERT: F 243 GLN cc_start: 0.8987 (tt0) cc_final: 0.8631 (tt0) REVERT: F 344 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7884 (mt-10) REVERT: F 364 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: F 400 ARG cc_start: 0.8105 (tpm-80) cc_final: 0.7836 (tpm-80) REVERT: F 418 GLU cc_start: 0.8751 (tp30) cc_final: 0.8227 (tp30) REVERT: F 422 GLN cc_start: 0.8147 (mt0) cc_final: 0.7755 (mt0) REVERT: F 513 MET cc_start: 0.7454 (tpp) cc_final: 0.6865 (tpp) outliers start: 37 outliers final: 19 residues processed: 286 average time/residue: 1.4479 time to fit residues: 456.3333 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 : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 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 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 466 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 164 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.097368 restraints weight = 21200.353| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.04 r_work: 0.3048 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3493 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= 0.143 Angle : 0.527 7.010 24774 Z= 0.265 Chirality : 0.039 0.132 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.963 15.226 2418 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.11 % Allowed : 18.25 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.29 (0.18), residues: 2136 helix: 2.45 (0.14), residues: 1248 sheet: 1.45 (0.40), residues: 180 loop : -0.17 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 134 HIS 0.003 0.001 HIS D 281 PHE 0.031 0.002 PHE E 149 TYR 0.015 0.001 TYR A 280 ARG 0.005 0.000 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 1086) hydrogen bonds : angle 4.03434 ( 3159) SS BOND : bond 0.00121 ( 6) SS BOND : angle 0.51471 ( 12) covalent geometry : bond 0.00335 (18270) covalent geometry : angle 0.52704 (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: 40 poor density : 274 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6027 (mmp-170) REVERT: A 217 GLN cc_start: 0.7686 (mt0) cc_final: 0.7436 (mt0) REVERT: A 344 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 350 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7188 (ttm110) REVERT: A 402 MET cc_start: 0.9088 (tpt) cc_final: 0.8847 (tpp) REVERT: A 418 GLU cc_start: 0.8770 (tp30) cc_final: 0.8421 (tp30) REVERT: B 172 LYS cc_start: 0.8321 (pttt) cc_final: 0.8097 (pttt) REVERT: B 186 MET cc_start: 0.8410 (mmt) cc_final: 0.7735 (mtp) REVERT: B 341 TYR cc_start: 0.8640 (t80) cc_final: 0.8329 (t80) REVERT: B 350 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7322 (ttm110) REVERT: B 371 LYS cc_start: 0.8769 (ttpp) cc_final: 0.8270 (ttpp) REVERT: B 412 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7868 (mp10) REVERT: B 418 GLU cc_start: 0.8751 (tp30) cc_final: 0.8198 (tp30) REVERT: B 422 GLN cc_start: 0.8248 (mt0) cc_final: 0.7859 (mt0) REVERT: C 172 LYS cc_start: 0.8426 (pttp) cc_final: 0.7493 (mtmt) REVERT: C 186 MET cc_start: 0.8260 (mmt) cc_final: 0.7577 (mtp) REVERT: C 243 GLN cc_start: 0.8967 (tt0) cc_final: 0.8626 (tt0) REVERT: C 344 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7878 (mt-10) REVERT: C 364 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: C 371 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8182 (ptmm) REVERT: C 400 ARG cc_start: 0.8066 (tpm-80) cc_final: 0.7784 (tpm-80) REVERT: C 412 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7808 (tp40) REVERT: C 418 GLU cc_start: 0.8766 (tp30) cc_final: 0.8176 (tp30) REVERT: C 422 GLN cc_start: 0.8129 (mt0) cc_final: 0.7705 (mt0) REVERT: C 459 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: C 513 MET cc_start: 0.7661 (tpp) cc_final: 0.7119 (tpp) REVERT: D 170 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.5908 (mmp-170) REVERT: D 344 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7972 (mt-10) REVERT: D 350 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7194 (ttm110) REVERT: D 364 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7727 (mt-10) REVERT: D 371 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8350 (mtmm) REVERT: D 418 GLU cc_start: 0.8782 (tp30) cc_final: 0.8432 (tp30) REVERT: E 117 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8248 (tm) REVERT: E 120 PHE cc_start: 0.7628 (t80) cc_final: 0.7069 (m-80) REVERT: E 148 LEU cc_start: 0.7882 (mt) cc_final: 0.7653 (mt) REVERT: E 170 ARG cc_start: 0.8000 (mtt180) cc_final: 0.6970 (mmp80) REVERT: E 186 MET cc_start: 0.8314 (mmt) cc_final: 0.7742 (mtp) REVERT: E 195 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.8067 (p) REVERT: E 217 GLN cc_start: 0.7542 (mt0) cc_final: 0.7326 (mt0) REVERT: E 344 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7941 (mt-10) REVERT: E 350 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7343 (ttm110) REVERT: E 418 GLU cc_start: 0.8645 (tp30) cc_final: 0.8212 (tp30) REVERT: E 466 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: F 120 PHE cc_start: 0.7625 (t80) cc_final: 0.7096 (m-80) REVERT: F 172 LYS cc_start: 0.8447 (pttp) cc_final: 0.7470 (mtpp) REVERT: F 186 MET cc_start: 0.8265 (mmt) cc_final: 0.7580 (mtp) REVERT: F 243 GLN cc_start: 0.8990 (tt0) cc_final: 0.8615 (tt0) REVERT: F 344 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7883 (mt-10) REVERT: F 364 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: F 371 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8211 (ptmm) REVERT: F 400 ARG cc_start: 0.8065 (tpm-80) cc_final: 0.7770 (tpm-80) REVERT: F 418 GLU cc_start: 0.8755 (tp30) cc_final: 0.8164 (tp30) REVERT: F 422 GLN cc_start: 0.8134 (mt0) cc_final: 0.7713 (mt0) REVERT: F 513 MET cc_start: 0.7404 (tpp) cc_final: 0.6782 (tpp) outliers start: 40 outliers final: 20 residues processed: 291 average time/residue: 1.4343 time to fit residues: 460.9704 Evaluate side-chains 297 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 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 132 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 0.4980 chunk 133 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 209 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 178 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098980 restraints weight = 21320.939| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.05 r_work: 0.3073 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3558 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= 0.117 Angle : 0.512 8.999 24774 Z= 0.257 Chirality : 0.038 0.131 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.832 14.298 2418 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.85 % Allowed : 18.62 % Favored : 79.54 % 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: 2.55 (0.14), residues: 1248 sheet: 1.40 (0.39), residues: 180 loop : -0.09 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 274 HIS 0.002 0.001 HIS E 230 PHE 0.033 0.002 PHE E 149 TYR 0.012 0.001 TYR A 280 ARG 0.005 0.000 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 1086) hydrogen bonds : angle 3.98211 ( 3159) SS BOND : bond 0.00116 ( 6) SS BOND : angle 0.51506 ( 12) covalent geometry : bond 0.00268 (18270) covalent geometry : angle 0.51249 (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 310 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6012 (mmp-170) REVERT: A 217 GLN cc_start: 0.7718 (mt0) cc_final: 0.7457 (mt0) REVERT: A 344 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 350 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7230 (ttm110) REVERT: A 418 GLU cc_start: 0.8777 (tp30) cc_final: 0.8399 (tp30) REVERT: B 172 LYS cc_start: 0.8358 (pttt) cc_final: 0.8127 (pttt) REVERT: B 186 MET cc_start: 0.8385 (mmt) cc_final: 0.7758 (mtp) REVERT: B 208 ARG cc_start: 0.7334 (tpp80) cc_final: 0.7097 (tpp80) REVERT: B 341 TYR cc_start: 0.8632 (t80) cc_final: 0.8294 (t80) REVERT: B 350 ARG cc_start: 0.7743 (ttm110) cc_final: 0.7344 (ttm110) REVERT: B 371 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8353 (ttpp) REVERT: B 418 GLU cc_start: 0.8770 (tp30) cc_final: 0.8209 (tp30) REVERT: B 422 GLN cc_start: 0.8250 (mt0) cc_final: 0.7849 (mt0) REVERT: C 172 LYS cc_start: 0.8417 (pttp) cc_final: 0.7455 (mtpp) REVERT: C 186 MET cc_start: 0.8263 (mmt) cc_final: 0.7579 (mtp) REVERT: C 243 GLN cc_start: 0.8961 (tt0) cc_final: 0.8606 (tt0) REVERT: C 344 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7854 (mt-10) REVERT: C 364 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: C 371 LYS cc_start: 0.8692 (ttpp) cc_final: 0.8210 (ptmm) REVERT: C 400 ARG cc_start: 0.8061 (tpm-80) cc_final: 0.7360 (tpp-160) REVERT: C 412 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7809 (tp40) REVERT: C 418 GLU cc_start: 0.8773 (tp30) cc_final: 0.8260 (tp30) REVERT: C 422 GLN cc_start: 0.8123 (mt0) cc_final: 0.7741 (mt0) REVERT: C 513 MET cc_start: 0.7575 (tpp) cc_final: 0.7068 (tpp) REVERT: D 149 PHE cc_start: 0.8256 (m-80) cc_final: 0.7693 (m-80) REVERT: D 170 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.5866 (mmp-170) REVERT: D 344 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 350 ARG cc_start: 0.7592 (ttm110) cc_final: 0.7172 (ttm110) REVERT: D 364 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7689 (mt-10) REVERT: D 371 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8335 (mtmm) REVERT: D 418 GLU cc_start: 0.8785 (tp30) cc_final: 0.8337 (tp30) REVERT: D 422 GLN cc_start: 0.8113 (mt0) cc_final: 0.7675 (mt0) REVERT: E 120 PHE cc_start: 0.7539 (t80) cc_final: 0.6949 (m-80) REVERT: E 170 ARG cc_start: 0.8001 (mtt180) cc_final: 0.6962 (mmp80) REVERT: E 186 MET cc_start: 0.8318 (mmt) cc_final: 0.7737 (mtp) REVERT: E 195 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.8055 (p) REVERT: E 217 GLN cc_start: 0.7390 (mt0) cc_final: 0.7156 (mt0) REVERT: E 341 TYR cc_start: 0.8566 (t80) cc_final: 0.8267 (t80) REVERT: E 344 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7853 (mt-10) REVERT: E 350 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7346 (ttm110) REVERT: E 418 GLU cc_start: 0.8655 (tp30) cc_final: 0.8243 (tp30) REVERT: F 120 PHE cc_start: 0.7664 (t80) cc_final: 0.7130 (m-80) REVERT: F 172 LYS cc_start: 0.8448 (pttp) cc_final: 0.7473 (mtpp) REVERT: F 186 MET cc_start: 0.8251 (mmt) cc_final: 0.7570 (mtp) REVERT: F 243 GLN cc_start: 0.8965 (tt0) cc_final: 0.8595 (tt0) REVERT: F 344 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7878 (mt-10) REVERT: F 364 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: F 371 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8276 (ptmm) REVERT: F 400 ARG cc_start: 0.8047 (tpm-80) cc_final: 0.7339 (tpp-160) REVERT: F 418 GLU cc_start: 0.8748 (tp30) cc_final: 0.8132 (tp30) REVERT: F 422 GLN cc_start: 0.8125 (mt0) cc_final: 0.7693 (mt0) REVERT: F 513 MET cc_start: 0.7474 (tpp) cc_final: 0.6873 (tpp) outliers start: 35 outliers final: 17 residues processed: 290 average time/residue: 1.4550 time to fit residues: 464.9331 Evaluate side-chains 290 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 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 D residue 484 ASP Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 177 optimal weight: 0.0970 chunk 68 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 459 GLN ** 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 = 0.3724 r_free = 0.3724 target = 0.136975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099127 restraints weight = 21245.018| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.06 r_work: 0.3074 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3585 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= 0.119 Angle : 0.521 10.059 24774 Z= 0.259 Chirality : 0.038 0.128 2808 Planarity : 0.004 0.037 3072 Dihedral : 3.812 14.107 2418 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.32 % Allowed : 19.51 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.18), residues: 2136 helix: 2.60 (0.14), residues: 1242 sheet: 1.33 (0.39), residues: 180 loop : -0.14 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 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 0.007 0.000 ARG C 350 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 1086) hydrogen bonds : angle 3.96911 ( 3159) SS BOND : bond 0.00117 ( 6) SS BOND : angle 0.50501 ( 12) covalent geometry : bond 0.00274 (18270) covalent geometry : angle 0.52055 (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: 25 poor density : 272 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5937 (mmt180) REVERT: A 217 GLN cc_start: 0.7682 (mt0) cc_final: 0.7441 (mt0) REVERT: A 344 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 350 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7160 (ttm110) REVERT: A 418 GLU cc_start: 0.8796 (tp30) cc_final: 0.8418 (tp30) REVERT: B 121 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7368 (mm) REVERT: B 172 LYS cc_start: 0.8350 (pttt) cc_final: 0.8118 (pttt) REVERT: B 186 MET cc_start: 0.8387 (mmt) cc_final: 0.7722 (mtp) REVERT: B 208 ARG cc_start: 0.7302 (tpp80) cc_final: 0.7092 (tpp80) REVERT: B 341 TYR cc_start: 0.8620 (t80) cc_final: 0.8322 (t80) REVERT: B 350 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7326 (ttm110) REVERT: B 371 LYS cc_start: 0.8830 (ttpp) cc_final: 0.8350 (ttpp) REVERT: B 418 GLU cc_start: 0.8767 (tp30) cc_final: 0.8194 (tp30) REVERT: B 422 GLN cc_start: 0.8256 (mt0) cc_final: 0.7837 (mt0) REVERT: C 172 LYS cc_start: 0.8418 (pttp) cc_final: 0.7515 (mtpt) REVERT: C 186 MET cc_start: 0.8271 (mmt) cc_final: 0.7591 (mtp) REVERT: C 243 GLN cc_start: 0.8959 (tt0) cc_final: 0.8598 (tt0) REVERT: C 344 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 364 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: C 371 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8244 (ptmm) REVERT: C 400 ARG cc_start: 0.8080 (tpm-80) cc_final: 0.7360 (tpp-160) REVERT: C 412 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7812 (tp40) REVERT: C 418 GLU cc_start: 0.8743 (tp30) cc_final: 0.8123 (tp30) REVERT: C 422 GLN cc_start: 0.8129 (mt0) cc_final: 0.7697 (mt0) REVERT: C 513 MET cc_start: 0.7578 (tpp) cc_final: 0.7079 (tpp) REVERT: D 170 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5896 (mmt180) REVERT: D 344 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7985 (mt-10) REVERT: D 350 ARG cc_start: 0.7603 (ttm110) cc_final: 0.7172 (ttm110) REVERT: D 371 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8342 (mtmm) REVERT: D 418 GLU cc_start: 0.8778 (tp30) cc_final: 0.8324 (tp30) REVERT: D 422 GLN cc_start: 0.8149 (mt0) cc_final: 0.7688 (mt0) REVERT: E 120 PHE cc_start: 0.7461 (t80) cc_final: 0.6925 (m-80) REVERT: E 170 ARG cc_start: 0.7999 (mtt180) cc_final: 0.6960 (mmp80) REVERT: E 186 MET cc_start: 0.8309 (mmt) cc_final: 0.7763 (mtp) REVERT: E 195 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8042 (p) REVERT: E 217 GLN cc_start: 0.7411 (mt0) cc_final: 0.7177 (mt0) REVERT: E 341 TYR cc_start: 0.8573 (t80) cc_final: 0.8273 (t80) REVERT: E 344 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7801 (mt-10) REVERT: E 350 ARG cc_start: 0.7663 (ttm110) cc_final: 0.7341 (ttm110) REVERT: F 120 PHE cc_start: 0.7624 (t80) cc_final: 0.7134 (m-80) REVERT: F 172 LYS cc_start: 0.8449 (pttp) cc_final: 0.7473 (mtpp) REVERT: F 186 MET cc_start: 0.8248 (mmt) cc_final: 0.7625 (mtp) REVERT: F 344 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7872 (mt-10) REVERT: F 364 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: F 371 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8164 (ptmm) REVERT: F 400 ARG cc_start: 0.8044 (tpm-80) cc_final: 0.7332 (tpp-160) REVERT: F 412 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7822 (tp40) REVERT: F 418 GLU cc_start: 0.8749 (tp30) cc_final: 0.8129 (tp30) REVERT: F 422 GLN cc_start: 0.8128 (mt0) cc_final: 0.7696 (mt0) REVERT: F 513 MET cc_start: 0.7448 (tpp) cc_final: 0.6870 (tpp) outliers start: 25 outliers final: 16 residues processed: 282 average time/residue: 1.4213 time to fit residues: 442.9213 Evaluate side-chains 284 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 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 435 LYS Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 415 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN C 459 GLN ** 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 = 0.3685 r_free = 0.3685 target = 0.133685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095242 restraints weight = 21243.840| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.04 r_work: 0.3019 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18276 Z= 0.201 Angle : 0.576 9.204 24774 Z= 0.289 Chirality : 0.041 0.147 2808 Planarity : 0.004 0.044 3072 Dihedral : 4.147 16.921 2418 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.69 % Allowed : 19.46 % Favored : 78.85 % 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: 2.17 (0.18), residues: 2136 helix: 2.30 (0.14), residues: 1248 sheet: 1.38 (0.39), residues: 180 loop : -0.09 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 134 HIS 0.005 0.001 HIS D 281 PHE 0.034 0.002 PHE E 149 TYR 0.019 0.002 TYR A 280 ARG 0.007 0.001 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 1086) hydrogen bonds : angle 4.15361 ( 3159) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.57662 ( 12) covalent geometry : bond 0.00477 (18270) covalent geometry : angle 0.57565 (24762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15378.99 seconds wall clock time: 264 minutes 43.88 seconds (15883.88 seconds total)